Gene-specific reactivation of X-linked genes upon Xist loss is linked to the chromatin states in extraembryonic endoderm and epiblast stem cells
RNA-seq (gene expression) · mouse · 13 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 13 samples: 5 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; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Lineage-specific dynamics of loss of X upregulation during inactive-X reactivationStem cell reports · 2024
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 GSE273917_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1144093 and SRA study SRP524095. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 11 samples.
How we read this: 5 replicated groups read from 13 sample titles; they account for 11 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.
- GSM8439540 WT XEN R1 WT XEN
- GSM8439541 WT XEN R2 WT XEN
- GSM8439542 △Xist-Pat-1 △Xist-Pat
- GSM8439543 △Xist-Pat-2 △Xist-Pat
- GSM8439544 △Xist-Pat-3 △Xist-Pat
- GSM8439545 WT-AZA-R1 WT-AZA
- GSM8439546 WT-AZA-R2 WT-AZA
- GSM8439547 △Xist-Pat-1-AZA
- GSM8439548 △Xist-Pat-2-AZA
- GSM8439549 WT EPI R1 WT EPI
- GSM8439550 WT EPI R2 WT EPI
- GSM8439551 △Xist-R1 △Xist
- GSM8439552 △Xist-R2 △Xist
- GSE243942 Spatio-temporal X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing [RNA-seq] 125 samples shares reactivation, x-linked, linked
- GSE243943 Spatio-temporal X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing 127 samples shares reactivation, x-linked, linked
- GSE288605 Context-Dependent and Gene-Specific Role of Chromatin Architecture Mediated by Histone Modifiers and Loop-extrusion Machinery 96 samples shares gene-specific, chromatin
- GSE295530 MeCP2 stabilizes the glucocorticoid system in active chromatin regions [RNA-seq] 723 samples shares chromatin
- GSE166225 Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates [RNA-seq] 288 samples shares chromatin
- GSE300757 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages 127 samples shares chromatin
- GSE290224 Intermittent Fasting Reprograms Chromatin Accessibility to Modulate Gene Expression in Brain and Muscle 96 samples shares chromatin
- GSE299114 Endothelial Cells retain inflammatory memory through chromatin remodeling [RNA-Seq 2] 53 samples shares chromatin
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.