3D Chromatin Remodeling in B-cell Development and B-cell Acute Lymphoblastic Leukemia
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 112 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
- 112 samples: 112 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.
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 GSE243299_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 PRJNA1017618 and SRA study SRP460620. 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 112 sample titles: 112 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.
- GSM7782655 ETV005 (ATAC-seq)
- GSM7782656 ETV006 (ATAC-seq)
- GSM7782657 ETV007 (ATAC-seq)
- GSM7782658 KMT2r001 (ATAC-seq)
- GSM7782659 KMT2r004 (ATAC-seq)
- GSM7782660 KMT2r005 (ATAC-seq)
- GSM7782661 PreB (ATAC-seq)
- GSM7782662 ImmatureB (ATAC-seq)
- GSM7782663 REH_sgERG#1 (ChIP-seq)
- GSM7782664 REH_sgERG#4 (ChIP-seq)
- GSM7782665 REH_sgERG#6 (ChIP-seq)
- GSM7782666 REH_sgCTRL#1 (ChIP-seq)
- GSM7782667 REH_sgCTRL#2 (ChIP-seq)
- GSM7782668 REH_CTCF#1 (ChIP-seq)
- GSM7782669 REH_CTCF#2 (ChIP-seq)
- GSM7782670 REH_ERG#1 (ChIP-seq)
- GSM7782671 REH_ERG#2 (ChIP-seq)
- GSM7782672 REH_ERG#3 (ChIP-seq)
- GSM7782673 REH_INPUT (ChIP-seq)
- GSM7782674 SEM_CTCF#1 (ChIP-seq)
- GSM7782675 SEM_CTCF#2 (ChIP-seq)
- GSM7782676 SEM_ERG#1 (ChIP-seq)
- GSM7782677 SEM_ERG#2 (ChIP-seq)
- GSM7782678 SEM_ERG#3 (ChIP-seq)
- GSM7782679 SEM_INPUT (ChIP-seq)
- GSM7782700 CLP001 (RNA-seq)
- GSM7782701 CLP002 (RNA-seq)
- GSM7782702 CLP003 (RNA-seq)
- GSM7782703 CLP004 (RNA-seq)
- GSM7782704 ETV001 (RNA-seq)
- GSM7782705 ETV002 (RNA-seq)
- GSM7782706 ETV003 (RNA-seq)
- GSM7782707 ETV004 (RNA-seq)
- GSM7782708 ETV005 (RNA-seq)
- GSM7782709 ETV006 (RNA-seq)
- GSM7782710 ETV007 (RNA-seq)
- GSM7782711 HD001 (RNA-seq)
- GSM7782712 ImmatureB001 (RNA-seq)
- GSM7782713 ImmatureB003 (RNA-seq)
- GSM7782714 ImmatureB004 (RNA-seq)
+ 72 more — browse all 112 samples with per-sample file links →
- GSE160298 The chromatin accessibility landscape of T-Cell Acute Lymphoblastic Leukemia 80 samples same disease briefing · shares lymphoblastic, chromatin, 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, b-cell, acute
- GSE12995 Expression data for diagnosis acute lymphoblastic leukemia samples 175 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 remodeling, 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
- GSE243298 3D Chromatin Remodeling in B-cell Development and B-cell Acute Lymphoblastic Leukemia [Hi-C] 35 samples shares lymphoblastic, remodeling, chromatin, leukemia, b-cell, 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.