CUT&RUN sequencing - E12 mouse embryonic cortices ZBTB7A - GATAD2B - H3K27ac…
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 18 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
- 18 samples: 6 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.
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 GSE294107_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 PRJNA1248393 and SRA study SRP577397. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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.
- GSM8898780 ZBTB7A CUT&RUN Repeat 1 ZBTB7A CUT&RUN Repeat
- GSM8898781 ZBTB7A CUT&RUN Repeat 2 ZBTB7A CUT&RUN Repeat
- GSM8898782 ZBTB7A CUT&RUN Repeat 3 ZBTB7A CUT&RUN Repeat
- GSM8898783 H3K4Me3 CUT&RUN Repeat 1 H3K4Me3 CUT&RUN Repeat
- GSM8898784 H3K4Me3 CUT&RUN Repeat 2 H3K4Me3 CUT&RUN Repeat
- GSM8898785 H3K4Me3 CUT&RUN Repeat 3 H3K4Me3 CUT&RUN Repeat
- GSM8898786 H3K27Ac CUT&RUN Repeat 1 H3K27Ac CUT&RUN Repeat
- GSM8898787 H3K27Ac CUT&RUN Repeat 2 H3K27Ac CUT&RUN Repeat
- GSM8898788 H3K27Ac CUT&RUN Repeat 3 H3K27Ac CUT&RUN Repeat
- GSM8898789 GATAD2B CUT&RUN Repeat 1 GATAD2B CUT&RUN Repeat
- GSM8898790 GATAD2B CUT&RUN Repeat 2 GATAD2B CUT&RUN Repeat
- GSM8898791 GATAD2B CUT&RUN Repeat 3 GATAD2B CUT&RUN Repeat
- GSM8898792 H3K4Me1 CUT&RUN Repeat 1 H3K4Me1 CUT&RUN Repeat
- GSM8898793 H3K4Me1 CUT&RUN Repeat 2 H3K4Me1 CUT&RUN Repeat
- GSM8898794 H3K4Me1 CUT&RUN Repeat 3 H3K4Me1 CUT&RUN Repeat
- GSM8898795 IgG CUT&RUN Repeat 1 IgG CUT&RUN Repeat
- GSM8898796 IgG CUT&RUN Repeat 2 IgG CUT&RUN Repeat
- GSM8898797 IgG CUT&RUN Repeat 3 IgG CUT&RUN Repeat
- GSE294144 RNA sequencing - E12 mouse embryonic cortices Emx1-Cre Zbtb7a-flox cKO vs WT 10 samples shares zbtb7a, e12, embryonic, cortices
- GSE326232 Lineage Plasticity Driven by GATA6 Loss Fuels Colorectal Cancer Metastasis [H3K27ac_CUT&RUN] 8 samples shares h3k27ac, cut, run
- 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
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.