Increased genomic instability and reshaping of tissue microenvironment underlie oncogenic properties of Arid1a mutations
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 31 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
- 31 samples: 14 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
- Increased genomic instability and reshaping of tissue microenvironment underlie oncogenic properties of Arid1a mutationsScience advances · 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 GSE212970_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 PRJNA878530 and SRA study SRP453346. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 28 samples.
How we read this: 14 replicated groups read from 31 sample titles; they account for 28 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.
- GSM7680796 Hepatocytes, ALB, Input
- GSM7680797 Hepatocytes, ALB, H3K27ac, ChIP, rep1 Hepatocytes, ALB, H3K27…
- GSM7680798 Hepatocytes, ALB, H3K27ac, ChIP, rep2 Hepatocytes, ALB, H3K27…
- GSM7680799 Hepatocytes, ALB, H3K4me1, ChIP, rep1 Hepatocytes, ALB, H3K4m…
- GSM7680800 Hepatocytes, ALB, H3K4me1, ChIP, rep2 Hepatocytes, ALB, H3K4m…
- GSM7680801 Hepatocytes, A1AKO, Input
- GSM7680802 Hepatocytes, A1AKO, H3K27ac, ChIP, rep1 Hepatocytes, A1AKO, H3K…
- GSM7680803 Hepatocytes, A1AKO, H3K27ac, ChIP, rep2 Hepatocytes, A1AKO, H3K…
- GSM7680804 Hepatocytes, A1AKO, H3K4me1, ChIP, rep1 Hepatocytes, A1AKO, H3K…
- GSM7680805 Hepatocytes, A1AKO, H3K4me1, ChIP, rep2 Hepatocytes, A1AKO, H3K…
- GSM7680806 Hepatocytes, A1ABDKO, Input
- GSM7680807 Hepatocytes, A1ABDKO, H3K27ac, ChIP, rep1 Hepatocytes, A1ABDKO, H…
- GSM7680808 Hepatocytes, A1ABDKO, H3K27ac, ChIP, rep2 Hepatocytes, A1ABDKO, H…
- GSM7680809 Hepatocytes, A1ABDKO, H3K4me1, ChIP, rep1 Hepatocytes, A1ABDKO, H…
- GSM7680810 Hepatocytes, A1ABDKO, H3K4me1, ChIP, rep2 Hepatocytes, A1ABDKO, H…
- GSM7680825 Arid1a/b DKO, 9gg, rep1 Arid1a/b DKO, 9gg,
- GSM7680826 Arid1a/b DKO, 9gg, rep2 Arid1a/b DKO, 9gg,
- GSM7680827 Arid1a KO, 30gg, rep1 Arid1a KO, 30gg,
- GSM7680828 Arid1a KO, 30gg, rep2 Arid1a KO, 30gg,
- GSM7680829 Arid1a KO, 9gg, rep1 Arid1a KO, 9gg,
- GSM7680830 Arid1a KO, 9gg, rep2 Arid1a KO, 9gg,
- GSM7680831 Arid1a KO/BcatEXON, rep1 Arid1a KO/BcatEXON,
- GSM7680832 Arid1a KO/BcatEXON, rep2 Arid1a KO/BcatEXON,
- GSM7680833 Arid1a KO, 30gg, TC, rep1 Arid1a KO, 30gg, TC,
- GSM7680834 Arid1a KO, 30gg, TC, rep2 Arid1a KO, 30gg, TC,
- GSM7680835 WT, 30gg, rep1 WT, 30gg,
- GSM7680836 WT, 30gg, rep2 WT, 30gg,
- GSM7680837 WT, 9gg, rep1 WT, 9gg,
- GSM7680838 WT, 9gg, rep2 WT, 9gg,
- GSM7680839 WT, 9gg, TC, rep1 WT, 9gg, TC,
- GSM7680840 WT, 9gg, TC, rep2 WT, 9gg, TC,
- GSE264527 Reshaping the Tumor Microenvironment of KRASG12D Pancreatic Ductal Adenocarcinoma with combined SOS1 and MEK Inhibition for Improved Immunotherapy Response 21 samples shares microenvironment, reshaping
- GSE241365 Oncogenic Calreticulin Induces Immune Escape by Stimulating TGF-β Expression and Regulatory T Cell Expansion in the Bone Marrow Microenvironment 12 samples shares microenvironment, oncogenic
- GSE269888 Oncogenic KRAS-dependent stromal interleukin-33 directs the pancreatic microenvironment to promote tumor growth [scRNA-seq] 11 samples shares microenvironment, oncogenic
- GSE217807 ARID1A suppresses R-loop mediated STING-Type I Interferon pathway activation of anti-tumor immunity 62 samples shares arid1a
- GSE269928 Arid1a mediates cell recovery upon gastric injury to prevent tumorigenesis [Multiome] 9 samples shares arid1a
- GSE254328 Epigenetic regulation of chromosomal instability by EZH2 methyltransferase 26 samples shares instability
- GSE290082 Enhancer-driven gene regulatory networks reveal transcription factors governing T cell adaptation and differentiation in the tumor microenvironment. 25 samples shares microenvironment
- GSE218178 Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance 183 samples shares microenvironment
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.