Topoisomerase I (TOP1) is a functional mitotic interactor of the bookmarking factor HNF1B
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 43 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
- Mus musculus (mouse)
- Samples
- 43 samples: 14 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.
- Paper
- HNF1β bookmarking involves Topoisomerase 1 activation and DNA topology relaxation in mitotic chromatinCell reports · 2024
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 GSE245087_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 PRJNA1026917 and SRA study SRP465696. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 34 samples.
How we read this: 14 replicated groups read from 43 sample titles; they account for 34 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.
- GSM7835583 KEC, Asy AQC, HNF1b, rep1 KEC, Asy AQC, HNF1b,
- GSM7835584 KEC, Asy AQC, HNF1b, rep2 KEC, Asy AQC, HNF1b,
- GSM7835585 KEC, Asy AQC, Inp1
- GSM7835586 KEC, Asy NAQC, HNF1b, rep1 KEC, Asy NAQC, HNF1b,
- GSM7835587 KEC, Asy NAQC, HNF1b, rep2 KEC, Asy NAQC, HNF1b,
- GSM7835588 KEC, Asy NAQC, Inp1
- GSM7835589 KEC, Mit AQC, HNF1b, rep1 KEC, Mit AQC, HNF1b,
- GSM7835590 KEC, Mit AQC, HNF1b, rep2 KEC, Mit AQC, HNF1b,
- GSM7835591 KEC, Mit AQC, Inp1
- GSM7835592 KEC, Mit NAQC, HNF1b, rep1 KEC, Mit NAQC, HNF1b,
- GSM7835593 KEC, Mit NAQC, HNF1b, rep2 KEC, Mit NAQC, HNF1b,
- GSM7835594 KEC, Mit NAQC, Inp1
- GSM7835595 KEC HNF1b-KO, Mit NAQC, Inp
- GSM7835596 KEC HNF1b-KO, Mit NAQC,TOP1, rep1 KEC HNF1b-KO, Mit NAQC,…
- GSM7835597 KEC HNF1b-KO, Mit NAQC,TOP1, rep2 KEC HNF1b-KO, Mit NAQC,…
- GSM7835598 KEC, Mit NAQC,TOP1, rep1 KEC, Mit NAQC,TOP1,
- GSM7835599 KEC, Mit NAQC,TOP1, rep2 KEC, Mit NAQC,TOP1,
- GSM7835600 786-O, HNF1B siRNA, rep 1 786-O, HNF1B siRNA,
- GSM7835601 786-O, HNF1B siRNA, rep 2 786-O, HNF1B siRNA,
- GSM7835602 786-O, HNF1B siRNA, rep 3 786-O, HNF1B siRNA,
- GSM7835603 786-O, Non Target siRNA, rep 1 786-O, Non Target siRN…
- GSM7835604 786-O, Non Target siRNA, rep 2 786-O, Non Target siRN…
- GSM7835605 786-O, Non Target siRNA, rep 3 786-O, Non Target siRN…
- GSM7835606 KEC, WT, rep1 KEC, WT,
- GSM7835607 KEC, WT, rep2 KEC, WT,
- GSM7835608 KEC, WT, rep3 KEC, WT,
- GSM7835609 KEC, HNF1B-KO, rep1 KEC, HNF1B-KO,
- GSM7835610 KEC, HNF1B-KO, rep2 KEC, HNF1B-KO,
- GSM7835611 KEC, HNF1B-KO, rep3 KEC, HNF1B-KO,
- GSM7835962 786-O, Asy AQC, HNF1b, rep1 786-O, Asy AQC, HNF1b,
- GSM7835963 786-O, Asy AQC, HNF1b, rep2 786-O, Asy AQC, HNF1b,
- GSM7835964 786-O, Asy AQC, HNF1b, rep3 786-O, Asy AQC, HNF1b,
- GSM7835965 786-O, Asy AQC, Inp
- GSM7835966 786-O, Asy NAQC, HNF1b, rep1 786-O, Asy NAQC, HNF1b,
- GSM7835967 786-O, Asy NAQC, HNF1b, rep2 786-O, Asy NAQC, HNF1b,
- GSM7835968 786-O, Asy NAQC, Inp
- GSM7835969 786-O, Mit AQC, HNF1b, rep1 786-O, Mit AQC, HNF1b,
- GSM7835970 786-O, Mit AQC, HNF1b, rep2 786-O, Mit AQC, HNF1b,
- GSM7835971 786-O, Mit AQC, HNF1b, rep3 786-O, Mit AQC, HNF1b,
- GSM7835972 786-O, Mit AQC, Inp
+ 3 more — browse all 43 samples with per-sample file links →
- GSE333477 Dynamicity of Topoisomerase 1 binding at super-enhancers regulates TLR-responsive gene expression program in macrophages 106 samples shares topoisomerase
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.