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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": "SRX11103796"} | 03072018-A04-NA18519 is a sample of in vitro differentiated cells derived from induced pluripotent stem cells (iPSCs) obtained from an individual named NA18519, as part of an experiment conducted on 03072018, batch b6, and well A04. No specific treatment was applied to this 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": "SRX4198075"} | Primary CD34+ hematopoietic cells from a donor, specifically the CD49d+ Band3- population, used in RNA sequencing 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": "SRX4198075"} | 18-hour treatment with CsA of a cultured Human Kidney Peritubular Microvascular Endothelial Cell (HKMEC) from a donor. The cells are CD144+/CD31+ phenotype and originated from the kidney tissue. | 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": "SRX4198075"} | 30.81-year-old female with parotid gland tissue sample (SJ312) showing no signs of inflammation (parotid and labial focus scores: 0, SSA: Negative, RF: Negative), negative ACR/EULAR score, and Group I parotid and labial infiltration phenotypes. CD45 expression is 0.22% in parotid gland tissue, while it is significant (4.75%) in labial tissue. ESSDAI score is relatively low (7.67). | 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": "SRX7446542"} | 40 year old female's SUM149PT cell line, which is a cell type of Invasive Ductal Carcinoma, a type of breast ductal adenocarcinoma and neoplasm, cultured for 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": "SRX7446542"} | Kidney tissue sample from a patient with Renal Cell Carcinoma (RCC). | 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": "SRX7446542"} | Macrophages (MDMs) derived from an individual named D3, treated with M-CSF and IL-4 to skew towards M2a-MDMs, and treated with Triumeq (T). Sample type: 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": "SRX4036249"} | DLD1 cell line, a model for colorectal cancer, treated with DMSO for one day. The cells can be either dormant or cycling. | 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": "SRX4036249"} | 10122017-A01-NA18489 is a sample of in vitro differentiated cells derived from induced pluripotent stem cells (iPSCs) of individual NA18489, which underwent experimental processes as part of batch b3 on 10122017. | 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": "SRX4036249"} | Lymphoblastoid cells from the HG02595 cell line treated with Interferon Gamma. | 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": "SRX11069377"} | 31-week-old male primary cells from a PBMC sample taken from a participant in the MANHICA site who received the RTSS vaccine, was not a case, and had no malaria before M3.5. The participant was exposed to high malaria transmission, had no parasitic infection, and had a malaria status of 0 at the time of sampling, which took place at M0 (2009-08-27) and M3.5 (2009-12-08). The time to malaria was 365 days, with a WAz score of 1.09, haz score of -1.1, and Hb level of 8.8. The stimulation was dmso, and there was 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": "SRX11069377"} | iCell Endothelials that have been treated with 087 kerosine at a dose of 10 in a study related to KER. | 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": "SRX11069377"} | G401 cancer cell line treated with DMSO, wild type genotype. | 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": "SRX8084534"} | Colorectal cancer cells treated with PDOX (patient-derived xenograft) using the Smart-seq2 protocol. | 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": "SRX8084534"} | Cryopreserved pancreatic islets from a nondiabetic male donor, 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": "SRX8084534"} | The sample, named "obcrn41\_es27", is a tissue sample taken from the myocardium (atrial biopsy) of a male individual with a BMI greater than 32 (34 specifically). The individual is of Caucasian background and is part of batch 2 in the study. The individual has two comorbidities and is considered multimorbid. | 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": "SRX3032004"} | MV-4-11-B CDX cell line treated with BI00894999 (1mg/kg) and Flavopiridol (2.5mg/kg) for 2 hours each, as part of a QUANT-seq study with replicate 4 and internal ID J5865. | 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": "SRX3032004"} | No information for this sample available | 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": "SRX3032004"} | Human induced pluripotent-stem-cell derived embryoid body sample treated with DAPT at a concentration of 3.75E-07 for factor analysis and model building, with positive teratogenicity. | 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": "SRX4911158"} | In-vitro differentiated Forward programmed megakaryocytes (hipsc line: A1ATD1c) at differentiation day 40 with negative transgene pattern. | 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": "SRX4911158"} | Metastatic melanoma cells derived from a patient, with over 100 passages, originating from a subcutaneous melanoma metastasis, undergoing control vector treatment for shRNA mediated knockdowns in Sample 6A-C. | 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": "SRX4911158"} | Heart failure patients after acute myocardial infarction with sacubitril/valsartan resistance. | 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": "SRX10058289"} | Natural Killer cells from donor E after 21 days in culture with retroviral transduction 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": "SRX10058289"} | IgAN_07 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": "SRX10058289"} | Non-small cell lung carcinoma (NSCLC) cells from a blood platelet (thrombocyte) 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": "SRX17581912"} | Hematopoietic stem cells (HSCs) derived from mobilized peripheral blood at day 0, with no treatment (NT), from donor mPB1, batch B1. Belonging to the stem cells sample type, specifically long-term hematopoietic stem cells (LT-HSCs). | 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": "SRX17581912"} | Paracancerous tissues from kidney cancer patients (NM\_02). | 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": "SRX17581912"} | Heart (Atrial Appendage) tissue from an (ICA)-positive individual with Ischemic Heart Disease (IHD) undergoing coronary artery bypass surgery. | 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": "SRX6959194"} | Aortic valve tissue from a sclerotic condition. | 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": "SRX6959194"} | 26 day old cultured embryonic stem cells with DCX+ cre line, not a control 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": "SRX6959194"} | 48 hour treated cardiac myocytes derived from induced pluripotent stem cells (iPSCs) line MSN01, with a concentration of 0.5 uM Prednisolone, RIN of 9, and 200 ng of RNA. | 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": "SRX15214205"} | 37-year-old male human tissue sample from the putamen with a body mass index of 38.1, pH of 6.6, and postmortem interval of 20.5 hours. The sample has been processed as a control for disease comparison and underwent RNA sequencing with library size of 30727065 and RIN of 6.4. The sample was stored for 132.59 hours and was obtained in an accidental manner. | 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": "SRX15214205"} | A skin fibroblast cell line (GM02596) from Individual 2, provided by Coriell Cell Repositories. The cells are part of the skin's zone and have not been treated with any agents. | 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": "SRX15214205"} | 35-day old eNb1 stem 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": "SRX958929"} | Primary cells from Bone marrow with acute myeloid leukemia (AML). This sample is part of a study on acute myeloid leukemia, specifically focusing on cells that are involved in diseases of cellular proliferation, neoplasms, leukemia, lymphoid neoplasm, cancer, and bone marrow disorders. No specific treatment is mentioned for 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": "SRX958929"} | 38-year-old male peripheral blood sample from an untreated individual with CD3+CD4-CD8+ surface markers. | 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": "SRX958929"} | 4-hour infected sample of Monocyte-derived dendritic cells with LT2 infection, primary 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": "SRX2883023"} | hiPSC-derived CPM-high cells isolated on day 21, in vitro differentiated cells, 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": "SRX2883023"} | 100:0 mixture of cultured human neurons and astrocytes, specifically human primary astrocytes (Lonza, #CC-2565) and 2-week differentiated human neural progenitors, containing total RNA. | 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": "SRX2883023"} | Primary pancreatic islet cells from an adult control subject. The cells have been curated as beta 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": "SRX4121401"} | Peripheral T-cell lymphoma, NOS cell line (OCILY12\_1) 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": "SRX4121401"} | Normal fallopian tube cells from a benign donor with ID 34350. | 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": "SRX4121401"} | iCell Cardiomyocytes treated with 008\_HFO\_1, a member of the HFO treatment class, and exposed to a dose of 1. | 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": "SRX8481838"} | Female carcinoma cell line, specifically NCI-H378, from a Caucasian individual, cultured and untreated. | 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": "SRX8481838"} | A prostate cancer tissue sample from a male subject, with molecular phenotype ARneg\_NEpos, taken from the LuCaP 93 PDX Tumor model. | 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": "SRX8481838"} | A tissue sample from a male stone forming kidney, specifically from the low medula region. | 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": "SRX8852762"} | 28-year-old female bone marrow sample from a non-SAA patient who has undergone treatment, 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": "SRX8852762"} | 50 ng/ml PMA-treated THP1-derived macrophages, transfected with 200 nM NC siRNA for 48 hours, and stimulated with 200 ng/ml LPS for 3 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": "SRX8852762"} | Primary lymphocytes (PBMCs) from a donor with the identifier I-3594, specifically at time point V2, and classified as TR phenotype. These cells are part of the hematopoietic system. | 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": "SRX17452841"} | A sample of H3.3K27M-glioma cells (BT869 cell line) with AAVS1 control knockout genotype, treated with nucleofection for 4 days. | 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": "SRX17452841"} | In-vitro differentiated megakaryocytes (A1ATD1 line) at differentiation day 40, with transgene pattern T, forward programmed. | 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": "SRX17452841"} | 199Z\_MSCB-015 are primary cells of neuronal progenitors obtained from a healthy donor. | 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": "SRX379966"} | 72 hours post serum-switch, human skeletal muscle myoblasts (HSMM) with debris present, no cells in well, primary cells, single-cell library protocol. | 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": "SRX379966"} | 13-year-old female's monocytes, unstimulated, collected 180 minutes post-treatment, as part of the control group 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": "SRX379966"} | 12-year-old male's peripheral blood sample, used in analysis and module construction, with a viral type (not RSV A, B, HKU1, NL63, PIV 1, 2, 3, 4, flu B, 229E, or cov), blood neutrophil differential of 80.6, lymphocyte differential of 11.8, monocyte differential of 6.6, eosinophil differential of 0.9, basophil differential of 0.1, white blood cell count of 7, platelet count of 168, erythrocytes count of 5.2, and library counts of 9.230438. | 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": "SRX7768086"} | 59-year-old non-SAA female bone marrow sample, untreated, 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": "SRX7768086"} | Neural stem cells derived from human induced pluripotent stem cells, sorted using MoFlo, and analyzed using RamDA-seq. | 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": "SRX7768086"} | Cervical squamous cells from a cervix tissue sample with late stage tumor and paracancer phenotype. | 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": "SRX7774284"} | 38-year-old male bone marrow sample from an untreated control subject with CD3+CD4-CD8+ surface markers. | 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": "SRX7774284"} | HNSCC cells with normal genotype, cell line sample from HNSCC study. 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": "SRX7774284"} | iCell Hepatocytes treated with 192_BITUMENS_1, a type of bitumen, with a dose of 1. | 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": "SRX12387682"} | 15-day old, hiPSC-derived cardiomyocytes (SCVI-111 TBX5-Lineage Reporter Line) cultured in vitro. | 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": "SRX12387682"} | Human peripheral blood cells from a patient with chronic lymphocytic leukemia (IGHV Mutated CLL), a type of lymphoid leukemia which is a chronic lymphatic system disease and cancer of the blood and hematological system. | 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": "SRX12387682"} | Sorted AFhi CD206+ CD45+ macrophages from the bronchoalveolar lavage fluid (BALF) of a smoker patient. | 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": "SRX2575319"} | siRNA-transfected BE(2)-C neuroblastoma cell line derived from bone marrow metastasis, with a disease focus on neuroblastoma. | 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": "SRX2575319"} | 2D_TSCM treated stem 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": "SRX2575319"} | 15-year-old female with previous tuberculosis diagnosis, providing primary T cells that were unstimulated at timepoint 360. | 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": "SRX1967198"} | The sample is a glioblastoma tumor tissue from patient BT\_S | 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": "SRX1967198"} | 6 hour primary monocytes sample from a male donor stimulated with N. meningitidis. | 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": "SRX1967198"} | U87 cells with multiplicity of infection (MOI) of 0, 4 hours post infection, in well D2 of plate 1001703005, 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": "SRX1304170"} | A primary cell sample from a pancreatic islet with a single, QC-passing beta cell, which has been processed with ERCC mix2 at a 1:1,000,000 dilution for single-cell RNA sequencing. | 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": "SRX1304170"} | 40 year old female's cell line SUM149PT, which is an Invasive Ductal Carcinoma, cultured cells, 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": "SRX1304170"} | 16-year-old female blood cells from a control subject at the SUN site. | 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": "SRX14426712"} | Tissue sample PT4\_PTP19 from study HS-2302\_L1\_823D87, with no specific treatment reported. | 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": "SRX14426712"} | middle temporal gyrus tissue sample from cluster pdzd2 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": "SRX14426712"} | 14-day post-infusion control CAR T cells collected from a tumor site, specifically of type T cell. | 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": "SRX19578821"} | Primary peripheral blood mononuclear cells from an asthma patient. | 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": "SRX19578821"} | 3-day old stem-like hematopoietic cells (ST-HSC T) derived from mobilized peripheral blood of a donor (mPB1) with GFP+PD- condition, from batch B1. | 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": "SRX19578821"} | 6-day old embryonic inner cell mass (ICM) cells cultured in vitro, 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": "SRX11509137"} | Kidney tissue sample from a heart failure time point. | 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": "SRX11509137"} | 33-year-old female donor's whole blood sample with bedtime cortisol level of 0.433718741 and awakening cortisol level of 1.170575738, measured during a period of emotional stress (5.46875). | 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": "SRX11509137"} | Primary hematopoietic cells from bone marrow, specifically granulocyte monocyte progenitor cells (GMP 123low 33+117+) that have passed quality control checks. | 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": "SRX4982846"} | Primary CD34+ hematopoietic stem and progenitor cells (HSPCs) from peripheral blood of a patient with myelofibrosis at baseline, as characterized by JAK2 mutation, 3'-TARGET-seq method, and IF0138 primer mix. | 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": "SRX4982846"} | Primary pancreatic cells from a adult with Type 1 Diabetes (T1D), specifically from the ducts of the pancreatic islets. | 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": "SRX4982846"} | Sample Control 2 is a cell line of striatal neurons that has undergone treatment with Cas13d/CAGEX at day 32. | 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": "SRX14272238"} | Biological Sample: Human intestinal organoids (tissue) with wildtype genotype (wt). The tissue of origin is the intestine. No treatment has been 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": "SRX14272238"} | Sample from a Xp11 renal cell carcinoma-5 tumor, specifically from the kidney tissue, which has been preserved using formalin-fixed paraffin-embedded (FFPE) method. This sample is not treated with any agents. | 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": "SRX14272238"} | Liver tissue from an Intrahepatic Cholangiocarcinoma (ICC) patient with molecular subtype LC4 and disease state ICC. | 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": "SRX16145234"} | B-NHL cell line carrying t(14;18)(q32;q21) with STAT6 N421K genotype, treated with IL4 for 20 minutes, washed, and incubated for 4 hours. Sample source is OCI-Ly1 cell line. | 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": "SRX16145234"} | Whole blood sample taken 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": "SRX16145234"} | 62-year-old male with Glioblastoma grade IV, a type of brain tumor and nervous system cancer. | 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": "SRX10844156"} | 6-hour treated CD138-selected bone marrow mononuclear cells (PMC14 cell line) with A-485 (1μM) using 3'-mRNA QuantSeq library prep. | 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": "SRX10844156"} | 11 week post-conception fetal tissue from the stomach mucosa and submucosa, 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": "SRX10844156"} | 19-year-old female bone marrow sample, treated for SAA (severe aplastic anemia), with surface markers Lin-CD34+. | 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": "SRX14777140"} | Kyse cell line derived from esophageal squamous cell carcinoma, treated with high concentration of EGF 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": "SRX14777140"} | Cryopreserved pancreatic islets from a nondiabetic male individual, not subjected to 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": "SRX14777140"} | 2hAux\_4h42C\_DoubleAID\_rep2: Colorectal adenocarcinoma cell line (DLD-1) with AFF1/4-AID OsTIR1 genotype, cultured at auxin growth temperature, indicating a potential investigation of colorectal adenocarcinoma or intestinal cancer. | 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": "SRX4330933"} | 81 year old female retina tissue sample with RIN value of 7.8 and post-mortem interval of 25.05 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": "SRX4330933"} | 18-N706-S502-F1.IPF010 is a tissue sample taken from the lung of a patient with idiopathic pulmonary fibrosis (IPF), a type of respiratory system disease and idiopathic interstitial pneumonia. 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": "SRX4330933"} | 19-year-old female from the non-Hispanic, White ethnic group, with a negative PCR test for SARS-CoV-2, provided a blood sample for RNA sequencing at enrollment (time point 0) as part of the Later Surveillance batch in the Control group. | 0 |
Subsets and Splits