Single-Cell Whole-Genome Bisulfite Sequencing for Analysis of Epigenetic Heterogeneity
Single-cell RNA-seq · mouse · 56 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Mus musculus (mouse)
- Samples
- 56 samples: 20 × Se vs 12 × MII vs 12 × 2i vs 7 × CTGroups 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; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Direct links to NCBI and ENA, 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, or the whole study as GSE56879_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
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 PRJNA244869 and SRA study SRP041257. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 51 samples.
How we read this: 4 replicated groups read from 56 sample titles; they account for 51 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.
- GSM1370522 MII_1 MII
- GSM1370523 MII_2 MII
- GSM1370524 MII_3 MII
- GSM1370525 MII_4 MII
- GSM1370526 MII_5 MII
- GSM1370527 MII_6 MII
- GSM1370528 MII_7 MII
- GSM1370529 MII_8 MII
- GSM1370530 MII_9 MII
- GSM1370531 MII_10 MII
- GSM1370532 MII_11 MII
- GSM1370533 MII_12 MII
- GSM1370534 MII_oocytes_bulk
- GSM1370535 2i_1 2i
- GSM1370536 2i_2 2i
- GSM1370537 2i_3 2i
- GSM1370538 2i_4 2i
- GSM1370539 2i_5 2i
- GSM1370540 2i_6 2i
- GSM1370541 2i_7 2i
- GSM1370542 2i_8 2i
- GSM1370543 2i_9 2i
- GSM1370544 2i_10 2i
- GSM1370545 2i_11 2i
- GSM1370546 2i_12 2i
- GSM1370547 2i_ESCs_bulk
- GSM1370548 CT_1 CT
- GSM1370549 CT_2 CT
- GSM1370550 CT_4 CT
- GSM1370551 CT_5 CT
- GSM1370552 CT_6 CT
- GSM1370553 CT_7 CT
- GSM1370554 CT_8 CT
- GSM1370555 Ser_1 Se
- GSM1370556 Ser_2 Se
- GSM1370557 Ser_3 Se
- GSM1370558 Ser_4 Se
- GSM1370559 Ser_5 Se
- GSM1370560 Ser_6 Se
- GSM1370561 Ser_7 Se
+ 16 more — browse all 56 samples with per-sample file links →
- GSE227108 Integrated single-cell analysis defines the epigenetic basis of castration-resistant prostate luminal cells (scRNA-seq) 18 samples shares single-cell, epigenetic
- GSE269748 A single-cell atlas deconstructs heterogeneity across multiple models in murine traumatic brain injury and identifies novel cell-specific targets 36 samples shares heterogeneity, single-cell
- GSE220691 Kidney Single-Cell Atlas Reveals Macrophage Heterogeneity in Progression and Regression of Cisplatin Induced AKI. 22 samples shares heterogeneity, single-cell
- GSE220675 Kidney Single-Cell Atlas Reveals Macrophage Heterogeneity in Progression and Regression of Cisplatin Induced AKI [scRNA-seq] 11 samples shares heterogeneity, single-cell
- GSE308939 Single-cell RNA-seq reveals the keratinocyte heterogeneity and increased interfollicular basal keratinocytes in wound-induced hair follicle neogenesis 6 samples shares heterogeneity, single-cell
- GSE192687 Single-cell RNAseq analysis of renal endothelial cells in murine diabetic nephropathy 5464 samples shares single-cell
- GSE215963 Subclonal evolution revealed by single-cell profiles of expressed mutations identifies adaptation mechanisms to immunotherapy in melanoma. 1497 samples shares single-cell
- GSE277789 Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [Smart-seq3-RNA-seq-add] 830 samples shares single-cell
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.