STAG2 Mutations Reshape the Cohesin-Structured Spatial Chromatin Architecture to Drive Gene Regulation in Acute myeloid Leukemia
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 541 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)
- Topic
- Acute myeloid leukemiaThis series is part of our curated briefing on it.
- Samples
- 541 samples: 296 distinct titles, 13 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
- STAG2 mutations reshape the cohesin-structured spatial chromatin architecture to drive gene regulation in acute myeloid leukemiaCell reports · 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 GSE268035_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 PRJNA1114077. Searching any of these in the dataset finder brings you back here.
How we read this: Read from the first 400 of 541 sample titles: 296 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.
- GSM8272861 ATAC_AML_ctr_10156
- GSM8272862 ATAC_AML_ctr_16911
- GSM8272863 ATAC_AML_ctr_18136
- GSM8272864 ATAC_AML_ctr_19416
- GSM8272865 ATAC_AML_ctr_21047
- GSM8272866 ATAC_AML_RAD21_27650
- GSM8272867 ATAC_AML_RAD21_AML0117
- GSM8272868 ATAC_AML_RAD21_UKR186
- GSM8272869 ATAC_AML_SA2_22525
- GSM8272870 ATAC_AML_SA2_24743
- GSM8272871 ATAC_AML_SA2_27493
- GSM8272872 ATAC_AML_SA2_29728
- GSM8272873 ATAC_CD34_14_3_siCtrl
- GSM8272874 ATAC_CD34_17_3_siCtrl
- GSM8272875 ATAC_CD34_18_4_siCtrl
- GSM8272876 ATAC_CD34_19_2_siCtrl
- GSM8272877 ATAC_CD34_20_6_siCtrl
- GSM8272878 ATAC_CD34_21_4_siCtrl
- GSM8272879 ATAC_CD34_22_3_siCtrl
- GSM8272880 ATAC_CD34_24_1_siCtrl
- GSM8272881 ATAC_CD34_27_4_siCtrl
- GSM8272882 ATAC_CD34_28_6_siCtrl
- GSM8272883 ATAC_CD34_14_4_Mock
- GSM8272884 ATAC_CD34_20_7_Mock
- GSM8272885 ATAC_CD34_18_1_Rad21
- GSM8272886 ATAC_CD34_20_1_Rad21
- GSM8272887 ATAC_CD34_22_1_RAD21
- GSM8272888 ATAC_CD34_27_1_Rad21
- GSM8272889 ATAC_CD34_28_1_Rad21
- GSM8272890 ATAC_CD34_14_1_SA1
- GSM8272891 ATAC_CD34_17_1_SA1
- GSM8272892 ATAC_CD34_18_2_SA1_SA2
- GSM8272893 ATAC_CD34_20_2_SA1_SA2
- GSM8272894 ATAC_CD34_20_4_SA1
- GSM8272895 ATAC_CD34_21_2_SA1
- GSM8272896 ATAC_CD34_27_3_SA1
- GSM8272897 ATAC_CD34_28_2_SA1_SA2
- GSM8272898 ATAC_CD34_28_4_SA1
- GSM8272899 ATAC_CD34_14_2_SA2
- GSM8272900 ATAC_CD34_17_2_SA2
+ 501 more — browse all 541 samples with per-sample file links →
- GSE137851 The long non-coding RNA HOXB-AS3 regulates ribosomal RNA transcription in NPM1-mutated acute myeloid leukemia 387 samples same disease briefing · shares leukemia
- GSE270185 Repurposing CD19-directed immunotherapies for pediatric t(8;21) acute myeloid leukemia 249 samples same disease briefing · shares leukemia
- GSE137574 Kevetrin induces apoptosis in TP53 wild-type and mutant acute myeloid leukemia cells 24 samples same disease briefing · shares leukemia
- GSE303795 Halofuginone exerts broad-spectrum cytotoxic effects by regulating p-eIF2α-S100A8/A9-calcium signaling, inhibiting global protein synthesis, and reversing the resistance of idarubicin in acute myeloid leukemia 6 samples same disease briefing · shares leukemia
- GSE129437 Genome-wde mapping of BRD9 binding sites and gene expression changes upon BRD9 knockdown 6 samples same disease briefing
- GSE122515 Bonn Dataset 3 of meta-analysis on AML classification, RNAseq dataset 0 samples same disease briefing
- GSE240343 STAG2 mutations and 3D genome organization, chromatin loops, and polycomb signaling in glioblastoma multiforme 20 samples shares stag2, mutations, chromatin
- GSE195611 3D chromatin architecture of drug-tolerant cancer cells at single-cell resolution 410 samples shares architecture, chromatin
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.