TOP2A & TOP2B occupancy in MCF7 plus and minus estradiol by ChiP-seq
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 10 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
- 10 samples: 10 samples, each with a distinct title — no replicated groupsGroups 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 GSE337189_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 PRJNA1484442 and SRA study SRP714239. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 10 sample titles: 10 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.
- GSM9850153 No estradiol, TOP2B antisera 30400 raised to CTD of TOP2B
- GSM9850154 No estradiol, TOP2A antisera 3116 raised to CTD of TOP2A
- GSM9850155 No estradiol, TOP2B antisera 3535 raised to last 116 amino acids of TOP2B
- GSM9850156 No estradiol, GFP antibody control
- GSM9850157 No estradiol, INPUT
- GSM9850158 30 minutes estradiol, TOP2B antisera 30400 raised to CTD of TOP2B
- GSM9850159 30 minutes estradiol, TOP2A antisera 3116 raised to CTD of TOP2A
- GSM9850160 30 minutes estradiol,TOP2B antisera 3535 raised to last 116 amino acids of TOP2B
- GSM9850161 30 minutes estradiol, GFP antibody control
- GSM9850162 30 minutes estradiol, INPUT
- GSE236412 Topological regulation of the estrogen transcriptional response by ZATT-mediated inhibition of TOP2B activity [ChIP-Seq] 69 samples shares top2b, chip-seq
- GSE68357 ChIP-seq of ER and PR in xenografted MCF7 tumors grown in mice [xenograft] 34 samples shares mcf7, chip-seq
- GSE292768 MCF7 ChIP-seq 10 samples shares mcf7, chip-seq
- GSE336731 Transcriptomic profiling of MCF7 ESR1-PARENT and ESR1-Y537S cells cultured under estrogen-depleted or estradiol-supplemented conditions following abemaciclib treatment and CCND1 knockdown 36 samples shares mcf7, estradiol
- GSE47043 Discovery of the p53 targetome in MCF7 cells from RNA-seq and ChIP-seq data 7 samples shares mcf7, chip-seq
- GSE251687 Polymerization of BTB transcription factors regulates chromatin occupancy [ChIP-Seq] 48 samples shares occupancy, chip-seq
- GSE272705 PBAF associates with repressed chromatin to enable REST occupancy (ChIP-seq) 31 samples shares occupancy, chip-seq
- GSE324916 Phosphorylation of serines 287/288 in DEK regulates cell-type-specific chromatin occupancy and compaction [ChIP-Seq] 24 samples shares occupancy, 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.