ChIP-Seq analysis of H3K4me3 and H3K27ac histone marks without and with METTL8 knockdown
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 24 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
- 24 samples: 12 conditions, mostly in duplicateGroups 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 GSE229482_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 PRJNA954736 and SRA study SRP432163. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 12 replicated groups read from 24 sample titles; they account for 24 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.
- GSM7164246 sh515_H3K4me3_IP_1 sh515_H3K4me3_IP
- GSM7164247 sh515_H3K4me3_IP_2 sh515_H3K4me3_IP
- GSM7164248 sh515_IN_H3K4me3_1 sh515_IN_H3K4me3
- GSM7164249 sh515_IN_H3K4me3_2 sh515_IN_H3K4me3
- GSM7164250 sh516_H3K4me3_IP_1 sh516_H3K4me3_IP
- GSM7164251 sh516_H3K4me3_IP_2 sh516_H3K4me3_IP
- GSM7164252 sh516_IN_H3K4me3_1 sh516_IN_H3K4me3
- GSM7164253 sh516_IN_H3K4me3_2 sh516_IN_H3K4me3
- GSM7164254 shNT_H3K4me3_IP_1 shNT_H3K4me3_IP
- GSM7164255 shNT_H3K4me3_IP_2 shNT_H3K4me3_IP
- GSM7164256 shNT_IN_H3K4me3_1 shNT_IN_H3K4me3
- GSM7164257 shNT_IN_H3K4me3_2 shNT_IN_H3K4me3
- GSM7164258 sh515_H3K27ac_IP1 sh515_H3K27ac_IP
- GSM7164259 sh515_H3K27ac_IP2 sh515_H3K27ac_IP
- GSM7164260 sh515_IN_H3K27ac_1 sh515_IN_H3K27ac
- GSM7164261 sh515_IN_H3K27ac_2 sh515_IN_H3K27ac
- GSM7164262 sh516_H3K27ac_IP1 sh516_H3K27ac_IP
- GSM7164263 sh516_H3K27ac_IP2 sh516_H3K27ac_IP
- GSM7164264 sh516_IN_H3K27ac_1 sh516_IN_H3K27ac
- GSM7164265 sh516_IN_H3K27ac_2 sh516_IN_H3K27ac
- GSM7164266 shNT_H3K27ac_IP1 shNT_H3K27ac_IP
- GSM7164267 shNT_H3K27ac_IP2 shNT_H3K27ac_IP
- GSM7164268 shNT_IN_H3K27ac_1 shNT_IN_H3K27ac
- GSM7164269 shNT_IN_H3K27ac_2 shNT_IN_H3K27ac
- GSE227793 H3K27ac and H3K4me3 ChIP-Seq profiling of a human paired left and right atrial cohort of atrial fibrillation and healthy sinus rhythm individuals 52 samples shares h3k4me3, h3k27ac, chip-seq
- GSE275303 Identifying RARG fusions or PML-RARA binding genes or analysis the epigenetic changes (H3K27ac, H3K4me1, and H3K4me3) in hCD34+ cells overexpressing CPSF6::RARG and NUP98::RARG. 34 samples shares h3k4me3, h3k27ac
- GSE306626 HMGN3 ChIP-seq in AC16 cells and Bulk-RNAseq in AC16 cell with and without HMGN3 knockdown 12 samples shares knockdown, chip-seq, without
- GSE280574 mChIP-seq for high-throughput epigenomic profiling reveals a decoupling of H2A.Z and H3K4me3 in cancer 576 samples shares h3k4me3, chip-seq
- GSE239270 Investigate FOXA2, NKX2-1, CTCF and P300 cistrome and enhancer (H3K27ac and H3k4me1) reprogramming during NEPC transformation by ChIP-seq. 104 samples shares h3k27ac, chip-seq
- GSE310167 Embryonic stem cell factors DPPA2/4 amplify active H3K4me3-H2AK119ub chromatin domains in non-small cell lung cancer (ChIP-seq) 54 samples shares h3k4me3, chip-seq
- GSE290054 H3K4me3 instructs transcription at intergenic active regulatory elements [ChIP-seq] 35 samples shares h3k4me3, chip-seq
- GSE308264 Genome-wide profiling of histone modification H3K27ac and CTCF transcription factor binding in Rett syndrome iPS cells 24 samples shares h3k27ac, histone
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.