Chromatin Modification Abnormalities by CHD7 and KMT2C Loss Promote Medulloblastoma Progression
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 71 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
- 71 samples: 23 conditions, mostly in triplicateGroups 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 GSE263362_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 PRJNA1096766 and SRA study SRP499986. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 68 samples.
How we read this: 23 replicated groups read from 71 sample titles; they account for 68 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.
- GSM8190180 Atoh1EGFP,Ptch1+/- spontaneous tumor rep1 Atoh1EGFP,Ptch1+/- spon…
- GSM8190181 Atoh1EGFP,Ptch1+/- spontaneous tumor rep2 Atoh1EGFP,Ptch1+/- spon…
- GSM8190182 Atoh1EGFP,Ptch1+/- spontaneous tumor rep3 Atoh1EGFP,Ptch1+/- spon…
- GSM8190183 sgPtch1 induced tumors rep1 sgPtch1 induced tumors
- GSM8190184 sgPtch1 induced tumors rep2 sgPtch1 induced tumors
- GSM8190185 sgPtch1 induced tumors rep3 sgPtch1 induced tumors
- GSM8190186 sgPtch1-sgChd7 tumors rep1 sgPtch1-sgChd7 tumors
- GSM8190187 sgPtch1-sgChd7 tumors rep2 sgPtch1-sgChd7 tumors
- GSM8190188 sgPtch1-sgChd7 tumors rep3 sgPtch1-sgChd7 tumors
- GSM8190189 sgPtch1-sgKmt2c tumors rep1 sgPtch1-sgKmt2c tumors
- GSM8190190 sgPtch1-sgKmt2c tumors rep2 sgPtch1-sgKmt2c tumors
- GSM8190191 sgPtch1-sgKmt2c tumors rep3 sgPtch1-sgKmt2c tumors
- GSM8190192 Group3 medulloblatoma rep1 Group3 medulloblatoma
- GSM8190193 Group3 medulloblatoma rep2 Group3 medulloblatoma
- GSM8190194 Group3 medulloblatoma rep3 Group3 medulloblatoma
- GSM8190195 GNP SAG(+) rep1 GNP SAG(+)
- GSM8190196 GNP SAG(+) rep2 GNP SAG(+)
- GSM8190197 GNP SAG(+) rep3 GNP SAG(+)
- GSM8190198 GNP SAG(-) rep1 GNP SAG(-)
- GSM8190199 GNP SAG(-) rep2 GNP SAG(-)
- GSM8190200 GNP SAG(-) rep3 GNP SAG(-)
- GSM8190201 Ptch1GNP ATAC_1 Ptch1GNP ATAC
- GSM8190202 Ptch1GNP ATAC_2 Ptch1GNP ATAC
- GSM8190203 Ptch1GNP ATAC_3 Ptch1GNP ATAC
- GSM8190204 PNC ATAC_1 PNC ATAC
- GSM8190205 PNC ATAC_2 PNC ATAC
- GSM8190206 PNC ATAC_3 PNC ATAC
- GSM8190207 Tumor ATAC_1 Tumor ATAC
- GSM8190208 Tumor ATAC_2 Tumor ATAC
- GSM8190209 Tumor ATAC_3 Tumor ATAC
- GSM8190210 Tumor Chd7_KO rep1 Tumor Chd7_KO
- GSM8190211 Tumor Chd7_KO rep2 Tumor Chd7_KO
- GSM8190212 NC H3K4me1 rep1 NC H3K4me1
- GSM8190213 NC H3K4me3 rep1 NC H3K4me3
- GSM8190214 NC H3K27ac rep1 NC H3K27ac
- GSM8190215 NC H3K27me3 rep1 NC H3K27me3
- GSM8190216 NC H3K4me1 rep2 NC H3K4me1
- GSM8190217 NC H3K4me3 rep2 NC H3K4me3
- GSM8190218 NC H3K27ac rep2 NC H3K27ac
- GSM8190219 NC H3K27me3 rep2 NC H3K27me3
+ 31 more — browse all 71 samples with per-sample file links →
- GSE263360 Chromatin Modification Abnormalities by CHD7 and KMT2C Loss Promote Medulloblastoma Progression [CUT&Tag] 36 samples shares kmt2c, chd7, medulloblastoma, abnormalities, modification, progression, chromatin, promote
- GSE263358 Chromatin Modification Abnormalities by CHD7 and KMT2C Loss Promote Medulloblastoma Progression [RNA-seq] 21 samples shares kmt2c, chd7, medulloblastoma, abnormalities, modification, progression, chromatin, promote
- GSE263359 Chromatin Modification Abnormalities by CHD7 and KMT2C Loss Promote Medulloblastoma Progression [ATAC-seq] 11 samples shares kmt2c, chd7, medulloblastoma, abnormalities, modification, progression, chromatin, promote
- GSE293000 Chromatin Modification Abnormalities by CHD7 and KMT2C Loss Promote Medulloblastoma Progression [scRNA-seq] 1 samples shares kmt2c, chd7, medulloblastoma, abnormalities, modification, progression, chromatin, promote
- GSE255571 Chromatin remodeler CHD7 regulates neurogenic gene expression via controlling chromatin accessibility and modifications of histone marks H3K27me3 and H3K4me3 [Mouse CUT&Tag] 10 samples shares chd7, modification, chromatin
- GSE255570 Chromatin remodeler CHD7 regulates neurogenic gene expression via controlling chromatin accessibility and modifications of histone marks H3K27me3 and H3K4me3 [Mouse RNA-seq] 4 samples shares chd7, modification, chromatin
- GSE274735 CHD7 promotes anti-viral short-lived effector CD8+ T cells 18 samples shares chd7, promote
- GSE274736 CHD7 promotes anti-viral short-lived effector CD8+ T cells [RNA-seq] 17 samples shares chd7, promote
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.