Cut&Run and MARS-seq on SU-DIPG13 cells treated Sulfopin/Vorinostat/Sulfopin+Vorinostat or DMSO
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 26 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
- Homo sapiens (human)
- Samples
- 26 samples: 18 distinct titles, 4 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
- Dual targeting of histone deacetylases and MYC as potential treatment strategy for H3-K27M pediatric gliomaseLife · 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 GSE221614_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 PRJNA915077 and SRA study SRP414499. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 6 samples read as cases, 5 as controls.
How we read this: Read from 26 sample titles: 18 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.
- GSM6890291 Cut& Run on SU-DIPG13 treated with DMSO using H3K27ac ab
- GSM6890292 Cut& Run on SU-DIPG13 treated with DMSO using H3K27me3 ab
- GSM6890293 Cut& Run on SU-DIPG13 treated with Sulfopin using H3K27ac ab
- GSM6890294 Cut& Run on SU-DIPG13 treated with Sulfopin using H3K27me3 ab
- GSM6890295 Cut& Run on SU-DIPG13 treated with Vorinostat using H3K27ac ab
- GSM6890296 Cut& Run on SU-DIPG13 treated with Vorinostat using H3K27me3 ab
- GSM6890297 Cut& Run on SU-DIPG13 treated with Sulfopin+Vorinostat using H3K27ac ab
- GSM6890298 Cut& Run on SU-DIPG13 treated with Sulfopin+Vorinostat using H3K27me3 ab
- GSM6890299 Cut& Run on SU-DIPG13 using HRP ab
- GSM6890300 DMSO1
- GSM6890301 DMSO2
- GSM6890302 DMSO3
- GSM6890303 Sulfo1
- GSM6890304 Sulfo2
- GSM6890305 Sulfo3
- GSM6890306 SulfoVorino1
- GSM6890307 SulfoVorino2
- GSM6890308 SulfoVorino3
- GSM6890309 Vorino1
- GSM6890310 Vorino2
- GSM6890311 Vorino3
- GSM6890312 DMSO2_12h
- GSM6890313 DMSO3_12h
- GSM6890314 Sulfo1_12h
- GSM6890315 Sulfo2_12h
- GSM6890316 Sulfo3_12h
- GSE221612 MARS-seq on SU-DIPG13 cells treated Sulfopin/Vorinostat/Sulfopin+Vorinostat or DMSO 17 samples shares su-dipg13, dmso, vorinostat, mars-seq, sulfopin, treated
- GSE221611 Cut&Run SU-DIPG13 cells treated Sulfopin/Vorinostat/Sulfopin+Vorinostat or DMSO 9 samples shares su-dipg13, dmso, vorinostat, sulfopin, treated
- GSE297268 Alterations of splicing and gene expression in DMSO or 4OHT treated-IMR90 ER:HRAS G12V cells upon knockdown of SF3B1 and RBM39 48 samples shares dmso, treated
- GSE22917 SAGE-Seq gene expression profiles of Hs578T, MCF7, and SUM159PT cells treated with STAT3 or non-targeting siRNAs, DMSO, or CXCR2, PTGIS, HAS1, PFKFB3, JAK, or NQO1 inhibitor 27 samples shares dmso, treated
- GSE333738 Genome-wide mapping of human H4K20me3 in the HN-SCC-151 HPV-negative head and neck squamous cell carcinoma cells treated with DMSO or the SUV420H1 inhibitor A-196/siNC (control) or siSUV420H1 siRNAs. 24 samples shares dmso, treated
- GSE232612 RNA-seq on DMSO or MAK683 treated cancer cells and xenograft tumor samples 24 samples shares dmso, treated
- GSE335198 RNA-seq and ONT full-length transcriptome profiling of HCT116 and WiDr cells treated with DMSO, GSK025, or GSK715 19 samples shares dmso, treated
- GSE211773 RNA-seq in human neuroblastoma SK-N-BE(2)-C cells treated with DMSO, TSA or E6R 9 samples shares dmso, treated
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.