Functional investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment
ChIP-seq / ATAC-seq (genome binding and open chromatin) · synthetic construct; Homo sapiens · 117 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
- synthetic construct; Homo sapiens
- Topic
- Acute lymphoblastic leukemiaThis series is part of our curated briefing on it.
- Samples
- 117 samples: 26 conditions, mostly with about 4 replicates eachGroups 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
- Investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatmentNature 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 GSE224204_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 PRJNA930066 and SRA study SRP422439. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 79 samples.
How we read this: 26 replicated groups read from 117 sample titles; they account for 79 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.
- GSM7011567 NALM6_igg
- GSM7011568 NALM6_PU1
- GSM7017373 697_PCap_HiC
- GSM7017374 Nalm6_PCap_HiC
- GSM7017375 RS411_PCap_HiC
- GSM7017376 CEM_PCap_HiC
- GSM7017377 REH_PCap_HiC
- GSM7017378 SUPB15_PCap_HiC
- GSM7017379 BALL1_PCap_HiC
- GSM7017380 SEM_PCap_HiC
- GSM7025658 ATAC_P12_1 ATAC_P12
- GSM7025659 ATAC_MOLT16_1 ATAC_MOLT16
- GSM7025660 ATAC_CEM_1 ATAC_CEM
- GSM7025661 ATAC_Loucy_1 ATAC_Loucy
- GSM7025662 ATAC_DND41_1 ATAC_DND41
- GSM7025663 ATAC_HSB2_1 ATAC_HSB2
- GSM7025664 ATAC_Jurkat_1 ATAC_Jurkat
- GSM7025665 ATAC_BALL1_1 ATAC_BALL1
- GSM7025666 ATAC_P12_2 ATAC_P12
- GSM7025667 ATAC_MOLT16_2 ATAC_MOLT16
- GSM7025668 ATAC_CEM_2 ATAC_CEM
- GSM7025669 ATAC_Loucy_2 ATAC_Loucy
- GSM7025670 ATAC_DND41_2 ATAC_DND41
- GSM7025671 ATAC_HSB2_2 ATAC_HSB2
- GSM7025672 ATAC_Jurkat_2 ATAC_Jurkat
- GSM7025673 ATAC_BALL1_2 ATAC_BALL1
- GSM7036225 NALM6_input
- GSM7036226 NALM6_polII_rep1 NALM6_polII
- GSM7036227 NALM6_polII_rep2 NALM6_polII
- GSM7042908 JurkatMPRA001 JurkatMPRA
- GSM7042909 JurkatMPRA002 JurkatMPRA
- GSM7042910 JurkatMPRA003 JurkatMPRA
- GSM7042911 JurkatMPRA004 JurkatMPRA
- GSM7042912 CEMMPRA001 CEMMPRA
- GSM7042913 CEMMPRA002 CEMMPRA
- GSM7042914 CEMMPRA003 CEMMPRA
- GSM7042915 CEMMPRA004 CEMMPRA
- GSM7042916 SUPB15MPRA001 SUPB15MPRA
- GSM7042917 SUPB15MPRA002 SUPB15MPRA
- GSM7042918 SUPB15MPRA003 SUPB15MPRA
+ 77 more — browse all 117 samples with per-sample file links →
- GSE12995 Expression data for diagnosis acute lymphoblastic leukemia samples 175 samples same disease briefing · shares lymphoblastic
- GSE160298 The chromatin accessibility landscape of T-Cell Acute Lymphoblastic Leukemia 80 samples same disease briefing · shares lymphoblastic
- 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
- 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
- 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
- GSE18198 Expression profile of human T-ALL cell lines treated with DMSO or SAHM1 12 samples same disease briefing
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.