Extensive folding variability between homologous chromosomes in mammalian cells
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 2239 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
- 2239 samples: 399 distinct titles, 1 of them repeatedGroups 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
- Extensive folding variability between homologous chromosomes in mammalian cellsMolecular systems biology · 2025
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 GSE254723_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 PRJNA1071571 and SRA study SRP487132. Searching any of these in the dataset finder brings you back here.
How we read this: Read from the first 400 of 2239 sample titles: 399 distinct titles with little repetition. 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.
- GSM8048457 totalRNAseq for mESC F123 Replicate1
- GSM8048458 totalRNAseq for mESC F123 Replicate2
- GSM8054226 ChIP-seq for H3K27me3 mark in mESC F123
- GSM8054227 ChIP-seq for RNAPII S5p in mESC F123
- GSM8054228 ChIP-seq for RNAPII S7p in mESC F123
- GSM8054341 F123 GAM library f123_0NP_GAM171024_E02_1_S13_R1_001
- GSM8054342 F123 GAM library f123_0NP_GAM171024_H04_1_S32_R1_001
- GSM8054343 F123 GAM library f123_0NP_GAM171108_H02_2_S112_R1_001
- GSM8054344 F123 GAM library f123_0NP_GAM171120_H02_1_S16_R1_001
- GSM8054345 F123 GAM library f123_0NP_GAM171120_H04_1_S32_R1_001
- GSM8054346 F123 GAM library f123_0NP_GAM171120_H09_1_S72_R1_001
- GSM8054347 F123 GAM library f123_0NP_GAM171120_H12_1_S96_R1_001
- GSM8054348 F123 GAM library f123_0NP_GAM171130_G12_1_S95_R1_001
- GSM8054349 F123 GAM library f123_0NP_GAM171130_H06_1_S48_R1_001
- GSM8054350 F123 GAM library f123_0NP_GAM171130_H11_1_S88_R1_001
- GSM8054351 F123 GAM library f123_0NP_GAM171130_H12_1_S96_R1_001
- GSM8054352 F123 GAM library f123_0NP_GAM171211_H06_1_S48_R1_001
- GSM8054353 F123 GAM library f123_0NP_GAM171211_H06_2_S144_R1_001
- GSM8054354 F123 GAM library f123_0NP_GAM171211_H12_1_S96_R1_001
- GSM8054355 F123 GAM library f123_0NP_GAM171211_H12_2_S192_R1_001
- GSM8054356 F123 GAM library f123_0NP_GAM171214_H02_1_S16_R1_001
- GSM8054357 F123 GAM library f123_0NP_GAM171221_H02_2_S112_R1_001
- GSM8054358 F123 GAM library f123_0NP_GAM171221_H04_2_S128_R1_001
- GSM8054359 F123 GAM library f123_0NP_GAM171221_H06_1_S48_R1_001
- GSM8054360 F123 GAM library f123_0NP_GAM171221_H06_2_S144_R1_001
- GSM8054361 F123 GAM library f123_0NP_GAM171221_H12_1_S96_R1_001
- GSM8054362 F123 GAM library f123_0NP_GAM180115_H12_1_S96_R1_001
- GSM8054363 F123 GAM library f123_0NP_GAM180116_H06_2_S144_R1_001
- GSM8054364 F123 GAM library f123_0NP_GAM180117_H06_2_S144_R1_001
- GSM8054365 F123 GAM library f123_0NP_GAM180123_A12_2_S185_R1_001
- GSM8054366 F123 GAM library f123_0NP_GAM180123_B06_2_S138_R1_001
- GSM8054367 F123 GAM library f123_0NP_GAM180207_H05_1_S40_R1_001
- GSM8054368 F123 GAM library f123_0NP_GAM180410_A07_2_S145_R1_001
- GSM8054369 F123 GAM library f123_0NP_GAM180410_B06_2_S138_R1_001
- GSM8054370 F123 GAM library f123_0NP_GAM180410_B07_2_S146_R1_001
- GSM8054371 F123 GAM library f123_0NP_GAM180410_C10_1_S75_R1_001
- GSM8054372 F123 GAM library f123_0NP_GAM180410_G06_1_S47_R1_001
- GSM8054373 F123 GAM library f123_0NP_GAM180716_B12_2_S186_R1_001
- GSM8054374 F123 GAM library f123_0NP_GAM180716_H03_2_S120_R1_001
- GSM8054375 F123 GAM library f123_0NP_GAM180716_H12_1_S96_R1_001
+ 2199 more — browse all 2239 samples with per-sample file links →
- GSE254710 Extensive folding variability between homologous chromosomes in mammalian cells [ChIP-Seq] 3 samples shares variability, chromosomes, homologous, extensive, mammalian, folding
- GSE254675 Extensive folding variability between homologous chromosomes in mammalian cells [RNA-seq] 2 samples shares variability, chromosomes, homologous, extensive, mammalian, folding
- GSE269952 Extensive mutual influences of SMC complexes shape 3D genome folding 176 samples shares extensive, folding
- GSE93730 Extensive Functional Redundancy of Mammalian Enhancers 52 samples shares extensive, mammalian
- GSE93728 Extensive Functional Redundancy of Mammalian Enhancers [ChIP-seq] 36 samples shares extensive, mammalian
- GSE93729 Extensive Functional Redundancy of Mammalian Enhancers [RNA-seq] 16 samples shares extensive, mammalian
- GSE339586 Extensive Crosstalk between BMP and Notch Signaling Pathways in Activated Adult Muscle Stem Cells [RNA-seq III] 24 samples shares extensive
- GSE305745 Extensive Crosstalk between BMP and Notch Signaling Pathways in Activated Adult Muscle Stem Cells [CUT&Tag] 14 samples shares extensive
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.