EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 34 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
- 34 samples: 8 conditions, mostly in triplicateGroups 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
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 GSE250267_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 PRJNA1053260 and SRA study SRP478205. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 6 samples read as cases, 6 as controls.
How we read this: 8 replicated groups read from 34 sample titles; they account for 21 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…
- GSM7976435 Capture HiC-seq at E18.5 in the male urogenital sinus.
- GSM7976436 Capture HiC-seq at E18.5 in the female urogenital sinus.
- GSM7976437 CUT&RUN against H3K27me3 in 16 hpf zebrafish posterior trunk replicate 1
- GSM7976438 CUT&RUN against H3K27ac in 16 hpf zebrafish posterior trunk replicate 1 CUT&RUN against H3K27ac…
- GSM7976439 CUT&RUN against H3K27ac in 16 hpf zebrafish posterior trunk replicate 2 CUT&RUN against H3K27ac…
- GSM7976440 RNA-seq in E18.5 mutant female urogenital sinus replicate 1 RNA-seq in E18.5 mutant…
- GSM7976441 RNA-seq in E18.5 mutant female urogenital sinus replicate 2 RNA-seq in E18.5 mutant…
- GSM7976442 RNA-seq in E18.5 mutant female urogenital sinus replicate 3 RNA-seq in E18.5 mutant…
- GSM7976443 RNA-seq in E18.5 mutant male urogenital sinus replicate 1 RNA-seq in E18.5 mutant…
- GSM7976444 RNA-seq in E18.5 mutant male urogenital sinus replicate 2 RNA-seq in E18.5 mutant…
- GSM7976445 RNA-seq in E18.5 mutant male urogenital sinus replicate 3 RNA-seq in E18.5 mutant…
- GSM7976446 RNA-seq in E18.5 wild type female urogenital sinus replicate 1 RNA-seq in E18.5 wild t…
- GSM7976447 RNA-seq in E18.5 wild type female urogenital sinus replicate 2 RNA-seq in E18.5 wild t…
- GSM7976448 RNA-seq in E18.5 wild type female urogenital sinus replicate 3 RNA-seq in E18.5 wild t…
- GSM7976449 RNA-seq in E18.5 wild type male urogenital sinus replicate 1 RNA-seq in E18.5 wild t…
- GSM7976450 RNA-seq in E18.5 wild type male urogenital sinus replicate 2 RNA-seq in E18.5 wild t…
- GSM7976451 RNA-seq in E18.5 wild type male urogenital sinus replicate 3 RNA-seq in E18.5 wild t…
- GSM7977989 ChIP against H3K27me3 in E18.5 mouse male urogenital sinus replicate 1
- GSM7977990 ChIP against H3K27ac in E18.5 mouse male urogenital sinus replicate 1
- GSM7977991 ChIP against H3K27ac in E18.5 mouse female urogenital sinus replicate 1
- GSE250263 EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS [ATAC-seq] 14 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.