Published October 28, 2025
| Version 1.1.0
Dataset
Open
Processed single-cell RNA-seq datasets of PBMC (1k, 3k, 4k, 8k) re-aligned with Cell Ranger v9.0.1 and GENCODE v48 (GRCh38.p14)
Description
This dataset contains processed single-cell RNA sequencing (scRNA-seq) data from peripheral blood mononuclear cells (PBMCs) with different cell counts (1k, 3k, 4k, 8k). The raw FASTQ files were downloaded from publicly available 10x Genomics datasets, and all samples were aligned using Cell Ranger v9.0.1 (February 6, 2025) with a custom-built reference genome based on GENCODE Release 48 (GRCh38.p14).
For each dataset, the following files are provided:
-
*_filtered_feature_bc_matrix.h5: filtered gene-barcode matrices -
*_raw_feature_bc_matrix.h5: unfiltered matrices
To facilitate data interpretation, the table below summarizes key metadata for each dataset, including sample source and assay details.
| Dataset | Number of cells | Species | Tissue | Disease | Assay |
|---|---|---|---|---|---|
| pbmc1k | ~1,000 | Human | Blood | Healthy | 10x 3' v3 |
| pbmc3k | ~3,000 | Human | Blood | Healthy | 10x 3' v1 |
| pbmc4k | ~4,000 | Human | Blood | Healthy | 10x 3' v2 |
| pbmc8k | ~8,000 | Human | Blood | Healthy | 10x 3' v2 |
Files
Files
(146.0 MB)
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md5:f720c2168531c1958cab2d81a28eb1fa
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6.7 MB | Download |
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md5:32b75eab73dfcf8b3df6264f5dfe12a4
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11.8 MB | Download |
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md5:9bf3c022611fab0f68174ae8bf1cda6b
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5.2 MB | Download |
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md5:3866c5925bc9b39ca70a096399143da1
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8.0 MB | Download |
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md5:5287da4e170d3829d15ac36d5a13ef21
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14.2 MB | Download |
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md5:9d45b6859311cacc6199728a5f142470
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24.4 MB | Download |
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md5:19d2152c8765d08c4e559c0c80de7440
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28.2 MB | Download |
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md5:2e7ce5d99d61800f86be86daf89d4874
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47.5 MB | Download |