EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS [ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 14 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
- 14 samples: 3 × ATAC-seq in fish 16 hpf posterior trunk vs 2 × ATAC-seq in mouse E18.5 male urogenital sinus vs 2 × ATAC-seq in mouse E18.5 female urogenital sinusGroups 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
- EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE DURING THE EMERGENCE OF DIGITS AND GENITALSbioRxiv : the preprint server for biology · 2024
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 GSE250263_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 PRJNA1053267 and SRA study SRP478199. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 7 samples.
How we read this: 3 replicated groups read from 14 sample titles; they account for 7 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.
- GSM7976421 ATAC-seq in fish 16 hpf head replicate 1
- GSM7976422 ATAC-seq in fish 16 hpf posterior trunk replicate 1 ATAC-seq in fish 16 hpf…
- GSM7976423 ATAC-seq in fish 30 hpf head replicate 1
- GSM7976424 ATAC-seq in fish 16 hpf posterior trunk replicate 2 ATAC-seq in fish 16 hpf…
- GSM7976425 ATAC-seq in fish 16 hpf posterior trunk replicate 3 ATAC-seq in fish 16 hpf…
- GSM7976426 ATAC-seq in fish 16 hpf anterior trunk replicate 1
- GSM7976427 ATAC-seq in fish 16 hpf rhombomeres replicate 1
- GSM7976428 ATAC-seq in fish 30 hpf cloaca replicate 1
- GSM7976429 ATAC-seq in fish 30 hpf tail bud replicate 1
- GSM7976430 ATAC-seq in fish 30 hpf trunk replicate 1
- GSM7976431 ATAC-seq in mouse E18.5 male urogenital sinus replicate 1 ATAC-seq in mouse E18.5…
- GSM7976432 ATAC-seq in mouse E18.5 female urogenital sinus replicate 1 ATAC-seq in mouse E18.5…
- GSM7976433 ATAC-seq in mouse E18.5 male urogenital sinus replicate 2 ATAC-seq in mouse E18.5…
- GSM7976434 ATAC-seq in mouse E18.5 female urogenital sinus replicate 2 ATAC-seq in mouse E18.5…
- GSE250267 EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS 34 samples shares genitals, cloacal, digits, evolutionary, regulatory, co-option, ancestral, emergence
- GSE250367 EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS [ChIP-seq] 3 samples shares genitals, cloacal, digits, evolutionary, regulatory, co-option, ancestral, emergence
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.