Rb-driven transcription limits its tumour suppressive effects in breast cancer
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 279 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
- 279 samples: 86 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 GSE303576_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 PRJNA1295849 and SRA study SRP602810. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 10 samples read as cases, 135 as controls.
How we read this: 86 replicated groups read from 279 sample titles; they account for 242 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.
- GSM9123560 MCF7 Parent DMSO Rb C&R replicate 1 MCF7 Parent DMSO Rb C&R
- GSM9123561 MCF7 Parent DMSO Rb C&R replicate 2 MCF7 Parent DMSO Rb C&R
- GSM9123562 MCF7 Parent palbociclib Rb C&R replicate 1 MCF7 Parent palbociclib…
- GSM9123563 MCF7 Parent palbociclib Rb C&R replicate 2 MCF7 Parent palbociclib…
- GSM9123564 MCF7 Parent palbociclib IgG2a C&R negative control
- GSM9123595 MCF7 Parent DMSO Rb C&R replicate 1.
- GSM9123596 MCF7 Parent DMSO Rb C&R replicate 2.
- GSM9123597 MCF7 Parent abemaciclib Rb C&R replicate 1 MCF7 Parent abemaciclib…
- GSM9123598 MCF7 Parent abemaciclib Rb C&R replicate 2 MCF7 Parent abemaciclib…
- GSM9123599 MCF7 RB1 KO DMSO Rb C&R replicate 1 MCF7 RB1 KO DMSO Rb C&R
- GSM9123600 MCF7 RB1 KO DMSO Rb C&R replicate 2 MCF7 RB1 KO DMSO Rb C&R
- GSM9123601 MCF7 RB1 KO abemaciclib Rb C&R replicate 1 MCF7 RB1 KO abemaciclib…
- GSM9123602 MCF7 RB1 KO abemaciclib Rb C&R replicate 2 MCF7 RB1 KO abemaciclib…
- GSM9123603 MCF7 Parent DMSO IgG2a C&R negative control
- GSM9123604 MCF7 RB1 KO abemaciclib H3K4me3 C&R positive control
- GSM9229425 MCF7_DMSO_rep1 MCF7_DMSO
- GSM9229426 MCF7_DMSO_rep2 MCF7_DMSO
- GSM9229427 MCF7_DMSO_rep3 MCF7_DMSO
- GSM9229428 MCF7_Abema_rep1 MCF7_Abema
- GSM9229429 MCF7_Abema_rep2 MCF7_Abema
- GSM9229430 MCF7_Abema_rep3 MCF7_Abema
- GSM9229431 MCF7_Fulv_rep1 MCF7_Fulv
- GSM9229432 MCF7_Fulv_rep2 MCF7_Fulv
- GSM9229433 MCF7_Fulv_rep3 MCF7_Fulv
- GSM9229434 MCF7_AbemaFulv_rep1 MCF7_AbemaFulv
- GSM9229435 MCF7_AbemaFulv_rep2 MCF7_AbemaFulv
- GSM9229436 MCF7_AbemaFulv_rep3 MCF7_AbemaFulv
- GSM9229437 ZR751_DMSO_rep1 ZR751_DMSO
- GSM9229438 ZR751_DMSO_rep2 ZR751_DMSO
- GSM9229439 ZR751_DMSO_rep3 ZR751_DMSO
- GSM9229440 ZR751_Abema_rep1 ZR751_Abema
- GSM9229441 ZR751_Abema_rep2 ZR751_Abema
- GSM9229442 ZR751_Abema_rep3 ZR751_Abema
- GSM9229443 ZR751_Fulv_rep2 ZR751_Fulv
- GSM9229444 ZR751_Fulv_rep3 ZR751_Fulv
- GSM9229445 ZR751_Fulv_rep1 ZR751_Fulv
- GSM9229446 ZR751_AbemaFulv_rep1 ZR751_AbemaFulv
- GSM9229447 ZR751_AbemaFulv_rep2 ZR751_AbemaFulv
- GSM9229448 ZR751_AbemaFulv_rep3 ZR751_AbemaFulv
- GSM9229449 MCF7 Parent DMSO H3K4me3 C&R replicate 1 MCF7 Parent DMSO H3K4me…
+ 239 more — browse all 279 samples with per-sample file links →
- GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 samples same disease briefing · shares transcription, 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
- GSE303346 Single-Cell RNA-Seq Reveals Immunosuppressive Effects of Triple-Negative Breast Cancer–Derived Exosomes on NK Cell Responses 16 samples shares suppressive, breast
- GSE259248 ZBTB7A is a modulator of KDM5-driven transcriptional networks in basal breast cancer (ChIP-Seq) 36 samples shares transcription, breast
- GSE307965 MiR-342 suppression of an E2F signaling network limits metastatic outgrowth of triple negative breast cancer 15 samples shares limits, 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.