The chromatin accessibility landscape of T-Cell Acute Lymphoblastic Leukemia
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 80 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 lymphoblastic leukemiaThis series is part of our curated briefing on it.
- Samples
- 80 samples: 73 distinct titles, 7 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.
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 GSE160298_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 PRJNA672916 and SRA study SRP289460. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 80 sample titles: 73 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.
- GSM4870905 6787 Diagnosis ATAC-seq
- GSM4870906 6787 Relapse ATAC-seq
- GSM4870907 7300 Diagnosis ATAC-seq
- GSM4870908 7300 Relapse ATAC-seq
- GSM4870909 6953 Diagnosis ATAC-seq
- GSM4870910 6953 Relapse ATAC-seq
- GSM4870911 PARGIR Diagnosis ATAC-seq
- GSM4870912 PARGIR Relapse ATAC-seq
- GSM4870913 PARMJA Diagnosis ATAC-seq
- GSM4870914 PARMJA Relapse ATAC-seq
- GSM4870915 PARPCK Diagnosis ATAC-seq
- GSM4870916 PARPCK Relapse ATAC-seq
- GSM4870917 PARVUE Diagnosis ATAC-seq
- GSM4870918 PARVUE Relapse ATAC-seq
- GSM4870919 PARYMD Diagnosis ATAC-seq
- GSM4870920 PARYMD Relapse ATAC-seq
- GSM4870921 PASJFJ Diagnosis ATAC-seq
- GSM4870922 PASJFJ Relapse ATAC-seq
- GSM4870923 PASRPK Diagnosis ATAC-seq
- GSM4870924 PASRPK Relapse ATAC-seq
- GSM4870925 PASVYP Diagnosis ATAC-seq
- GSM4870926 PASVYP Relapse ATAC-seq
- GSM4870927 PATDDT Diagnosis ATAC-seq
- GSM4870928 PATDDT Relapse ATAC-seq
- GSM4870929 PATENL Diagnosis ATAC-seq
- GSM4870930 PATENL Relapse ATAC-seq
- GSM4870931 PATVDU Diagnosis ATAC-seq
- GSM4870932 PATVDU Relapse ATAC-seq
- GSM4870933 CUL-76 Diagnosis ATAC-seq
- GSM4870934 CUL-249 Diagnosis ATAC-seq
- GSM4870935 CUL-297 Diagnosis ATAC-seq
- GSM4870936 13684 Diagnosis ATAC-seq
- GSM4870937 22259 Diagnosis ATAC-seq
- GSM4870938 20165 Diagnosis ATAC-seq
- GSM4870939 27596 Diagnosis ATAC-seq
- GSM4870940 CD34-Cd1a-Negative ATAC-seq 1
- GSM4870941 CD34-Cd1a-Negative ATAC-seq 2
- GSM4870942 CD34-Cd1a-Positive ATAC-seq 1
- GSM4870943 CD34-Cd1a-Positive ATAC-seq 2
- GSM4870944 ISP ATAC-seq 1
+ 40 more — browse all 80 samples with per-sample file links →
- GSE12995 Expression data for diagnosis acute lymphoblastic leukemia samples 175 samples same disease briefing · shares lymphoblastic, leukemia, acute
- GSE115656 Alternative splicing analysis of pediatric B-cell acute lymphoblastic leukemia compared to normal bone marrow derived pro-B cells 38 samples same disease briefing · shares lymphoblastic, leukemia, acute
- 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 same disease briefing · shares chromatin
- GSE13425 Expression data from ALL patients included in the set used to construct a classification signature (COALL cohort) 190 samples same disease briefing
- GSE154675 PHF6 Interacts with LMO2 During Normal Haematopoiesis and in Leukaemia and Regulates the Level of Gene Expression and Genome Integrity 41 samples same disease briefing
- GSE18198 Expression profile of human T-ALL cell lines treated with DMSO or SAHM1 12 samples same disease briefing
- GSE243299 3D Chromatin Remodeling in B-cell Development and B-cell Acute Lymphoblastic Leukemia 112 samples shares lymphoblastic, chromatin, leukemia, acute
- GSE243298 3D Chromatin Remodeling in B-cell Development and B-cell Acute Lymphoblastic Leukemia [Hi-C] 35 samples shares lymphoblastic, chromatin, leukemia, acute
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.