Genomic context sensitizes regulatory elements to genetic disruption
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 154 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
- 154 samples: 154 samples, each with a distinct title — no replicated groupsGroups 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
- Genomic context sensitizes regulatory elements to genetic disruptionMolecular cell · 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 GSE241708_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 PRJNA1009152 and SRA study SRP457013. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 154 sample titles: 154 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.
- GSM7734070 mESC-dPiga-CUT&RUN-CTCF-BS10373A
- GSM7734071 mesendoderm-dPiga-CUT&RUN-CTCF-BS10382A
- GSM7734072 mesendoderm-LP300-CUT&RUN-CTCF-BS10383A
- GSM7734073 mesendoderm-Igf2_Igf2_157kb~Igf2SV-CUT&RUN-CTCF-BS10384A
- GSM7734074 mesendoderm-Igf2_Igf2_miICR~Igf2SV-CUT&RUN-CTCF-BS10387A
- GSM7734075 mesendoderm-Igf2_Igf2_dCTCFinICR-CUT&RUN-CTCF-BS10389A
- GSM7734076 BAC-Igf2_Igf2_157kb~Igf2SV-BS08196A
- GSM7734077 BAC-Igf2_Igf2_miICR~Igf2SV-BS08664A
- GSM7734078 BAC-Igf2_Igf2_dEnh~miICR~Igf2SV-BS08667A
- GSM7734079 BAC-Sox2_DistalLCR_H19enh-BS11097A
- GSM7734080 BAC-Sox2_DistalLCR_H19enh~inverted-BS11098A
- GSM7734081 BAC-Igf2_Igf2_dCTCFinICR-BS09866A
- GSM7734082 BAC-Igf2_Igf2_dEnh~dCTCFinICR-BS09687A
- GSM7734083 BAC-Igf2_Igf2_Sox2DistalLCR~miICR-BS11125A
- GSM7734084 BAC-Igf2_Igf2_Sox2DistalLCR~dCTCFinICR-BS11128A
- GSM7734085 BAC-Igf2_Igf2_Sox2DistalLCR~inverted~miICR-BS11131A
- GSM7734086 BAC-Igf2_Igf2_Sox2DistalLCR~inverted~dCTCFinICR-BS11137A
- GSM7734087 BAC-Igf2_Igf2_inverted~miICR-BS12671A
- GSM7734088 BAC-Igf2_Igf2_inverted~dCTCFinICR-BS14102A
- GSM7734089 BAC-Igf2_Igf2_inverted~dEnh~miICR-BS12529A
- GSM7734090 BAC-Igf2_Igf2_inverted~dEnh~dCTCFinICR-BS12675A
- GSM7734091 BAC-Igf2_Igf2_miICR~dIgf2~Sox2-BS16232A
- GSM7734092 BAC-Igf2_Igf2_dCTCFinICR~dIgf2~Sox2-BS15912A
- GSM7734093 BAC-Sox2_Sox2_dDistalLCR~H19Enh-BS17632A
- GSM7734094 BAC-Sox2_Sox2_dDistalLCR~H19Enh~inverted-BS17635A
- GSM7734095 mESC-LP300-BS08269A
- GSM7734096 mESC-Sox2_Sox2_143kb-BS08611A
- GSM7734097 mESC-Sox2_Sox2_143kb-BS08612A
- GSM7734098 mESC-Sox2_Sox2_143kb-BS08615A
- GSM7734099 mESC-Sox2_Sox2_46kbp~dDistalLCR-BS08616A
- GSM7734100 mESC-Sox2_Sox2_46kbp~dDistalLCR-BS08617A
- GSM7734101 mESC-Sox2_Sox2_46kbp~dDistalLCR-BS08618A
- GSM7734102 mESC-Igf2_Igf2_157kb~Igf2SV-BS09964A
- GSM7734103 mESC-Igf2_Igf2_miICR~Igf2SV-BS09207A
- GSM7734104 mESC-Igf2_Igf2_miICR~Igf2SV-BS09209A
- GSM7734105 mESC-Igf2_Igf2_miICR~Igf2SV-BS09210A
- GSM7734106 mESC-Igf2_Igf2_dEnh~miICR~Igf2SV-BS09212A
- GSM7734107 mESC-Igf2_Igf2_dEnh~miICR~Igf2SV-BS09214A
- GSM7734108 mESC-Igf2_Igf2_dCTCFinICR-BS10031A
- GSM7734109 mESC-Igf2_Igf2_dCTCFinICR-BS10033A
+ 114 more — browse all 154 samples with per-sample file links →
No close match found for this topic, so these are simply the most-viewed datasets of the same kind.
- GSE237089 Non-CG DNA methylation and MeCP2 stabilize repeated tuning of long genes that distinguish closely related neuron types. 108 samples
- GSE273615 In vivo armed macrophages curb liver metastasis through tumor reactive T cell rejuvenation 36 samples
- GSE314329 Inflammatory Monocytes Constrain YAP-Induced Cell Proliferation 34 samples
- GSE266690 Single cell approaches define neural stem cell niches and identify microglial ligands that enhance precursor-mediated remyelination 33 samples
- GSE102346 Regulation of m6A transcripts by the 3ʹ→5ʹ RNA helicase YTHDC2 is essential for a successful meiotic program in the mammalian germline 32 samples
- GSE60615 miRNAs in Treg-derived Exosomes 24 samples
- GSE260699 Spatially tuneable multi-omics sequencing using light-driven combinatorial barcoding of molecules in tissues 17 samples
- GSE274621 Single cell transcriptomes and spatial architecture of pancreatic pre-invasive lesions reveal acinar metaplastic cells' heterogeneity 2 samples
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.