Integration of ATAC-seq and RNA-seq identifies typing and prognosis evaluation target molecules of triple negative breast cancer
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 19 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
- Homo sapiens (human)
- Topic
- Breast cancerThis series is part of our curated briefing on it.
- Samples
- 19 samples: 19 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.
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 GSE254212_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 PRJNA1069018 and SRA study SRP485947. 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 19 sample titles: 19 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.
- GSM8036086 OA1-A
- GSM8036087 OA1-P
- GSM8036088 OA3-A
- GSM8036089 OA3-P
- GSM8036090 OA4-A
- GSM8036091 OA4-P
- GSM8036092 OA5-A
- GSM8036093 OA5-P
- GSM8036094 OA6-A
- GSM8036095 OA6-P
- GSM8036096 OA7-A
- GSM8036097 OA9-A
- GSM8036098 OA9-P
- GSM8036099 OA10-A
- GSM8036100 OA10-P
- GSM8036101 OA13-A
- GSM8036102 OA13-P
- GSM8036103 OA15-A
- GSM8036104 OA15-P
- GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 samples same disease briefing · shares negative
- GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
- GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 samples same disease briefing
- GSE104193 Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-β signalling and malignant features in vitro and in vivo 32 samples same disease briefing
- GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 samples same disease briefing
- GSE278751 A stem cell model identifies two alternative cell fates in CBFA2T3::GLIS2-driven acute megakaryoblastic leukemia initiation (Multiome scRNA-seq/scATAC-seq) 14 samples shares identifies, atac-seq, rna-seq
- GSE282258 Imaging-based drug screening combined with moleuclar profiling identifies signatures and drivers of therapy resistance in pediatric AML [ATAC-seq] 44 samples shares identifies, atac-seq
- GSE251778 Sex-specific and multiomic integration enhance accuracy of peripheral blood biomarkers of major depressive disorder [RNA-Seq] 169 samples shares integration, rna-seq
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.