Coordination between transcriptional orientation and nucleoprotein complexes generate chromatin configuration of IgH locus
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 96 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
- 96 samples: 47 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.
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 GSE241741_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 PRJNA1009442 and SRA study SRP456959. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 94 samples.
How we read this: 47 replicated groups read from 96 sample titles; they account for 94 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.
- GSM7732848 Capture Hi-C EF1a For #1 rep1 Capture Hi-C EF1a For #1
- GSM7732849 Capture Hi-C EF1a For #1 rep2 Capture Hi-C EF1a For #1
- GSM7732850 Capture Hi-C EF1a Rev #1 rep1 Capture Hi-C EF1a Rev #1
- GSM7732851 Capture Hi-C EF1a Rev #1 rep2 Capture Hi-C EF1a Rev #1
- GSM7732852 Capture Hi-C EF1a Rev #2 rep1 Capture Hi-C EF1a Rev #2
- GSM7732853 Capture Hi-C EF1a Rev #2 rep2 Capture Hi-C EF1a Rev #2
- GSM7732854 Capture Hi-C EF1a For #2 rep1 Capture Hi-C EF1a For #2
- GSM7732855 Capture Hi-C EF1a For #2 rep2 Capture Hi-C EF1a For #2
- GSM7732856 Capture Hi-C Eu-- #2 rep1 Capture Hi-C Eu-- #2
- GSM7732857 Capture Hi-C Eu-- #2 rep2 Capture Hi-C Eu-- #2
- GSM7732858 Capture Hi-C Eu-- #1 rep1 Capture Hi-C Eu-- #1
- GSM7732859 Capture Hi-C Eu-- #1 rep2 Capture Hi-C Eu-- #1
- GSM7732860 Capture Hi-C WT rep1 Capture Hi-C WT
- GSM7732861 Capture Hi-C WT rep2 Capture Hi-C WT
- GSM7733041 Directional RNA-Seq Eu-- #2 rep1 Directional RNA-Seq Eu-…
- GSM7733042 Directional RNA-Seq Eu-- #2 rep2 Directional RNA-Seq Eu-…
- GSM7733043 Directional RNA-Seq Eu-- #1 rep1 Directional RNA-Seq Eu-…
- GSM7733044 Directional RNA-Seq Eu-- #1 rep2 Directional RNA-Seq Eu-…
- GSM7733045 Directional RNA-Seq EF1a Rev #2 rep1 Directional RNA-Seq EF1…
- GSM7733046 Directional RNA-Seq EF1a Rev #2 rep2 Directional RNA-Seq EF1…
- GSM7733047 Directional RNA-Seq EF1a For #2 rep1 Directional RNA-Seq EF1…
- GSM7733048 Directional RNA-Seq EF1a For #2 rep2 Directional RNA-Seq EF1…
- GSM7733049 Directional RNA-Seq EF1a For #1 rep1 Directional RNA-Seq EF1…
- GSM7733050 Directional RNA-Seq EF1a For #1 rep2 Directional RNA-Seq EF1…
- GSM7733051 Directional RNA-Seq EF1a Rev #1 rep1 Directional RNA-Seq EF1…
- GSM7733052 Directional RNA-Seq EF1a Rev #1 rep2 Directional RNA-Seq EF1…
- GSM7733053 Directional RNA-Seq WT rep2 Directional RNA-Seq WT
- GSM7733054 Directional RNA-Seq 3'CBEs-- rep1 Directional RNA-Seq 3'C…
- GSM7733055 Directional RNA-Seq 3'CBEs-- rep2 Directional RNA-Seq 3'C…
- GSM7733056 Directional RNA-Seq WT rep1 Directional RNA-Seq WT
- GSM7733057 Directional RNA-Seq 3'CBEs Inv #1 rep1 Directional RNA-Seq 3'C…
- GSM7733058 Directional RNA-Seq 3'CBEs Inv #1 rep2 Directional RNA-Seq 3'C…
- GSM7733059 Directional RNA-Seq 3'CBEs Inv #2 rep1 Directional RNA-Seq 3'C…
- GSM7733060 Directional RNA-Seq 3'CBEs Inv #2 rep2 Directional RNA-Seq 3'C…
- GSM7733061 CTCF ChIP-Seq WT rep1 CTCF ChIP-Seq WT
- GSM7733062 Rad21 ChIP-Seq WT rep1 Rad21 ChIP-Seq WT
- GSM7733063 CTCF ChIP-Seq WT rep2 CTCF ChIP-Seq WT
- GSM7733064 Rad21 ChIP-Seq WT rep2 Rad21 ChIP-Seq WT
- GSM7733065 Rad21 ChIP-Seq EF1a Rev #2 rep1 Rad21 ChIP-Seq EF1a Re…
- GSM7733066 Rad21 ChIP-Seq EF1a Rev #2 rep2 Rad21 ChIP-Seq EF1a Re…
+ 56 more — browse all 96 samples with per-sample file links →
- GSE241668 Coordination between transcriptional orientation and nucleoprotein complexes generate chromatin configuration of IgH locus [ChIP-Seq] 48 samples shares nucleoprotein, configuration, coordination, orientation, complexes, chromatin, generate, locus
- GSE241667 Coordination between transcriptional orientation and nucleoprotein complexes generate chromatin configuration of IgH locus [Directional RNA-Seq] 20 samples shares nucleoprotein, configuration, coordination, orientation, complexes, chromatin, generate, locus
- GSE308516 Resf1 is required for normal placental development and configuration of trophoblast cell-specific heterochromatin [ChIP-seq] 25 samples shares configuration, chromatin
- GSE308515 Resf1 is required for normal placental development and configuration of trophoblast cell-specific heterochromatin [RNA-seq] 17 samples shares configuration, chromatin
- GSE262263 The chromatin accessibility landscape of mouse oocytes during configuration transition (CUT&Tag) 12 samples shares configuration, chromatin
- GSE299391 Chromatin-intrinsic mechanisms determine orientation-specific class switch recombination [ChIP-Seq] 8 samples shares orientation, chromatin
- GSE261972 The chromatin accessibility landscape of mouse oocytes during configuration transition 8 samples shares configuration, chromatin
- GSE262265 The chromatin accessibility landscape of mouse oocytes during configuration transition (RNA-Seq) 4 samples shares configuration, 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.