Effect of ZIC1 on group 3 medulloblastoma cell lines and granule neuron progenitor [ChIP-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 13 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
- 13 samples: 11 distinct titles, 2 of them repeatedGroups 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
- ZIC1 is a context-dependent medulloblastoma driver in the rhombic lipNature genetics · 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 GSE217638_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 PRJNA899866 and SRA study SRP407041. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 13 sample titles: 11 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.
- GSM6723638 D283_ZIC1NF_294_IP
- GSM6723639 D283_ZIC1NF_301_IP
- GSM6723640 D283_ZIC1NF_WT1_IP
- GSM6723641 D283_ZIC1NF_WT2_IP
- GSM8073637 GNP_ZIC1NF_no_virus_IP
- GSM8073638 GNP_ZIC1NF_301_IP_1
- GSM8073639 GNP_ZIC1NF_301_IP_2
- GSM8073640 GNP_ZIC1NF_294_IP
- GSM8073641 GNP_ZIC1NF_WT1_IP_1
- GSM8073642 GNP_ZIC1NF_WT1_IP_2
- GSM8501035 MB051_Xeno_27Ac
- GSM8501036 MB051_Xeno_27me3
- GSM8501037 MB051_Xeno_inp
- GSE276321 Chromodomain protein CDYL confers forebrain identity to human cortical organoids by inhibiting neuronatin [ChIP-seq] 9 samples shares chip-seq, neuron
- GSE270069 Species-specific progenitor domain extends neurogenesis and increases motor neuron production 3 samples shares progenitor, neuron
- GSE294966 ChIP-seq for beta-catenin, EZH2, EED, KMT2B, H3K4me3, H3K27me3 and sequential chipseq 148 samples shares chip-seq
- GSE205245 H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs [ChIP-seq] 105 samples shares chip-seq
- GSE271891 The PNUTS phosphatase complex controls transcription pause release [ChIP-Seq] 94 samples shares chip-seq
- GSE255372 Targeting CDK7 function in the RNA Polymerase II transcription cycle in inflammatory arthritis [ChIP-seq] 69 samples shares chip-seq
- GSE244510 KDM6A Regulates Immunogenicity of Multiple Myeloma (ChIP-seq) 24 samples shares chip-seq
- GSE294955 ZFTA–RELA ependymomas make itaconate to epigenetically drive fusion expression [ChIP-Seq] 18 samples shares 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.