SINE-MIR enhancer rewiring by Esrrb architecturally reprogram the pluripotency spectrum
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 78 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
- 78 samples: 69 distinct titles, 9 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.
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 GSE215453_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 PRJNA890291 and SRA study SRP401932. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 78 sample titles: 69 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.
- GSM6626450 Esrrb_sh1_E14_2i
- GSM6626451 Esrrb_sh1_E14_LS
- GSM6626452 Esrrb_sh2_E14_2i
- GSM6626453 Esrrb_sh2_E14_LS
- GSM6626454 shEV_E14_2i
- GSM6626455 shEV_E14_LS
- GSM6626456 CRISPRi_1sgScrmbl
- GSM6626457 CRISPRi_3sgMIR
- GSM6626458 CRISPRi_sgMIR22
- GSM6626459 CRISPRi_sgMIR23
- GSM6626460 CRISPRi_sgScrmbl
- GSM6626461 EPSC_Esrrb_sh1
- GSM6626462 EPSC_Esrrb_sh2
- GSM6626463 EPSC_shEV
- GSM6626464 shEV
- GSM6626465 Yy1_sh1
- GSM6626466 Yy1_sh2
- GSM6626467 1__Esrrb_ChIP_Input
- GSM6626468 2__H3K4me3_ChIP_Input
- GSM6626469 3__Esrrb_ChIP_Sample
- GSM6626470 4__H3K4me3_ChIP_Sample
- GSM6626471 sgMIR22_Cas9_IP
- GSM6626472 sgMIR22_Input
- GSM6626473 sgMIR23_Cas9_IP
- GSM6626474 sgMIR23_Input
- GSM6626475 ScrmblESRRB
- GSM6626476 ScrmblInput
- GSM6626477 sgMIR22ESRRB
- GSM6626478 sgMIR23ESRRB
- GSM6626479 sgMIR23Input
- GSM6626480 YY1_ChIP_in_shESRRB-sh1_Input
- GSM6626481 YY1_ChIP_in_shESRRB-sh1_Sample
- GSM6626482 YY1_ChIP_in_shEV_Input
- GSM6626483 YY1_ChIP_in_shEV_Sample
- GSM6637440 HiC_ESC-rep1
- GSM6637441 HiC_2i-rep1
- GSM6637442 HiC_EPSC-rep1
- GSM6637444 HiC_RA-rep1
- GSM6637445 HiC_ESC-rep2
- GSM6637446 HiC_2i-rep2
+ 38 more — browse all 78 samples with per-sample file links →
- GSE313769 SATB1 Lowers The TCR Signaling Threshold For Thymocytes Positive Selection via Super-enhancer Reprogramming 122 samples shares reprogram, enhancer
- GSE278100 Foxa1-Mediated Chromatin Remodeling and Enhancer Reprogramming Promotes Gemcitabine Resistance in Pancreatic Cancer 54 samples shares reprogram, enhancer
- GSE282319 Long read RNA sequencing reveals a new long non-coding RNA that regulates somatic cell reprogramming and pluripotency 45 samples shares pluripotency, reprogram
- GSE294457 TCA cycle rewiring underpins histone acetylation sourcing and cell-fate transitions during exit from naive pluripotency 12 samples shares pluripotency, rewiring
- GSE237954 Oncofetal reprogramming drives phenotypic plasticity in WNT-dependent colorectal cancer 122 samples shares reprogram
- GSE248534 Lamin A/C-regulated cysteine catabolic flux modulates stem cell fate through epigenome reprogramming 72 samples shares reprogram
- GSE294258 Intracellular iron homeostasis-regulated epigenetic reprogramming contributes to -7/del(7q) leukemia 71 samples shares reprogram
- GSE267452 Loss of Nuclear Receptor Nr4a3 Alleviates Cellular Senescence to Promote Adult Direct Cardiac Reprogramming 54 samples shares reprogram
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.