TEX cell fate and differentiation are shaped by 3D genome reorganization and chromatin architecture integrity [RNA-seq]
RNA-seq (gene expression) · mouse · 18 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
- 18 samples: 6 conditions, mostly in triplicateGroups 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 GSE275499_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 PRJNA1151122 and SRA study SRP528150. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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.
- GSM8478617 RNAseq D3_WT_Tex-eff_rep1 RNAseq D3_WT_Tex-eff
- GSM8478618 RNAseq D3_WT_Tex-eff_rep2 RNAseq D3_WT_Tex-eff
- GSM8478619 RNAseq D3_WT_Tex-prec_rep1 RNAseq D3_WT_Tex-prec
- GSM8478620 RNAseq D3_WT_Tex-prec_rep2 RNAseq D3_WT_Tex-prec
- GSM8478621 RNAseq D3_WT_Tex-prec_rep3 RNAseq D3_WT_Tex-prec
- GSM8478622 RNAseq D3_CTCFKO_Tex-eff_rep1 RNAseq D3_CTCFKO_Tex-eff
- GSM8478623 RNAseq D3_CTCFKO_Tex-eff_rep2 RNAseq D3_CTCFKO_Tex-eff
- GSM8478624 RNAseq D3_CTCFKO_Tex-eff_rep3 RNAseq D3_CTCFKO_Tex-eff
- GSM8478625 RNAseq D3_CTCFKO_Tex-prec_rep1 RNAseq D3_CTCFKO_Tex-pr…
- GSM8478626 RNAseq D3_CTCFKO_Tex-prec_rep2 RNAseq D3_CTCFKO_Tex-pr…
- GSM8478627 RNAseq D3_CTCFKO_Tex-prec_rep3 RNAseq D3_CTCFKO_Tex-pr…
- GSM8478628 RNAseq D3_CTCFKO_Tex-prec_rep4 RNAseq D3_CTCFKO_Tex-pr…
- GSM8478629 RNAseq D8_Tex-eff_rep1 RNAseq D8_Tex-eff
- GSM8478630 RNAseq D8_Tex-eff_rep2 RNAseq D8_Tex-eff
- GSM8478631 RNAseq D8_Tex-eff_rep3 RNAseq D8_Tex-eff
- GSM8478632 RNAseq D8_Tex-prec_rep1 RNAseq D8_Tex-prec
- GSM8478633 RNAseq D8_Tex-prec_rep2 RNAseq D8_Tex-prec
- GSM8478634 RNAseq D8_Tex-prec_rep3 RNAseq D8_Tex-prec
- GSE288605 Context-Dependent and Gene-Specific Role of Chromatin Architecture Mediated by Histone Modifiers and Loop-extrusion Machinery 96 samples shares tex, architecture, chromatin
- GSE330674 Glucocorticoid resistance during chronic social stress in mice: RNA-seq of prefrontal cortex 24 samples shares tex, rna-seq
- GSE277487 Single-nucleus RNA-seq of mouse cortex following CCI-induced traumatic brain injury across multiple time points 12 samples shares tex, rna-seq
- GSE327645 BACH1 acts as a pioneer repressor to enable macrophage plasticity and adaptation across tissues and inflammatory contexts [RNA-seq/ATAC-seq] 28 samples shares tex, rna-seq
- GSE283662 Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning 22 samples shares tex, 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, rna-seq
- GSE299114 Endothelial Cells retain inflammatory memory through chromatin remodeling [RNA-Seq 2] 53 samples shares chromatin, rna-seq
- GSE200323 Establishment of chromatin architecture interplays with embryo hypertranscription 158 samples shares architecture, 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.