CTCF binding polarity determines chromatin looping
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 506 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
- 506 samples: 34 conditions, mostly with about 7 replicates eachGroups 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 GSE72720_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 PRJNA294741 and SRA study SRP063007. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 325 samples.
How we read this: 34 replicated groups read from the first 400 of 506 sample titles; they account for 325 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.
- GSM1828650 CTCF_ChIPseq_E14_ESC
- GSM1828651 CTCF_ChIPseq_E14_NPC
- GSM1864278 ESC_chr10_57142766 ESC_chr10
- GSM1864279 ESC_chr10_57168814 ESC_chr10
- GSM1864280 ESC_chr10_57190786 ESC_chr10
- GSM1864281 ESC_chr10_57454886 ESC_chr10
- GSM1864282 ESC_chr10_57463988 ESC_chr10
- GSM1864283 ESC_chr10_57473250 ESC_chr10
- GSM1864284 ESC_chr10_57515889 ESC_chr10
- GSM1864285 ESC_chr10_57568589 ESC_chr10
- GSM1864286 ESC_chr10_69781902 ESC_chr10
- GSM1864287 ESC_chr10_79132358 ESC_chr10
- GSM1864288 ESC_chr10_79639380 ESC_chr10
- GSM1864289 ESC_chr11_102160656 ESC_chr11
- GSM1864290 ESC_chr11_102263652 ESC_chr11
- GSM1864291 ESC_chr11_102273033 ESC_chr11
- GSM1864292 ESC_chr11_102282204 ESC_chr11
- GSM1864293 ESC_chr11_102295886 ESC_chr11
- GSM1864294 ESC_chr11_102348013 ESC_chr11
- GSM1864295 ESC_chr11_102552165 ESC_chr11
- GSM1864296 ESC_chr11_102755095 ESC_chr11
- GSM1864297 ESC_chr11_102762586 ESC_chr11
- GSM1864298 ESC_chr11_102854422 ESC_chr11
- GSM1864299 ESC_chr11_102864574 ESC_chr11
- GSM1864300 ESC_chr11_103194723 ESC_chr11
- GSM1864301 ESC_chr11_31537749 ESC_chr11
- GSM1864302 ESC_chr11_32041144 ESC_chr11
- GSM1864303 ESC_chr11_32138087 ESC_chr11
- GSM1864304 ESC_chr11_32149201 ESC_chr11
- GSM1864305 ESC_chr11_32224410 ESC_chr11
- GSM1864306 ESC_chr11_32609632 ESC_chr11
- GSM1864307 ESC_chr11_77487588 ESC_chr11
- GSM1864308 ESC_chr12_30412470 ESC_chr12
- GSM1864309 ESC_chr12_74319439 ESC_chr12
- GSM1864310 ESC_chr13_72906854
- GSM1864311 ESC_chr14_77361458 ESC_chr14
- GSM1864312 ESC_chr14_77370919 ESC_chr14
- GSM1864313 ESC_chr15_8564527 ESC_chr15
- GSM1864314 ESC_chr15_8577349 ESC_chr15
- GSM1864315 ESC_chr15_89028294 ESC_chr15
+ 466 more — browse all 506 samples with per-sample file links →
- GSE72539 CTCF binding polarity determines chromatin looping [4C] 504 samples shares ctcf, determines, chromatin, polarity, binding, looping
- GSE306869 The RNA binding protein LIN28A mediates chromatin dynamics during neuronal differentiation 24 samples shares chromatin, binding
- GSE262521 Disentangling the architectural and non-architectural functions of CTCF and cohesin in global gene regulation 68 samples shares ctcf
- GSE234248 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [RNA-seq] 24 samples shares ctcf
- GSE234251 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [Mnase-seq] 21 samples shares ctcf
- GSE264193 H3K27 dimethylation dynamics reveal stepwise establishment of facultative heterochromatin in early mouse embryos [ChIP-seq] 57 samples shares 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
- GSE237534 INO80 / SWR remodelers regulate Pol II transcription through BRD2 and chromatin landscape 217 samples shares 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.