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{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX3111576"} | 198Z\_MSCB-067 sample contains primary cells that are neuronal progenitors from patient type WB\_1. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX3111576"} | Bone marrow-derived mesenchymal stromal cells, primary cells obtained from Rooster Bio. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX3111576"} | Paracancerous tissues from kidney cancer patients (NM\_08) in a kidney cancer study. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX7834244"} | CD8+ T cells from a healthy skin sample, labeled C4, from plate rep1, well E6, sequencing batch b7, which passed QC, and clustered as 2\_Resid. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX7834244"} | 14-year-old male's blood T cells (PBMCs) with no virus reads and 68799 mapped human reads, serving as a control sample in a study. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX7834244"} | Breast biopsy tissue from a healthy subject before Mifepristone treatment. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX3112138"} | 201Z\_MSCB-083 is a sample of primary neuronal progenitor cells from patient MD1 with no reported treatment. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX3112138"} | KYSE150 cells, which are an ESCC (Esophageal Squamous Cell Carcinoma) cell line derived from ESC (Esophageal Squamous Cell), were used in this study as a control in the experiment CP-4. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX3112138"} | BJ Fibroblasts cell line treated with WT (wild type). | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX17804318"} | Paracancerous normal liver tissue. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX17804318"} | 100,000 primary blood cells (buffy coat) from a donor, fraction positive control, collected in lysis/binding buffer, and run on NextSeq Zeus flowcell id HV3T2BGXG at 6 hours timepoint. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX17804318"} | GIST-T1/816 cells treated with GDC0980 for 4 hours. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11179446"} | Human induced pluripotent stem cells (iPSCs) that were separately cultured, derived from embryonic tissue, and previously fibroblasts. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11179446"} | Descending colon pinch biopsy tissue from a patient with UC inactive condition. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11179446"} | K562 cell line derived from a patient with Chronic Myelogenous Leukemia, with no sgRNA treatment. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX10022110"} | CD3+ T cells from a tumor tissue that have been treated with a POST (type unspecified) treatment, sorted into live/dead, CD14-, CD20-, CD45+CD3+ fractions. The cells are primary cells, and they have been modified to express a disease of cellular proliferation, CD8-positive, alpha-beta T cell, T cell, hematopoietic cell, neoplasm, leukocyte, disease, CD4-positive, alpha-beta T cell phenotype. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX10022110"} | Colorectal cancer cells (Colorectal cancer) that have undergone a patient-derived xenograft (PDOX) treatment. The sample was processed using the Smart-seq2 protocol. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX10022110"} | A gastric cancer PDX tumor sample from a Nude mouse that has undergone FOLFOX treatment and developed AcquiredResistance. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX13867163"} | 293T cell line with Ehhadh K572R overexpression, cultured cells from a late embryonic stage. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX13867163"} | A skin tissue sample from donor APC87 with condition AD (Alzheimer's Disease). | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX13867163"} | A2780 cells treated with citric acid (CA). | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX1772827"} | 23-year-old non-diabetic male with African American (AA) ethnicity primary pancreatic islet cells, specifically alpha cells, with no treatment. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX1772827"} | middle temporal gyrus tissue sample from the WG960039\_H12 study, part of the gaba\_sox6\_tac1 cluster with no reported treatment. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX1772827"} | 65-year-old male patient with de novo acute myeloid leukemia (AML) and BMMC (bone marrow mononuclear cells) sample. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX7771286"} | 14-year-old male bone marrow sample from an untreated control subject, with surface markers Lin-CD34+. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX7771286"} | MDA-MB231-Myc cell line treated with Doxycycline for 120 hours. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX7771286"} | A tissue sample from chorionic villi of a female placenta, treated with in-vitro fertilization (IVF) at gestational age 83 days, with Caucasian, Asian, or Biracial race and NonHispanic ethnicity. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX1519709"} | 58-60 passaged H9 human embryonic stem cells treated with 50 ng/mL Activin A for 6 hours. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX1519709"} | Sample_815\_AM\_uninf is a tissue sample from the lung of a non-infected donor with ID 815, specifically consisting of alveolar macrophages (AM). | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX1519709"} | A sample of stably transfected C4-2B prostate cancer cells with the pcDNA 3.1 vector only, representing prostate cancer cells in culture. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX3941109"} | Female breast epithelial cells from adult human breast tissue, specifically from the luminal location, with no reported treatment. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX3941109"} | 0.05 µM BAY-1251152 treated OCI-AML3 acute myeloid leukemia cell line with NMP mutation after 8 hours of treatment. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX3941109"} | 1957 is a donor of naive CD4 T cells, which were taken from the donor when they were at an old developmental stage. The cells are of type alpha-beta T cell, which are hematopoietic cells and a type of leukocyte and lymphocyte. The cells were not treated with anything before being used for the study. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX5428506"} | IgAN (IgA nephropathy) patient renal biopsies sample IgAN\_17, with IgAN disease state. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX5428506"} | Healthy control, Human Intestinal Lymphatic Endothelial cells (HILEC) taken from healthy colonic mucosa. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX5428506"} | 23-year-old female blood cells from a control subject, collected 6 months after exposure, with no treatment. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX9219114"} | 32nd oocyte sample with ID S22 at germinal vesicle (GV) maturation stage, which is a type of germ cell. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX9219114"} | 50915BCG, Matched Group 10, M.tb-uninfected, CMV-infected cell line sample with genotype BCG and treated with D-7. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX9219114"} | PC-3 prostate cancer cell line treated with shCDGAP. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX10022607"} | CD3+ T cells from a tumor sample that have been sorted as live, CD14-, CD20-, CD45+CD3+ and treated with PRE. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX10022607"} | The sample is a cell line derived from adult brain tissue, with no reported treatment. The genome build used is hg38. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX10022607"} | Induced pluripotent stem cell-derived cardiomyocytes from a male, Caucasian donor, treated with re-oxygenation2. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX10715630"} | Primary cells from a peripheral blood monocyte-derived macrophage sample, with M2 polarization and donor 8, that has not been treated. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX10715630"} | Colon tissue sample from a study named "rRNA depletion US-1493173" with sample source name "Sample\_US-1493173" and mapped ontology term "colon". The sample was not treated with any specific agent or condition. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX10715630"} | Early embryonic, stem cell line H1 hESC that has been cultured in mTSER and overexpressed in primed state. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX9632992"} | CD8+ T cells from an intestinal transplant recipient donor, with CD103pos status, taken from the small intestine. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX9632992"} | Glioblastoma tissue sample from a study on glioblastoma, a type of nervous system cancer and a form of astrocytoma located in the central nervous system. The sample does not indicate any treatment. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX9632992"} | 112-day-old cultured human embryonic stem cell (H9, WA09) derived retinal organoid, specifically Rod3 cell type, from time group 5, in the final dataset with no removal reason. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX2490645"} | Cultured embryonic stem cells, Cre line DCX-, after 54 days in culture. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX2490645"} | A sample of total RNA-seq from a male, neonate HFF-hTERT clone 6 cell line, specifically HFFc6, which was derived from a normal, preserved donor with the ID ENCDO737WWC. This cell line was cultured and underwent 19 passages before being flash-frozen for preservation. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX2490645"} | 15-18 passage MCF-7 breast cancer cell line treated with siRNF181. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX9107042"} | The sample is an iPSC-derived neuron, specifically the SBAD3 cell line, that has been cultured in vitro. It has not passed quality control (QC) and was obtained from dermal fibroblasts that were differentiated into iPS cells. No treatment was applied to this sample. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX9107042"} | Blood tissue sample from a subject with no reported history of PTSD (ptsd: Never) and replicate number 185 (replicates: NvrRep185). | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX9107042"} | Blood cells from a female donor, treated with LAIV8-IIV5/AS03 at Day 0. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11069963"} | 22-week-old male primary cells (PBMCs) from a healthy, older individual who received the RTSS vaccine and was part of a malaria study in Bagamoyo with high transmission rates. The individual did not have malaria before or at the time of sample collection (M0), and the time to malaria was 365 days. The individual was a control subject, matched with case 33, and had a -0.24 weight-for-age z-score (WAZ) and -0.12 height-for-age z-score (HAZ), as well as a hemoglobin (Hb) level of 9.6 g/dL. The cells were stimulated with hbs and collected at plate location G4, plate SSF-1780. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11069963"} | 8-year-old male liver tissue from a control group. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11069963"} | K562 cell line, which is a human immortalized myelogenous leukemia line, cultured cells that have undergone 20-22 passages, and have not received any treatment. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX8496337"} | Nasal airway epithelium tissue from an asthmatic individual. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX8496337"} | 2D culture of MDAMB231 cancer cell line with HSF2 knockdown and HSF1 knockdown, sourced from pleural effusion of a female adult Caucasian patient with adenocarcinoma. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX8496337"} | U4 is a primary cell sample from a subject with status UC (Ulcerative Colitis), specifically from the rectum, enriched for immune cells with surface markers CD45+. The cells have been characterized as leukocytes and hematopoietic cells. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX2806427"} | Normal human islet inlet cells. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX2806427"} | This sample contains embryonic stem cells (hESC H9 SOX17mCHERRY/wRUNX1CGFP/w) that have undergone Day 18 differentiation, and have been subjected to two treatments: DMSO (drug vehicle) treatment from day 2 to day 4, and orbital shear plate treatment from Day 10 to day 18. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX2806427"} | 8 days post induced viral expression of OSKM in BJ foreskin fibroblast cell line, with negative bdd2-c8 enrichment. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX1964980"} | Neoplastic astrocytes from the periphery of a glioblastoma patient (BT\_S1) tissue sample, specifically from plate id 1001000028, well F6, and cluster 11, as characterized by TSNE analysis. The cells have been genetically modified to express HEPACAM for selection purposes. This sample originates from a brain tissue and has been diagnosed with glioblastoma multiforme, which is a type of nervous system cancer and a disease of cellular proliferation. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX1964980"} | U3013 glioma cell line treated with NC-Empty. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX1964980"} | 8-month-old retinal organoid tissue sample, named Organoid8M\_R61\_C64. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX13700008"} | A cell line sample from a female Caucasian patient with adenocarcinoma, specifically MDA-MB-231, which has been sorted into subclone 13. This sample was obtained from liver metastasis in an adult organism, specifically from mouse number M1, and it has not undergone retransplantation. The sample was taken as a technical replicate. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX13700008"} | 40 year old female with Invasive Ductal Carcinoma (SUM149PT cell line) treated and used in Chip91481_r21_c55 experiment. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX13700008"} | 71-year-old female bone marrow sample containing Lin - CD34+ CD38- hematopoietic stem and progenitor cells, which are part of the hematopoietic system. The cells are primary cells, and no treatment was applied. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX12032550"} | A sample of lung adenocarcinoma, a type of non-small cell lung carcinoma, derived from a cell line. The cells are of epithelial origin, which is consistent with lung adenocarcinoma. This sample is part of a study on lung disease, specifically lung carcinoma, including its subtype adenocarcinoma, and is associated with abnormal cellular proliferation and respiratory system disease. The treatment for this sample is not specified. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX12032550"} | HeLa cells treated with SpliceostatinA in the Yoshida Lab. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX12032550"} | A sample of glioblastoma, a type of nervous system cancer, specifically a grade IV astrocytoma (also known as glioblastoma multiforme), which is untreated. The cells come from a patient-derived xenograft, meaning they were taken from a human patient and implanted into a different species to grow. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX6813650"} | A blood plasma sample from a pancreatic ductal adenocarcinoma (PDAC) patient, part of the PDAC\_272 study. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX6813650"} | 25-year-old female patient with severe dengue, whose blood sample (containing PBMCs) consists of B cells, a type of lymphocyte of B lineage, with 1,863,888 human uniquely mapped reads and no virus reads. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX6813650"} | Bone marrow sample with BCR-ABL positive status, at 6 months post TKI treatment, consisting of Lin-CD34+CD38- cells. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX7549249"} | 35-year-old female donor's (313C) single hematopoietic stem cell or multipotent progenitor (HSC or MPP) taken from peripheral blood, obtained through donation after circulatory death (DCD). Sample type is stem cells. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX7549249"} | Cryopreserved pancreatic islets from a female donor with Type 2 Diabetes (T2D). The sample is primary cells, and no treatment was given. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX7549249"} | Naive H9 stem cells treated with PXGL. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX8030912"} | Primary cells from sorted bone marrow macrophages (CD14+CD163+) with no treatment. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX8030912"} | IgAN_10 renal biopsy sample from a patient with IgAN (IgA nephropathy), a kidney disease. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX8030912"} | 31 is a sample of LSCC tissue from a subject with stage 4 LSCC, who has a history of tobacco smoking and alcohol consumption. The sample is relevant to nicotine dependence. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX2784758"} | hPSC-derived retinal cells (D218) from the Human Retina tissue. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX2784758"} | Colorectal cancer cells treated with PDOX (Patient-Derived Organoid Xenograft) using the Smart-seq2 protocol. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX2784758"} | A673 cells treated with SP-2509 at 2uM concentration, replicate 3, with hypersensitivity to SP-2509. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX9820584"} | Sample of human cells in a mouse xenograft model, with wild-type genotype, exposed to hypoxia treatment. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX9820584"} | 18-day differentiated motor neurons derived from induced pluripotent stem cells (iPSCs) of a sporadic amyotrophic lateral sclerosis (ALS) patient, aligned to hg19 genome, part of Batch B. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX9820584"} | Human induced pluripotent stem cell derived cardiomyocytes (iPSCs) with control overexpression, sample 2, rep 2, cell line WTC-11, in vitro differentiated cells. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11928008"} | 20476 is a female donor with new onset T1D. The sample consists of primary CD4-positive, alpha-beta T cells that have been isolated and sorted using plate sort method. The cells were obtained from a 16 year old individual. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11928008"} | A sample of MCF-7 human breast cancer epithelial cells, cultured and derived from a Caucasian adult female with pleural effusion breast cancer. The sample has not undergone any treatment. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11928008"} | 22-hour prostate cancer cell sample (LNCaP) treated with R1881 1nM and Enzalutamide 2uM. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX12326420"} | 35-year-old male patient with de novo acute myeloid leukemia (AML) and a lymphoid neoplasm, specifically leukemia blast cells, which are non-terminally differentiated cells. This primary cell sample has not received any treatment. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX12326420"} | MCF7 cells treated with 1 uM Bisphenol A for 6 hours in DMEM + 10% HI-FBS media. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX12326420"} | Primary peripheral blood morphonuclear cells unstimulated culture from a donor with high interferon-γ producing asthma. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX5348386"} | Normal esophagus tissue from the Nov28 cell isolation batch, cluster 2. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX5348386"} | 54 year old female systemic sclerosis patient, visit at month 12, treated with cyclophosphamide, diffuse subset. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX5348386"} | Plasmacytoid Dendritic Cell (pDC) sample, lineage: Dendritic Cell Lineage, antibodies: CD14-, BDCA1-, BDCA2+, CD123hi, isolated from Peripheral Blood. Cultured cell, hematopoietic cell, leukocyte, and blood cell line. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX14405611"} | 8 Gy X-ray irradiated HPV-positive head and neck squamous cell carcinoma (HNSCC) cell line, UD-SCC2, after 4 hours of treatment. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX14405611"} | 14-year-old female with case group status, who provided primary T cells for RNA sequencing after stimulation with ESAT antigen at timepoint 540, and tested positive for QFT. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX14405611"} | iPS-derived endothelial cells at passage 6, cultured in vitro, with the phenotype FPAH (familial pulmonary arterial hypertension). | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX4354063"} | 24-year-old female patient with dengue fever, whose blood sample (containing Peripheral Blood Mononuclear Cells or PBMCs) contains primary monocyte cells with 65,203 uniquely mapped human reads and no virus reads. | 1 |
Subsets and Splits