Zinc finger homeobox-3 (ZFHX3) exerts genome-wide regulation of dailygene expression in the suprachiasmatic nucleus
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 65 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
- 65 samples: 17 conditions, mostly with about 4 replicates eachGroups 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
- Zinc finger homeobox-3 (ZFHX3) orchestrates genome-wide daily gene expression in the suprachiasmatic nucleuseLife · 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 GSE261795_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 PRJNA1089097 and SRA study SRP497273. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 24 samples read as cases, 38 as controls.
How we read this: 17 replicated groups read from 65 sample titles; they account for 61 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.
- GSM8143850 SCN, control1, 2hours, rep1 SCN, control1, 2hours,
- GSM8143851 SCN, control1, 2hours, rep2 SCN, control1, 2hours,
- GSM8143852 SCN, control1, 2hours, rep3 SCN, control1, 2hours,
- GSM8143853 SCN, control1, 2hours, rep4 SCN, control1, 2hours,
- GSM8143854 SCN, control1, 6hours, rep1 SCN, control1, 6hours,
- GSM8143855 SCN, control1, 6hours, rep2 SCN, control1, 6hours,
- GSM8143856 SCN, control1, 6hours, rep3 SCN, control1, 6hours,
- GSM8143857 SCN, control1, 6hours, rep4 SCN, control1, 6hours,
- GSM8143858 SCN, control1, 10hours, rep1 SCN, control1, 10hours,
- GSM8143859 SCN, control1, 10hours, rep2 SCN, control1, 10hours,
- GSM8143860 SCN, control1, 10hours, rep3 SCN, control1, 10hours,
- GSM8143861 SCN, control1, 10hours, rep4 SCN, control1, 10hours,
- GSM8143862 SCN, control1, 14hours, rep1 SCN, control1, 14hours,
- GSM8143863 SCN, control1, 14hours, rep2 SCN, control1, 14hours,
- GSM8143864 SCN, control1, 14hours, rep3 SCN, control1, 14hours,
- GSM8143865 SCN, control1, 14hours, rep4 SCN, control1, 14hours,
- GSM8143866 SCN, control1, 18hours, rep1 SCN, control1, 18hours,
- GSM8143867 SCN, control1, 18hours, rep2 SCN, control1, 18hours,
- GSM8143868 SCN, control1, 18hours, rep3 SCN, control1, 18hours,
- GSM8143869 SCN, control1, 18hours, rep4 SCN, control1, 18hours,
- GSM8143870 SCN, control1, 22hours, rep1 SCN, control1, 22hours,
- GSM8143871 SCN, control1, 22hours, rep2 SCN, control1, 22hours,
- GSM8143872 SCN, control1, 22hours, rep3 SCN, control1, 22hours,
- GSM8143873 SCN, control1, 22hours, rep4 SCN, control1, 22hours,
- GSM8143874 SCN, mutant, 2hours, rep1 SCN, mutant, 2hours,
- GSM8143875 SCN, mutant, 2hours, rep2 SCN, mutant, 2hours,
- GSM8143876 SCN, mutant, 2hours, rep3 SCN, mutant, 2hours,
- GSM8143877 SCN, mutant, 2hours, rep4 SCN, mutant, 2hours,
- GSM8143878 SCN, mutant, 6hours, rep1 SCN, mutant, 6hours,
- GSM8143879 SCN, mutant, 6hours, rep2 SCN, mutant, 6hours,
- GSM8143880 SCN, mutant, 6hours, rep3 SCN, mutant, 6hours,
- GSM8143881 SCN, mutant, 6hours, rep4 SCN, mutant, 6hours,
- GSM8143882 SCN, mutant, 10hours, rep1 SCN, mutant, 10hours,
- GSM8143883 SCN, mutant, 10hours, rep2 SCN, mutant, 10hours,
- GSM8143884 SCN, mutant, 10hours, rep3 SCN, mutant, 10hours,
- GSM8143885 SCN, mutant, 10hours, rep4 SCN, mutant, 10hours,
- GSM8143886 SCN, mutant, 14hours, rep1 SCN, mutant, 14hours,
- GSM8143887 SCN, mutant, 14hours, rep2 SCN, mutant, 14hours,
- GSM8143888 SCN, mutant, 14hours, rep3 SCN, mutant, 14hours,
- GSM8143889 SCN, mutant, 14hours, rep4 SCN, mutant, 14hours,
+ 25 more — browse all 65 samples with per-sample file links →
- GSE261429 Zinc finger homeobox-3 (ZFHX3) exerts genome-wide regulation of dailygene expression in the suprachiasmatic nucleus [RNA-seq] 62 samples shares homeobox-3, zfhx3, suprachiasmatic, genome-wide, dailygene, finger, exerts, zinc
- GSE288012 Genome-wide screen identifies Runx2 as a novel regulator of hematopoietic stem cell expansion and T-cell commitment 20 samples shares genome-wide
- GSE169312 Next-generation sequencing Facilitates Quantitative Analysis of Wild Type and EED-/- mice cerebellum Transcriptomes and Genome-wide maps of chromatin state in Wild Type and EED-/- mice cerebellum 12 samples shares genome-wide
- GSE262791 LaminB1 DamID, RNA-seq and Genome-wide analysis of replication timing in RIF1 depleted preimplantation mouse embryos 468 samples shares genome-wide
- GSE241542 A phosphate transporter in VIPergic neurons of the suprachiasmatic nucleus gates locomotor activity during the light/dark transition in mice 298 samples shares suprachiasmatic
- GSE278949 Genome-wide DNA replication profiling and full-length total RNA sequencing from the same single cell [03_CBMS1_mESC] 168 samples shares genome-wide
- GSE92605 Allelic genome-wide maps of open chromatin state in zygotes and early embryo 69 samples shares genome-wide
- GSE254806 Differential genome-wide profile of histone modifications upon treatment with gamma-secretase inibithor (GSI) DAPT [ChIP-seq] 57 samples shares genome-wide
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.