Identification and targeting of extremely high-risk gamma delta T-ALL in children [HiChIP, ChIP and ATAC]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 62 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
- 62 samples: 20 conditions, mostly in duplicateGroups 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
- Biologic and Clinical Analysis of Childhood Gamma Delta T-ALL Identifies LMO2/STAG2 Rearrangements as Extremely High RiskCancer discovery · 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 GSE243772_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 PRJNA1019788 and SRA study SRP462596. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 42 samples.
How we read this: 20 replicated groups read from 62 sample titles; they account for 42 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.
- GSM7795535 MOLT-14_HiChIP_H3K27ac
- GSM7795536 PER-117_HiChIP_H3K27ac
- GSM7795537 MOLT14_EV_H3K27ac_rep1 MOLT14_EV_H3K27ac
- GSM7795538 MOLT14_EV_H3K27ac_rep2 MOLT14_EV_H3K27ac
- GSM7795539 MOLT14_EV_input_rep1 MOLT14_EV_input
- GSM7795540 MOLT14_EV_input_rep2 MOLT14_EV_input
- GSM7795541 MOLT14_EV_STAG1_rep1 MOLT14_EV_STAG1
- GSM7795542 MOLT14_EV_STAG1_rep2 MOLT14_EV_STAG1
- GSM7795543 MOLT14_EV_STAG2_rep1 MOLT14_EV_STAG2
- GSM7795544 MOLT14_EV_STAG2_rep2 MOLT14_EV_STAG2
- GSM7795545 MOLT14_STAG2_H3K27ac_rep1 MOLT14_STAG2_H3K27ac
- GSM7795546 MOLT14_STAG2_H3K27ac_rep2 MOLT14_STAG2_H3K27ac
- GSM7795547 MOLT14_STAG2_input_rep1 MOLT14_STAG2_input
- GSM7795548 MOLT14_STAG2_input_rep2 MOLT14_STAG2_input
- GSM7795549 MOLT14_STAG2_STAG1_rep1 MOLT14_STAG2_STAG1
- GSM7795550 MOLT14_STAG2_STAG1_rep2 MOLT14_STAG2_STAG1
- GSM7795551 MOLT14_STAG2_STAG2_rep1 MOLT14_STAG2_STAG2
- GSM7795552 MOLT14_STAG2_STAG2_rep2 MOLT14_STAG2_STAG2
- GSM7795553 PF382_SA19_WT_H3K27ac
- GSM7795554 PF382_SA19_WT_input
- GSM7795555 PF382_SA19_WT_STAG1 PF382_SA19_WT_STAG
- GSM7795556 PF382_SA19_WT_STAG2 PF382_SA19_WT_STAG
- GSM7795557 PF382_SA20_STAG2KO_homo_H3K27ac
- GSM7795558 PF382_SA20_STAG2KO_homo_input
- GSM7795559 PF382_SA20_STAG2KO_homo_STAG1 PF382_SA20_STAG2KO_homo…
- GSM7795560 PF382_SA20_STAG2KO_homo_STAG2 PF382_SA20_STAG2KO_homo…
- GSM7795561 PF382_SA28_WT_H3K27ac
- GSM7795562 PF382_SA28_WT_input
- GSM7795563 PF382_SA28_WT_STAG1 PF382_SA28_WT_STAG
- GSM7795564 PF382_SA28_WT_STAG2 PF382_SA28_WT_STAG
- GSM7795565 PF382_SB23_STAG2KO_homo_H3K27ac
- GSM7795566 PF382_SB23_STAG2KO_homo_input
- GSM7795567 PF382_SB23_STAG2KO_homo_STAG1 PF382_SB23_STAG2KO_homo…
- GSM7795568 PF382_SB23_STAG2KO_homo_STAG2 PF382_SB23_STAG2KO_homo…
- GSM8244884 MOLT-14_ChIPseq_CTCF
- GSM8244885 MOLT-14_ChIPseq_CTCF_input
- GSM8244886 MOLT-14_ChIPseq_CTCF_EV_rep1 MOLT-14_ChIPseq_CTCF_EV
- GSM8244887 MOLT-14_ChIPseq_CTCF_EV_rep2 MOLT-14_ChIPseq_CTCF_EV
- GSM8244888 MOLT-14_ChIPseq_CTCF_EV_rep1_input
- GSM8244889 MOLT-14_ChIPseq_CTCF_EV_rep2_input
+ 22 more — browse all 62 samples with per-sample file links →
- GSE291386 Chromatin accessibility profiling of HSPC-derived erythroblast differentiation [ATAC-seq] 165 samples shares atac
- GSE289805 Histone H4 lysine 20 tri-methylation safeguards breast cancer lineage fidelity and unfolded protein response [ChIP-seq/ATAC-seq] 126 samples shares atac
- GSE270684 The EZH2 and EZH1 inhibitor valemetostat derepresses p16INK4a to induce early endomitotic exit in megakaryocytes [scATAC-Seq] 66 samples shares atac
- GSE327580 Acquired genetic and cell state changes in IDH-mutant glioma progression [snATAC] 48 samples shares atac
- GSE282258 Imaging-based drug screening combined with moleuclar profiling identifies signatures and drivers of therapy resistance in pediatric AML [ATAC-seq] 44 samples shares atac
- GSE334112 Reversible epiblast regionalisation determines differentiation potential of human PSCs [ATAC-seq] 38 samples shares atac
- GSE316389 Chromatin accessibility and gene expression profiling of primary and metastatic ER+ breast cancer [ATAC-seq] 36 samples shares atac
- GSE286146 Two parallel neural ectoderm populations contribute to the developing brain [ATAC-seq] 30 samples shares atac
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.