Promoter- and Enhancer-Dependent Cohesin Loading Initiates Chromosome Looping to Fold Tcrb Loci for Long-Range Recombination [CUT&RUN]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 42 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
- 42 samples: 34 distinct titles, 8 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
- Promoter- and enhancer-dependent cohesin loading initiates chromosome looping to fold Tcrb loci for long-range recombinationCell reports · 2025
Read the full summary ↓
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 GSE296305_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 PRJNA1258901 and SRA study SRP583225. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 42 sample titles: 34 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.
- GSM8968340 R1KO_RNAPol2Ser20821CR_DN_1
- GSM8968341 R1KO_RNAPol2Ser20905CR_DN_2
- GSM8968342 V1TxS_RNAPol2Ser20821CR_DN_1
- GSM8968343 V1TxS_RNAPol2Ser20905CR_DN_2
- GSM8968344 Misc_IgGcntrl0821CR_DN
- GSM8968345 Misc_IgGcntrl0905CR_DN
- GSM8968346 EbKO_H3K27ac10727CR_DN_1
- GSM8968347 EbKO_H3K27ac10727CR_DN_2
- GSM8968348 R1KO_H3K27ac0727CR_DN_1
- GSM8968349 R1KO_H3K27ac0727CR_DN_2
- GSM8968350 V1TxS_H3K27ac0724CR_DN_1
- GSM8968351 V1TxS_H3K27ac0727CR_DN_2
- GSM8968352 HTS_SO85_03_RCTKO_Nipbl1030CR_DN_1_S3
- GSM8968353 HTS_SO85_07_RCTKO_Nipbl1206CR_DN_2_S7
- GSM8968354 HTS_SO85_11_EbKO_Nipbl1206CR_DN_3_S11
- GSM8968355 HTS_SO85_21_EbKO_Nipbl1212CR_DN_4_S21
- GSM8968356 R1KO_Nipbl0816CR_DN_1
- GSM8968357 R1KO_Nipbl0816CR_DN_2
- GSM8968358 V1CScr_Nipbl0816CR_DN_1
- GSM8968359 V1CScr_Nipbl0821CR_DN_2
- GSM8968360 V1PKO_Nipbl0816CR_DN_1
- GSM8968361 V1PKO_Nipbl0816CR_DN_2
- GSM8968362 V1TxS_Nipbl0816CR_DN_1
- GSM8968363 V1TxS_Nipbl0816CR_DN_2
- GSM8968364 HTSSO52_V1TxS_Rad210712CR_DN_2
- GSM8968365 HTSSO57_V1TxS_Rad210712CR_DN_1
- GSM8968366 HTS_SO85_02_RCTKO_Rad211030CR_DN_1_S2
- GSM8968367 HTS_SO85_06_RCTKO_Rad211206CR_DN_2_S6
- GSM8968368 HTS_SO85_10_EbKO_Rad211206CR_DN_3_S10
- GSM8968369 HTS_SO85_20_EbKO_Rad211212CR_DN_4_S20
- GSM8968370 R1KO_Rad210712CR_DN_1
- GSM8968371 R1KO_Rad210712CR_DN_2
- GSM8968372 V1CScr_Rad210712CR_DN_1
- GSM8968373 V1CScr_Rad210712CR_DN_2
- GSM8968374 V1PKO_Rad21712CR_DN_1
- GSM8968375 V1PKO_Rad21712CR_DN_2
- GSM8968376 HTS_SO85_01_RCTKO_CTCF1030CR_DN_1_S1
- GSM8968377 HTS_SO85_09_RCTKO_CTCF1206CR_DN_2_S9
- GSM8968378 HTS_SO85_12_EbKO_CTCF1206CR_DN_1_S12
- GSM8968379 HTS_SO85_22_EbKO_CTCF1212CR_DN_2_S22
+ 2 more — browse all 42 samples with per-sample file links →
- GSE295964 Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at the promoters of genes expressed during meiosis [CUT&RUN] 13 samples shares cut, run, promoter
- GSE289642 Noncanonical PRC2 chromatin association reveals a key role of EZHIP in intergenerational epigenetic memory transition [ChIP-Seq, Cut & Run] 107 samples shares cut, run
- GSE303384 Mechanism of maintenance and establishment of repression by the Mtg16 tumor suppressor [CUT&RUN, ChIP-Seq] 92 samples shares cut, run
- GSE306261 Astrocyte glucocorticoid receptor signaling restricts neuronal plasticity [CUT&RUN] 50 samples shares cut, run
- GSE313359 Hippocampal estrogen levels, receptor types and epigenetics contribute to sex-specific memory-vulnerabilities to concurrent acute stresses [Cut & Run] 45 samples shares cut, run
- GSE292333 H2AK119ub1-MLL2 counteraction underlies heritable H3K27me3 formation in oocytes [CATCH-seq and CUT&RUN] 44 samples shares cut, run
- GSE298002 Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [CUT&Run] 38 samples shares cut, run
- GSE274875 A mutant ASXL1-EHMT complex contributes to heterochromatin dysfunction in clonal hematopoiesis and chronic monomyelocytic leukemia [Cut & Run] 38 samples shares cut, run
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.