A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 17 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
- 17 samples: 16 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
- A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survivalNature communications · 2024
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 GSE232887_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 PRJNA974358 and SRA study SRP438595. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 17 sample titles: 16 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.
- GSM7385429 CHiC_FL_E115-WT
- GSM7385430 CHiC_MD_E115-WT
- GSM7385431 CHiC_H_E115-WT
- GSM7385432 ATAC_H_E115-WT_rep1
- GSM7385433 ATAC_H_E115-WT_rep2
- GSM7385434 12570_PCW17_LV_H3K27ac [re-analysis]
- GSM7385435 12570_PCW17_LV_input [re-analysis]
- GSM7385436 12570_PCW17_RV_H3K27ac
- GSM7385437 12570_PCW17_RV_input
- GSM7385438 12570_PCW17_LA_H3K27ac
- GSM7385439 12570_PCW17_LA_input
- GSM7385440 12570_PCW17_RA_H3K27ac
- GSM7385441 12570_PCW17_RA_input
- GSM7385442 12570_LV_PCW17_RNA [re-analysis]
- GSM7385443 12570_LA_PCW17_RNA
- GSM7385444 12570_RV_PCW17_RNA
- GSM7385445 12570_RA_PCW17_RNA
- GSE202126 Single-cell Total-RNA Profiling Unveils Regulatory Hubs of Transcription Factors 1089 samples shares regulatory
- GSE297013 Transcriptomic and Epigenomic Profiling of MYADM and RhoA Regulatory Networks in Metastatic Cancer Models 52 samples shares regulatory
- GSE63281 Targeted disruption of DNMT1, 3A and 3B in human embryonic stem cells 34 samples shares embryonic
- GSE306837 Unraveling Enteroendocrine Cell lineage dynamics and associated gene regulatory networks during intestinal development 13 samples shares regulatory
- GSE253161 Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease [NIH-3T3_K562_RNA_without_blocking] 1 samples shares regulatory
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.