Genome-wide analysis of RUNX3 binding and histone modification alteration after RUNX3 Knock out
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 18 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
- 18 samples: 9 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.
- Paper
- Aberrant Upregulation of RUNX3 Activates Developmental Genes to Drive Metastasis in Gastric CancerCancer research communications · 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 GSE198664_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 PRJNA816429 and SRA study SRP364133. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 9 replicated groups read from 18 sample titles; they account for 18 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.
- GSM5954525 HGC27_WT_Input_rep1 HGC27_WT_Input
- GSM5954526 HGC27_WT_Input_rep2 HGC27_WT_Input
- GSM5954527 HGC27_RUNX3KO_Input_rep1 HGC27_RUNX3KO_Input
- GSM5954528 HGC27_RUNX3KO_Input_rep2 HGC27_RUNX3KO_Input
- GSM5954529 HGC27_WT_RUNX3_rep1 HGC27_WT_RUNX3
- GSM5954530 HGC27_WT_RUNX3_rep2 HGC27_WT_RUNX3
- GSM5954531 HGC27_WT_H3K27ac_rep1 HGC27_WT_H3K27ac
- GSM5954532 HGC27_WT_H3K27ac_rep2 HGC27_WT_H3K27ac
- GSM5954533 HGC27_RUNX3KO_H3K27ac_rep1 HGC27_RUNX3KO_H3K27ac
- GSM5954534 HGC27_RUNX3KO_H3K27ac_rep2 HGC27_RUNX3KO_H3K27ac
- GSM5954535 HGC27_WT_H3K4me3_rep1 HGC27_WT_H3K4me3
- GSM5954536 HGC27_WT_H3K4me3_rep2 HGC27_WT_H3K4me3
- GSM5954537 HGC27_RUNX3KO_H3K4me3_rep1 HGC27_RUNX3KO_H3K4me3
- GSM5954538 HGC27_RUNX3KO_H3K4me3_rep2 HGC27_RUNX3KO_H3K4me3
- GSM5954539 HGC27_WT_H3K4me1_rep1 HGC27_WT_H3K4me1
- GSM5954540 HGC27_WT_H3K4me1_rep2 HGC27_WT_H3K4me1
- GSM5954541 HGC27_RUNX3KO_H3K4me1_rep1 HGC27_RUNX3KO_H3K4me1
- GSM5954542 HGC27_RUNX3KO_H3K4me1_rep2 HGC27_RUNX3KO_H3K4me1
- GSE308264 Genome-wide profiling of histone modification H3K27ac and CTCF transcription factor binding in Rett syndrome iPS cells 24 samples shares modification, genome-wide, binding, histone
- GSE193713 Genome-wide maps of chromatin state for histone modifications and chromatin remodeling factors in WT and PHF6-KO conditions in Jurkat T-ALL cells. 20 samples shares modification, genome-wide, histone
- GSE271703 Integrated ChIP-seq and Transcriptomic Profiling of Histone Modifications Across Breast Cancer Progression in MCF10A-Derived Cell Lines [ChIP-Seq] 60 samples shares modification, histone
- GSE326102 Genome-wide histone acetylation underscores tumor intrinsic immune signaling induced by photothermal therapy in ovarian cancer 56 samples shares genome-wide, histone
- GSE269841 Genome-wide Mapping of Topoisomerase Binding Sites Suggests Topoisomerase 3a (TOP3A) as a Reader of Transcription-Replication Conflicts (TRC) 15 samples shares genome-wide, binding
- GSE304098 Profiling of histone modifications reveal tumor microenvironment-acquired super-enhancer regulates progression of esophageal squamous cell carcinoma 11 samples shares modification, histone
- GSE237282 Integrative Analysis of Genome-Wide Epigenetic and Transcriptomic Alterations Reveals Molecular Markers for Diagnosing Pediatric Obstructive Sleep Apnea in Black Females 37 samples shares genome-wide, alteration
- GSE288172 Influence of NIPBL Knockdown-Induced Alterations in Cohesin Loop Extrusion on CTCF Loops, Enhancer-Promoter Connectivity, and PRC Domain Contacts During hESC Differentiation into Pancreatic Lineages 263 samples shares alteration, knock
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.