TEX cell fate and differentiation are shaped by 3D genome reorganization and chromatin architecture integrity [D3]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 18 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- 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 GSE284090_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1197112 and SRA study SRP551141. 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.
- GSM8478587 ATAC D3_WT_Tex-prec_rep1 ATAC D3_WT_Tex-prec
- GSM8478588 ATAC D3_WT_Tex-eff_rep1 ATAC D3_WT_Tex-eff
- GSM8478589 ATAC D3_WT_Tex-prec_rep2 ATAC D3_WT_Tex-prec
- GSM8478590 ATAC D3_WT_Tex-eff_rep2 ATAC D3_WT_Tex-eff
- GSM8478591 ATAC D3_WT_Tex-prec_rep3 ATAC D3_WT_Tex-prec
- GSM8478592 ATAC D3_WT_Tex-eff_rep3 ATAC D3_WT_Tex-eff
- GSM8478593 ATAC D3_CTCFKO_Tex-prec_rep1 ATAC D3_CTCFKO_Tex-prec
- GSM8478594 ATAC D3_CTCFKO_Tex-eff_rep1 ATAC D3_CTCFKO_Tex-eff
- GSM8478595 ATAC D3_CTCFKO_Tex-prec_rep2 ATAC D3_CTCFKO_Tex-prec
- GSM8478596 ATAC D3_CTCFKO_Tex-eff_rep2 ATAC D3_CTCFKO_Tex-eff
- GSM8478597 ATAC D3_CTCFKO_Tex-prec_rep3 ATAC D3_CTCFKO_Tex-prec
- GSM8478598 ATAC D3_CTCFKO_Tex-eff_rep3 ATAC D3_CTCFKO_Tex-eff
- GSM8478605 CTCF CUTRUN D3_Tex-prec_rep1 CTCF CUTRUN D3_Tex-prec
- GSM8478606 CTCF CUTRUN D3_Tex-prec_rep2 CTCF CUTRUN D3_Tex-prec
- GSM8478607 CTCF CUTRUN D3_Tex-prec_rep3 CTCF CUTRUN D3_Tex-prec
- GSM8478608 CTCF CUTRUN D3_Tex-eff_rep1 CTCF CUTRUN D3_Tex-eff
- GSM8478609 CTCF CUTRUN D3_Tex-eff_rep2 CTCF CUTRUN D3_Tex-eff
- GSM8478610 CTCF CUTRUN D3_Tex-eff_rep3 CTCF CUTRUN D3_Tex-eff
- GSE288605 Context-Dependent and Gene-Specific Role of Chromatin Architecture Mediated by Histone Modifiers and Loop-extrusion Machinery 96 samples shares tex, architecture, chromatin
- GSE283662 Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning 22 samples shares tex, chromatin
- GSE304211 H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [CUTnTAG] 128 samples shares reorganization, chromatin
- GSE310322 Mapping self-associating chromatin hubs identifies Id proteins as key determinants of exhausted T cell fate 37 samples shares chromatin, fate
- GSE292285 Depletion of lamin-associated polypeptide 2 alpha leads to chromatin reorganization and redistribution of A-type lamins to open genomic regions [ChIP-seq] 22 samples shares reorganization, chromatin
- GSE233039 The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [ATAC-Seq] 18 samples shares chromatin, integrity
- GSE200323 Establishment of chromatin architecture interplays with embryo hypertranscription 158 samples shares architecture, chromatin
- GSE307620 Spatial chromatin architecture and accessibility co-profiling of mammalian tissues 2 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.