Phase Separation of ARID1A Chromatin Remodeling Factor Promotes Oncogenic Potential of Ewing’s Sarcoma
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 30 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
- 30 samples: 30 samples, each with a distinct title — no replicated groupsGroups 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
- Prion-like domain mediated phase separation of ARID1A promotes oncogenic potential of Ewing's sarcomaNature 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 GSE234239_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 PRJNA980606 and SRA study SRP441348. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 30 sample titles: 30 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.
- GSM7457918 A673 WT RNA-seq
- GSM7457919 A673 ARID1A WT RE1 RNA-seq
- GSM7457920 A673 ARID1A WT RE2 RNA-seq
- GSM7457921 A673 ARID1A WT RE3 RNA-seq
- GSM7457922 A673 ARID1A WT RE4 RNA-seq
- GSM7457923 A673 ARID1A WT RE5 RNA-seq
- GSM7457924 A673 ARID1A KO RNA-seq
- GSM7457925 A673 ARID1A DD1,2 1 RNA-seq
- GSM7457926 A673 ARID1A DD1,2 2 RNA-seq
- GSM7457927 A673 ARID1A DD1,2 3 RNA-seq
- GSM7457928 A673 ARID1A DD1,2 4 RNA-seq
- GSM7457929 A673 ARID1A DD1,2 5 RNA-seq
- GSM7457930 A673 ARID1A PRLD Y/S RNA-seq
- GSM7457931 A673 WT ATAC-seq
- GSM7457932 A673 ARID1A WT RE1 ATAC-seq
- GSM7457933 A673 ARID1A WT RE2 ATAC-seq
- GSM7457934 A673 ARID1A WT RE3 ATAC-seq
- GSM7457935 A673 ARID1A WT RE4 ATAC-seq
- GSM7457936 A673 ARID1A WT RE5 ATAC-seq
- GSM7457937 A673 ARID1A KO ATAC-seq
- GSM7457938 A673 ARID1A DD1,2 1 ATAC-seq
- GSM7457939 A673 ARID1A DD1,2 2 ATAC-seq
- GSM7457940 A673 ARID1A DD1,2 3 ATAC-seq
- GSM7457941 A673 ARID1A DD1,2 4 ATAC-seq
- GSM7457942 A673 ARID1A DD1,2 5 ATAC-seq
- GSM7457943 A673 ARID1A PRLD Y/S ATAC-seq
- GSM7457944 A673 ARID1A WT RE2 in situ Hi-C
- GSM7457945 A673 ARID1A WT RE3 in situ Hi-C
- GSM7457946 A673 ARID1A DD1,2 2 in situ Hi-C
- GSM7457947 A673 ARID1A DD1,2 4 in situ Hi-C
- GSE314155 BRD9 Reads Lactate-Induced H3K18 Lactylation to Drive Oncogenic Chromatin Remodeling in Hepatocellular Carcinoma 17 samples shares remodeling, chromatin, oncogenic
- GSE215328 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [hESC_H9_d049_ChIP_Seq] 135 samples shares remodeling, chromatin
- GSE243299 3D Chromatin Remodeling in B-cell Development and B-cell Acute Lymphoblastic Leukemia 112 samples shares remodeling, chromatin
- GSE278512 Phase separation of chimeric antigen receptor promotes immunological synapse maturation and persistent cytotoxicity 45 samples shares separation, promotes
- GSE253694 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [HEK293T_siNURD_CTCF_ChIP_Seq] 36 samples shares remodeling, chromatin
- GSE243298 3D Chromatin Remodeling in B-cell Development and B-cell Acute Lymphoblastic Leukemia [Hi-C] 35 samples shares remodeling, chromatin
- GSE215326 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [HEK293T_IAA72h_ChIP_Seq] 30 samples shares remodeling, chromatin
- GSE247982 The chromatin landscape of high-grade serous ovarian cancer metastasis identifies potential regulatory drivers of chemoresistant tumour cells 10 samples shares chromatin, potential
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.