Progesterone receptor directs a distinct estrogen receptor-alpha chromatin binding profile in breast cancer to elicit good clinical outcome
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 197 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
- 197 samples: 155 distinct titles, 6 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.
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 GSE68359_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 PRJNA282502 and SRA study SRP057755. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 197 sample titles: 155 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.
- GSM1669011 JC1553_T47D_ER_Full_Media_3hr r1
- GSM1669012 JC1563_T47D_ER_Full_Media_3hr r2
- GSM1669013 JC1573_T47D_ER_Full_Media_3hr r3
- GSM1669014 JC1554_T47D_ER_Progesterone_3hr r1
- GSM1669015 JC1564_T47D_ER_Progesterone_3hr r2
- GSM1669016 JC1574_T47D_ER_Progesterone_3hr r3
- GSM1669017 JC1555_T47D_ER_R5020_3hr r1
- GSM1669018 JC1565_T47D_ER_R5020_3hr r2
- GSM1669019 JC1575_T47D_ER_R5020_3hr r3
- GSM1669020 JC1562_T47D_Input_Full_Media_3hr r1
- GSM1669021 JC1572_T47D_Input_Full_Media_3hr r2
- GSM1669022 JC1582_T47D_Input_Full_Media_3hr r3
- GSM1669023 JC1559_T47D_p300_Full_Media_3hr r1
- GSM1669024 JC1569_T47D_p300_Full_Media_3hr r2
- GSM1669025 JC1579_T47D_p300_Full_Media_3hr r3
- GSM1669026 JC1560_T47D_p300_Progesterone_3hr r1
- GSM1669027 JC1570_T47D_p300_Progesterone_3hr r2
- GSM1669028 JC1580_T47D_p300_Progesterone_3hr r3
- GSM1669029 JC1561_T47D_p300_R5020_3hr r1
- GSM1669030 JC1571_T47D_p300_R5020_3hr r2
- GSM1669031 JC1581_T47D_p300_R5020_3hr r3
- GSM1669032 JC1556_T47D_PR_Full_Media_3hr r1
- GSM1669033 JC1566_T47D_PR_Full_Media_3hr r2
- GSM1669034 JC1576_T47D_PR_Full_Media_3hr r3
- GSM1669035 JC1557_T47D_PR_Progesterone_3hr r1
- GSM1669036 JC1567_T47D_PR_Progesterone_3hr r2
- GSM1669037 JC1577_T47D_PR_Progesterone_3hr r3
- GSM1669038 JC1558_T47D_PR_R5020_3hr r1
- GSM1669039 JC1568_T47D_PR_R5020_3hr r2
- GSM1669040 JC1578_T47D_PR_R5020_3hr r3
- GSM1669041 JC1378_NA_p300_Progesterone_3hr r0
- GSM1669042 JC1523_MCF7_ER_Full_Media_3hr r1
- GSM1669043 JC1533_MCF7_ER_Full_Media_3hr r2
- GSM1669044 JC1543_MCF7_ER_Full_Media_3hr r3
- GSM1669045 JC1524_MCF7_ER_Progesterone_3hr r1
- GSM1669046 JC1534_MCF7_ER_Progesterone_3hr r2
- GSM1669047 JC1544_MCF7_ER_Progesterone_3hr r3
- GSM1669048 JC1525_MCF7_ER_R5020_3hr r1
- GSM1669049 JC1535_MCF7_ER_R5020_3hr r2
- GSM1669050 JC1545_MCF7_ER_R5020_3hr r3
+ 157 more — browse all 197 samples with per-sample file links →
- GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing · shares distinct
- GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 samples same disease briefing
- GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 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
- GSE287902 BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction [Cut&Run] 40 samples shares chromatin, receptor
- GSE280618 H3K27me3 chromatin heterogeneity reveals variable cell responses to estrogen and endocrine treatment 34 samples shares chromatin, estrogen
- GSE314776 Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer [ChIP-Seq] 24 samples shares chromatin, distinct
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.