Identification of genomic features that uniquely impact estrogen receptor alpha binding and its effects on gene expression in endometrial cancer
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 37 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
- Endometrial cancerThis series is part of our curated briefing on it.
- Samples
- 37 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.
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 GSE312906_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 PRJNA1377578 and SRA study SRP705832. 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 37 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.
- GSM9343569 Trial1_PreTreatment_Ctrl
- GSM9343570 Trial1_E2_GFP_Neg
- GSM9343571 Trial1_E2_GFP_Low
- GSM9343572 Trial1_E2_GFP_Med
- GSM9343573 Trial1_E2_GFP_High
- GSM9343574 Trial2_PreTreatment_Ctrl
- GSM9343575 Trial2_E2_GFP_Neg
- GSM9343576 Trial2_E2_GFP_Low
- GSM9343577 Trial2_E2_GFP_Med
- GSM9343578 Trial2_E2_GFP_High
- GSM9343579 Ishikawa_SOX17_DMSO
- GSM9343580 Ishikawa_input
- GSM9778040 HCI_ATAC_DMSO_Rep1 HCI_ATAC_DMSO
- GSM9778041 HCI_ATAC_DMSO_Rep2 HCI_ATAC_DMSO
- GSM9780674 HCIEC23_DMSO_input
- GSM9780675 HCIEC23_DMSO_H3K4me1_Rep1 HCIEC23_DMSO_H3K4me1
- GSM9780676 HCIEC23_DMSO_H3K4me1_Rep2 HCIEC23_DMSO_H3K4me1
- GSM9780677 HCIEC23_DMSO_SOX17
- GSM9780678 Ishikawa_SOX17KO_cloneA3_E2_ER
- GSM9780679 Ishikawa_SOX17KO_cloneE3_E2_ER
- GSM9780680 Ishikawa_Cnt_cloneF3_E2_ER
- GSM9780717 SOX17KO_cloneA3_E2_Rep1 SOX17KO_cloneA3_E2
- GSM9780718 SOX17KO_cloneA3_E2_Rep2 SOX17KO_cloneA3_E2
- GSM9780719 SOX17KO_cloneA3_DMSO_Rep1 SOX17KO_cloneA3_DMSO
- GSM9780720 SOX17KO_cloneA3_DMSO_Rep2 SOX17KO_cloneA3_DMSO
- GSM9780721 SOX17KO_cloneE3_E2_Rep1 SOX17KO_cloneE3_E2
- GSM9780722 SOX17KO_cloneE3_E2_Rep2 SOX17KO_cloneE3_E2
- GSM9780723 SOX17KO_cloneE3_DMSO_Rep1 SOX17KO_cloneE3_DMSO
- GSM9780724 SOX17KO_cloneE3_DMSO_Rep2 SOX17KO_cloneE3_DMSO
- GSM9780725 Cnt_cloneE5_E2_Rep1 Cnt_cloneE5_E2
- GSM9780726 Cnt_cloneE5_E2_Rep2 Cnt_cloneE5_E2
- GSM9780727 Cnt_cloneE5_DMSO_Rep1 Cnt_cloneE5_DMSO
- GSM9780728 Cnt_cloneE5_DMSO_Rep2 Cnt_cloneE5_DMSO
- GSM9780729 Cnt_cloneF3_E2_Rep1 Cnt_cloneF3_E2
- GSM9780730 Cnt_cloneF3_E2_Rep2 Cnt_cloneF3_E2
- GSM9780731 Cnt_cloneF3_DMSO_Rep1 Cnt_cloneF3_DMSO
- GSM9780732 Cnt_cloneF3_DMSO_Rep2 Cnt_cloneF3_DMSO
- GSE334100 Identification of genomic features that uniquely impact estrogen receptor alpha binding and its effects on gene expression in endometrial cancer [RNA-seq] 16 samples same disease briefing · shares endometrial, features, uniquely, estrogen, receptor, binding, impact, alpha
- GSE312323 Identification of genomic features that uniquely impact estrogen receptor alpha binding and its effects on gene expression in endometrial cancer [SOX17_ChIPseq] 2 samples same disease briefing · shares endometrial, features, uniquely, estrogen, receptor, binding, impact, alpha
- GSE303681 Pre-receptor regulation of 11-oxyandrogens differs between normal and cancerous endometrium and across endometrial cancer grades and molecular subtypes 18 samples same disease briefing · shares endometrial, receptor
- GSE307568 Patient-derived organoid – immune cell co-culture platform for therapeutics discovery in high-grade endometrial cancer 189 samples same disease briefing · shares endometrial
- GSE212217 Distinct Mechanisms of Mismatch-Repair Deficiency Delineate Two Modes of Response to Anti–PD-1 Immunotherapy in Endometrial Carcinoma 104 samples same disease briefing · shares endometrial
- GSE17025 Gene Expression Analysis of Stage I Endometrial Cancers 103 samples same disease briefing · shares endometrial
- GSE323968 Transcriptional signatures indicating RB function may predict response to CDK4/6 inhibition in endometrial cancer 56 samples same disease briefing · shares endometrial
- GSE247793 Cell cycle checkpoint proficiency of endometrial cancer cells 42 samples same disease briefing · shares endometrial
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.