Brca1 haploinsufficiency promotes early tumor onset and epigenetic alterations in a mouse model of hereditary breast cancer
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 38 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
- 38 samples: 25 distinct titles, 4 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
- Brca1 haploinsufficiency promotes early tumor onset and epigenetic alterations in a mouse model of hereditary breast cancerNature genetics · 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 GSE247454_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 PRJNA1037576 and SRA study SRP471174. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 10 samples read as cases, 18 as controls.
How we read this: Read from 38 sample titles: 25 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.
- GSM7890131 Tumor_WT_a
- GSM7890132 Tumor_WT_b
- GSM7890133 Tumor_WT_c
- GSM7890134 Tumor_HET_a
- GSM7890135 Tumor_HET_b
- GSM7890136 Tumor_HET_c
- GSM7890137 Tumor_HET_d
- GSM7890138 Young_WT_a
- GSM7890139 Young_WT_b
- GSM7890140 Young_WT_c
- GSM7890141 Young_HET_a
- GSM7890142 Young_HET_b
- GSM7890143 Young_HET_c
- GSM7890144 Aged_WT_a
- GSM7890145 Aged_WT_b
- GSM7890146 Aged_WT_c
- GSM7890147 Aged_WT_d
- GSM7890148 Aged_HET_a
- GSM7890149 Aged_HET_b
- GSM7890150 Aged_HET_c
- GSM7890151 Aged_HET_d
- GSM7890184 Normal_WT_5430
- GSM7890185 Normal_WT_5468
- GSM7890186 Normal_WT_5434
- GSM7890187 Normal_WT_5440
- GSM7890188 Normal_HET_5433
- GSM7890189 Normal_HET-5431
- GSM7890190 Normal_HET-5438
- GSM7890191 Normal_HET_5469
- GSM7890192 Normal_HET_5428
- GSM7890193 Normal_HET_5472
- GSM7890194 Normal_HET_5425
- GSM7890195 Tumor_WT_6971
- GSM7890196 Tumor_WT-6982
- GSM7890197 Tumor_WT-6992
- GSM7890198 Tumor_HET-6934
- GSM7890199 Tumor_HET-6986
- GSM7890200 Tumor_HET-6989
- GSE224209 Macrophage epigenetic memories of early life injury drive neonatal nociceptive priming. 21 samples shares epigenetic, early
- GSE252418 Subchronic elevation in ambient temperature drives alterations to the sperm epigenome and accelerates early embryonic development in mice 83 samples shares alterations, early
- GSE316619 Epigenetic memory of colitis promotes tumour growth 47 samples shares epigenetic, promotes
- GSE289856 Convergence of aging- and rejuvenation-related epigenetic alterations on PRC2 targets 39 samples shares alterations, epigenetic
- GSE252551 Disease-associated astrocyte epigenetic memory promotes CNS pathology [ATAC-Seq and RNA-Seq] 32 samples shares epigenetic, promotes
- GSE288348 Disease-associated astrocyte epigenetic memory promotes CNS pathology [sgEp300, sgACLY astrocytes bulk RNA-Seq dataset] 18 samples shares epigenetic, promotes
- GSE301448 Epigenetic Reactivation of CNS Endothelial Developmental Programs Triggers Adult Brain Angiogenesis, Promotes Post-Stroke Revascularization and Neuroregeneration [RNAseq-Stroke] 18 samples shares epigenetic, promotes
- GSE238201 Loss of PPARα function promotes epigenetic dysregulation of lipid homeostasis driving ferroptosis and pyroptosis lipotoxicity in Metabolic Dysfunction Associated Steatotic Liver Disease (MASLD) [RNA-seq] 12 samples shares epigenetic, promotes
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.