The Hira complex regulates Gli3R-dependent transcription in Hedgehog signaling and medulloblastoma cell growth and migration
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 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
- Mus musculus (mouse)
- Samples
- 10 samples: 2 × NIH/3T3 cells treated with DMSO vs 2 × NIH/3T3 cells treated with Dox in order to induce HA-Gli3R expression vs 2 × NIH/3T3 with Hira loss-of-function cells treated with DMSO vs 2 × NIH/3T3 with Hira loss-of-function cells treated with Dox in order to induce HA-Gli3R expressionGroups 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
- The Hira complex regulates Gli3R-dependent transcription in Hedgehog signaling and medulloblastoma cell growth and migrationScientific reports · 2025
Read the full summary ↓
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 GSE291945_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 PRJNA1236220 and SRA study SRP570420. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 4 replicated groups read from 10 sample titles; they account for 8 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.
- GSM8844855 NIH/3T3 cells treated with DMSO_1 NIH/3T3 cells treated w…
- GSM8844856 NIH/3T3 cells treated with DMSO_2 NIH/3T3 cells treated w…
- GSM8844857 NIH/3T3 cells treated with Dox in order to induce HA-Gli3R expression_1 NIH/3T3 cells treated w…
- GSM8844858 NIH/3T3 cells treated with Dox in order to induce HA-Gli3R expression_2 NIH/3T3 cells treated w…
- GSM8844859 NIH/3T3 with Hira loss-of-function cells treated with DMSO_1 NIH/3T3 with Hira loss-…
- GSM8844860 NIH/3T3 with Hira loss-of-function cells treated with DMSO_2 NIH/3T3 with Hira loss-…
- GSM8844861 NIH/3T3 with Hira loss-of-function cells treated with Dox in order to induce HA-Gli3R expression_1 NIH/3T3 with Hira loss-…
- GSM8844862 NIH/3T3 with Hira loss-of-function cells treated with Dox in order to induce HA-Gli3R expression_2 NIH/3T3 with Hira loss-…
- GSM8844863 NIH/3T3 cells treated with DMSO (INPUT)
- GSM8844864 NIH/3T3 cells treated with Dox (INPUT)
- GSE272888 Dynamic transcriptional and epigenetic changes define postnatal tendon growth 54 samples shares transcription, growth
- GSE283958 Cohesin recruitment to promoters and enhancers by general transcription factors and chromatin regulators 47 samples shares transcription
- GSE268172 Stable maintenance of MERVL-positive embryonic stem cells reveals sustained transcriptional programs and enhancer remodeling 45 samples shares transcription
- GSE326173 Nuclear receptor Nur77 resolves the inflammatory response of macrophages primarily by regulating expression of AP-1 transcription factors and their target genes [ChIP-seq] 42 samples shares transcription
- GSE294521 Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [CUTnTAG] 34 samples shares transcription
- GSE271884 GFI1-driven transcriptional and epigenetic programs maintain memory CD8+ T cell persistence [ATAC-seq]. 30 samples shares transcription
- GSE324864 HP1B and H3K9me3 Regulate Olfactory Receptor Choice and 2 Transcriptional Identity [ChIP-seq] 28 samples shares transcription
- GSE339012 Mega-Enhancers Compartmentalize Transcriptionally Active Long Genes in the Brain [ChIP-Seq] 22 samples shares transcription
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.