Epiregulon: Inference of single-cell transcription factor activity to dissect mechanisms of lineage plasticity and drug response
Single-cell RNA-seq · human · 38 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Samples
- 38 samples: 10 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI.
Direct links to NCBI, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need.
Whole study · RAW.tar
Everything the authors deposited as one archive (GSE252883_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.
What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1062865. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 10 replicated groups read from 38 sample titles; they account for 20 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM7990798 VCaP, GEX
- GSM7990799 LNCaP, GEX LNCaP, GEX
- GSM7990800 VCaP, ATAC, 1 VCaP, ATAC,
- GSM7990801 VCaP, ATAC, 2 VCaP, ATAC,
- GSM7990802 LNCaP, ATAC, 1 LNCaP, ATAC,
- GSM7990803 LNCaP, ATAC, 2 LNCaP, ATAC,
- GSM7990804 VCaP, HTO
- GSM7990805 LNCaP, HTO LNCaP, HTO
- GSM7990806 H660, GEX
- GSM7990807 H660, ATAC
- GSM7990808 H660, HTO
- GSM7990809 DU145, GEX
- GSM7990810 DU145, ATAC
- GSM7990811 DU145, HTO
- GSM7990812 LNCaP, GEX LNCaP, GEX
- GSM7990813 LNCaP, ATAC
- GSM7990814 LNCaP, HTO LNCaP, HTO
- GSM8605967 DU145, DMSO, input
- GSM8605968 DU145, DMSO, SMARCA4
- GSM8605969 DU145, DMSO, FOSL1
- GSM8605970 DU145, DMSO, TEAD1
- GSM8605971 DU145, SMARCA2/4 degrader, input
- GSM8605972 DU145, SMARCA2/4 degrader, SMARCA4
- GSM8605973 DU145, SMARCA2/4 degrader, FOSL1
- GSM8605974 DU145, SMARCA2/4 degrader, TEAD1
- GSM8605975 MDA-PCa-2b, DMSO, SMARCA4, rep1 MDA-PCa-2b, DMSO, SMAR…
- GSM8605976 MDA-PCa-2b, DMSO, SMARCA4, rep2 MDA-PCa-2b, DMSO, SMAR…
- GSM8605977 MDA-PCa-2b, SMARCA2/4 degrader, SMARCA4, rep1 MDA-PCa-2b, SMARCA2/4 d…
- GSM8605978 MDA-PCa-2b, SMARCA2/4 degrader, SMARCA4, rep2 MDA-PCa-2b, SMARCA2/4 d…
- GSM8605979 MDA-PCa-2b, DMSO, AR, rep1 MDA-PCa-2b, DMSO, AR,
- GSM8605980 MDA-PCa-2b, DMSO, AR, rep2 MDA-PCa-2b, DMSO, AR,
- GSM8605981 MDA-PCa-2b, SMARCA2/4 degrader, AR, rep1 MDA-PCa-2b, SMARCA2/4 d…
- GSM8605982 MDA-PCa-2b, SMARCA2/4 degrader, AR, rep2 MDA-PCa-2b, SMARCA2/4 d…
- GSM8605983 MDA-PCa-2b, DMSO, FOXA1, rep1 MDA-PCa-2b, DMSO, FOXA…
- GSM8605984 MDA-PCa-2b, DMSO, FOXA1, rep2 MDA-PCa-2b, DMSO, FOXA…
- GSM8605985 MDA-PCa-2b, SMARCA2/4 degrader, FOXA1, rep1 MDA-PCa-2b, SMARCA2/4 d…
- GSM8605986 MDA-PCa-2b, SMARCA2/4 degrader, FOXA1, rep2 MDA-PCa-2b, SMARCA2/4 d…
- GSM8605987 MDA-PCa-2b, input
- GSE324131 A single-cell and spatial atlas of prostate cancer reveals the combinatorial nature of gene modules underlying lineage plasticity and metastasis 38 samples shares single-cell, plasticity, lineage
- GSE307215 Spatiotemporal Single-Cell Profiling Reveals T Cell Clonal Dynamics and Phenotypic Plasticity in Human Graft-versus-Host Disease 104 samples shares single-cell, plasticity
- GSE296831 Epigenetic Context Defines the Transcriptional Activity of Canonical and Noncanonical NF-kappaB Signaling in Pancreatic Cancer [ChIP-Seq] 48 samples shares transcription, activity
- GSE335480 Single-cell tracking reveals tumor-reactive T cell plasticity during melanoma TIL therapy 38 samples shares single-cell, plasticity
- GSE332630 Multimodal single-cell analyses reveal distinct fusion-regulated transcriptional programs in Ewing sarcoma 22 samples shares transcription, single-cell
- GSE287976 Single-Cell Omics Analysis of Human Basophils Reveals Two Transcriptionally Distinct Populations 12 samples shares transcription, single-cell
- GSE270503 Epigenetic heterogeneity and state-specific transcriptional programs determine differential drug response in osteosarcoma [Cut&Run] 56 samples shares transcription
- GSE274113 Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes [10x ATAC + GEX Multiome] 42 samples shares transcription
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.