GEO series

Coordination between transcriptional orientation and nucleoprotein complexes generate chromatin configuration of IgH locus [ChIP-Seq]

GSE241668 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 48 samples Submitted 2025/01/22 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 48 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: 48 samples: 23 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.

Summary (written by the submitters)

In this study we combined epigenetic, transcriptional and recombinational assays of wild type and mutated Igh alleles to uncover structure function relationships between sequences that configure the locus for the first step of gene assembly.

This dataset

Open GSE241668 in finder → Find more mouse ChIP / ATAC / CUT&Tag datasets →

Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE241668_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1009088 and SRA study SRP456968. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

23 conditions, mostly in duplicate

CTCF ChIP-Seq WT ×2 Rad21 ChIP-Seq WT ×2 Rad21 ChIP-Seq EF1a Rev #2 ×2 CTCF ChIP-Seq EF1a Rev #1 ×2 H3K4me3 ChIP-Seq EF1a Rev #1 ×2 H3K27ac ChIP-Seq EF1a Rev #1 ×2 CTCF ChIP-Seq EF1a Rev #2 ×2 H3K4me3 ChIP-Seq EF1a Rev #2 ×2 +17 more

Supports a between-group comparison across 46 samples.

How we read this: 23 replicated groups read from 48 sample titles; they account for 46 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.

Samples in this study

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…
GSM7733067 CTCF ChIP-Seq EF1a Rev #1 rep1 CTCF ChIP-Seq EF1a Rev…
GSM7733068 CTCF ChIP-Seq EF1a Rev #1 rep2 CTCF ChIP-Seq EF1a Rev…
GSM7733069 H3K4me3 ChIP-Seq EF1a Rev #1 rep1 H3K4me3 ChIP-Seq EF1a …
GSM7733070 H3K4me3 ChIP-Seq EF1a Rev #1 rep2 H3K4me3 ChIP-Seq EF1a …
GSM7733071 H3K27ac ChIP-Seq EF1a Rev #1 rep1 H3K27ac ChIP-Seq EF1a …
GSM7733072 H3K27ac ChIP-Seq EF1a Rev #1 rep2 H3K27ac ChIP-Seq EF1a …
GSM7733073 Rad21 ChIP-Seq EF1a Rev #1 rep1
GSM7733074 Rad21ChIP-Seq EF1a Rev #1 rep2
GSM7733075 CTCF ChIP-Seq EF1a Rev #2 rep1 CTCF ChIP-Seq EF1a Rev …
GSM7733076 CTCF ChIP-Seq EF1a Rev #2 rep2 CTCF ChIP-Seq EF1a Rev …
GSM7733077 H3K4me3 ChIP-Seq EF1a Rev #2 rep1 H3K4me3 ChIP-Seq EF1a R…
GSM7733078 H3K4me3 ChIP-Seq EF1a Rev #2 rep2 H3K4me3 ChIP-Seq EF1a R…
GSM7733079 H3K27ac ChIP-Seq EF1a Rev #2 rep1 H3K27ac ChIP-Seq EF1a R…
GSM7733080 H3K27ac ChIP-Seq EF1a Rev #2 rep2 H3K27ac ChIP-Seq EF1a R…
GSM7733081 CTCF ChIP-Seq EF1a For #2 rep1 CTCF ChIP-Seq EF1a For …
GSM7733082 CTCF ChIP-Seq EF1a For #2 rep2 CTCF ChIP-Seq EF1a For …
GSM7733083 H3K4me3 ChIP-Seq EF1a For #2 rep1 H3K4me3 ChIP-Seq EF1a F…
GSM7733084 H3K4me3 ChIP-Seq EF1a For #2 rep2 H3K4me3 ChIP-Seq EF1a F…
GSM7733085 H3K27ac ChIP-Seq EF1a For #2 rep1 H3K27ac ChIP-Seq EF1a F…
GSM7733086 Rad21 ChIP-Seq EF1a For #2 rep1 Rad21 ChIP-Seq EF1a For…
GSM7733087 H3K27ac ChIP-Seq EF1a For #2 rep2 H3K27ac ChIP-Seq EF1a F…
GSM7733088 Rad21 ChIP-Seq EF1a For #2 rep2 Rad21 ChIP-Seq EF1a For…
GSM7733089 CTCF ChIP-Seq EF1a For #1 rep1 CTCF ChIP-Seq EF1a For …
GSM7733090 CTCF ChIP-Seq EF1a For #1 rep2 CTCF ChIP-Seq EF1a For …
GSM7733091 H3K4me3 ChIP-Seq EF1a For #1 rep1 H3K4me3 ChIP-Seq EF1a F…
GSM7733092 H3K4me3 ChIP-Seq EF1a For #1 rep2 H3K4me3 ChIP-Seq EF1a F…
GSM7733093 H3K27ac ChIP-Seq EF1a For #1 rep1 H3K27ac ChIP-Seq EF1a F…
GSM7733094 H3K27ac ChIP-Seq EF1a For #1 rep2 H3K27ac ChIP-Seq EF1a F…
GSM7733095 Rad21 ChIP-Seq EF1a For #1 rep1 Rad21 ChIP-Seq EF1a For…
GSM7733096 Rad21 ChIP-Seq EF1a For #1 rep2 Rad21 ChIP-Seq EF1a For…
GSM7733097 Rad21 ChIP-Seq Eu-- rep2 Rad21 ChIP-Seq Eu
GSM7733098 CTCF ChIP-Seq Eu-- rep1 CTCF ChIP-Seq Eu
GSM7733099 CTCF ChIP-Seq Eu-- rep2 CTCF ChIP-Seq Eu
GSM7733100 H3K4me3 ChIP-Seq Eu-- rep1 H3K4me3 ChIP-Seq Eu

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

GSE241741 Coordination between transcriptional orientation and nucleoprotein complexes generate chromatin configuration of IgH locus 96 samples shares nucleoprotein, configuration, coordination, orientation, complexes, chromatin, generate
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
GSE308516 Resf1 is required for normal placental development and configuration of trophoblast cell-specific heterochromatin [ChIP-seq] 25 samples shares configuration, chromatin, chip-seq
GSE299391 Chromatin-intrinsic mechanisms determine orientation-specific class switch recombination [ChIP-Seq] 8 samples shares orientation, chromatin, chip-seq
GSE262263 The chromatin accessibility landscape of mouse oocytes during configuration transition (CUT&Tag) 12 samples shares configuration, chromatin
GSE261972 The chromatin accessibility landscape of mouse oocytes during configuration transition 8 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
GSE262265 The chromatin accessibility landscape of mouse oocytes during configuration transition (RNA-Seq) 4 samples shares configuration, chromatin

Search all mouse ChIP / ATAC / CUT&Tag datasets in GEO →

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