GPS2 and HDAC3 ChIP-Seq and RNA-Seq in GPS2-KO MCF-7
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 14 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)
- Samples
- 14 samples: 3 × RNA-Seq of GPS2-KO MCF-7 vs 3 × RNA-Seq of WT MCF-7 vs 2 × GPS2 ChIP-Seq in GPS2-KO MCF-7 vs 2 × GPS2 ChIP-Seq in WT MCF-7Groups 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.
- Paper
- Nonproteolytic ubiquitination regulates chromatin occupancy by the NCoR/SMRT/HDAC3 corepressor complex in MCF-7 breast cancer cellsProceedings of the National Academy of Sciences of the United States of America · 2025
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 GSE250076_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 PRJNA1051979 and SRA study SRP477657. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 4 replicated groups read from 14 sample titles; they account for 10 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.
- GSM7971875 GPS2 ChIP-Seq in GPS2-KO MCF-7 - Replicate 1 GPS2 ChIP-Seq in GPS2-K…
- GSM7971876 GPS2 ChIP-Seq in GPS2-KO MCF-7 - Replicate 2 GPS2 ChIP-Seq in GPS2-K…
- GSM7971877 HDAC3 ChIP-Seq in GPS2-KO MCF-7 - Replicate 2
- GSM7971878 Input DNA of GPS2-KO MCF-7
- GSM7971879 GPS2 ChIP-Seq in WT MCF-7 - Replicate 1 GPS2 ChIP-Seq in WT MCF…
- GSM7971880 GPS2 ChIP-Seq in WT MCF-7 - Replicate 2 GPS2 ChIP-Seq in WT MCF…
- GSM7971881 HDAC3 ChIP-Seq in WT MCF-7 - Replicate 2
- GSM7971882 Input DNA of WT MCF-7
- GSM7973572 RNA-Seq of GPS2-KO MCF-7 - Replicate 1 RNA-Seq of GPS2-KO MCF-7
- GSM7973573 RNA-Seq of GPS2-KO MCF-7 - Replicate 2 RNA-Seq of GPS2-KO MCF-7
- GSM7973574 RNA-Seq of GPS2-KO MCF-7 - Replicate 3 RNA-Seq of GPS2-KO MCF-7
- GSM7973575 RNA-Seq of WT MCF-7 - Replicate 1 RNA-Seq of WT MCF-7
- GSM7973576 RNA-Seq of WT MCF-7 - Replicate 2 RNA-Seq of WT MCF-7
- GSM7973577 RNA-Seq of WT MCF-7 - Replicate 3 RNA-Seq of WT MCF-7
- GSE250040 GPS2 and HDAC3 ChIP-Seq in GPS2-KO MCF-7 [ChIP-Seq] 8 samples shares gps2-ko, hdac3, mcf-7, gps2, chip-seq
- GSE250075 GPS2 and HDAC3 RNA-Seq in GPS2-KO MCF-7 [RNA-Seq] 6 samples shares gps2-ko, hdac3, mcf-7, gps2, rna-seq
- GSE246361 MCF-7 RPMI ERa and FOXA1 ChIP-seq in GDC-9545 and GNE-858 18 samples shares mcf-7, chip-seq
- GSE246364 RNA-seq data for MCF-7 cells with ER knockdown or GDC-9545 treatment 14 samples shares mcf-7, rna-seq
- GSE302670 Enhanced efficacy of a specific HDAC3 inhibitor in combination with 5-Azacitidine against diffuse large B-cell lymphoma [ChIP-seq] 13 samples shares hdac3, chip-seq
- GSE246363 RNA-seq of MCF-7 cells with ER or FOXA1 knockout and/or GDC-9545 treatment 10 samples shares mcf-7, rna-seq
- GSE216922 ChIP-Seq of MYC in MCF-7 cells with EPIC1 knockdown or overexpression. 10 samples shares mcf-7, chip-seq
- GSE252695 RNA-dependent ChIP-Seq (rChIP-Seq) of MYC and TBP in MCF-7 cells 10 samples shares mcf-7, chip-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.