Epigenetic and 3D Genome Changes Drive Primary Trastuzumab Resistance in HER2+ Breast Cancer
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 20 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
- 20 samples: 10 conditions, mostly in duplicateGroups 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 GSE297715_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 PRJNA1265766 and SRA study SRP586721. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 10 replicated groups read from 20 sample titles; they account for 20 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.
- GSM8997256 SKBR3 H3K27me3 rep1 SKBR3 H3K27me3
- GSM8997257 SKBR3 H3K27me3 rep2 SKBR3 H3K27me3
- GSM8997258 SKBR3 H3K4me3 rep1 SKBR3 H3K4me3
- GSM8997259 SKBR3 H3K4me3 rep2 SKBR3 H3K4me3
- GSM8997260 SKBR3 H3K27ac rep1 SKBR3 H3K27ac
- GSM8997261 SKBR3 H3K27ac rep2 SKBR3 H3K27ac
- GSM8997262 SKBR3 CTCF rep1 SKBR3 CTCF
- GSM8997263 SKBR3 CTCF rep2 SKBR3 CTCF
- GSM8997264 SKBR3 RNApolII rep1 SKBR3 RNApolII
- GSM8997265 SKBR3 RNApolII rep2 SKBR3 RNApolII
- GSM8997266 JIMT1 H3K27me3 rep1 JIMT1 H3K27me3
- GSM8997267 JIMT1 H3K27me3 rep2 JIMT1 H3K27me3
- GSM8997268 JIMT1 H3K4me3 rep1 JIMT1 H3K4me3
- GSM8997269 JIMT1 H3K4me3 rep2 JIMT1 H3K4me3
- GSM8997270 JIMT1 H3K27ac rep1 JIMT1 H3K27ac
- GSM8997271 JIMT1 H3K27ac rep2 JIMT1 H3K27ac
- GSM8997272 JIMT1 CTCF rep1 JIMT1 CTCF
- GSM8997273 JIMT1 CTCF rep2 JIMT1 CTCF
- GSM8997274 JIMT1 RNApolII rep1 JIMT1 RNApolII
- GSM8997275 JIMT1 RNApolII rep2 JIMT1 RNApolII
- GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 samples same disease briefing · shares resistance, breast
- GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 samples same disease briefing · shares breast
- GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 samples same disease briefing · shares breast
- 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 · shares breast
- GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
- GSE300628 HER2 heterogeneous breast cancer models reveal novel therapeutic targets and subclonal dynamics during evolution to resistance to HER2-targeted therapies 60 samples shares her2, resistance, breast
- GSE231526 DUSP6 inhibition overcomes neuregulin/HER3-driven therapy tolerance in HER2+ breast cancer 18 samples shares her2, breast, drive
- GSE317345 Genomic accesssment of patients with HR+/HER2- metastatic breast cancer treated with palbociclib (PROMISE study) 39 samples shares her2, breast
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.