Highly multiplexed single cell chromatin regulator and accessibility profiling elucidates chromatin dynamics in human B cell development and oncogenesis, and reveals an adverse prognostic gene expression signature in B lymphoblastic leukemias [patient]
Single-cell RNA-seq · human · 12 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Topic
- Acute lymphoblastic leukemiaThis series is part of our curated briefing on it.
- Samples
- 12 samples: 3 × Patient1_tech vs 3 × Patient2_tech vs 3 × Patient3_tech vs 3 × Patient4_techGroups 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.
Read the full summary ↓
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 GSE269118_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1120342 and SRA study SRP511922. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8306617 Patient1_techrep1 Patient1_tech
- GSM8306618 Patient1_techrep2 Patient1_tech
- GSM8306619 Patient1_techrep3 Patient1_tech
- GSM8306620 Patient2_techrep1 Patient2_tech
- GSM8306621 Patient2_techrep2 Patient2_tech
- GSM8306622 Patient2_techrep3 Patient2_tech
- GSM8306623 Patient3_techrep1 Patient3_tech
- GSM8306624 Patient3_techrep2 Patient3_tech
- GSM8306625 Patient3_techrep3 Patient3_tech
- GSM8306626 Patient4_techrep1 Patient4_tech
- GSM8306627 Patient4_techrep2 Patient4_tech
- GSM8306628 Patient4_techrep3 Patient4_tech
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- 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
- GSE12995 Expression data for diagnosis acute lymphoblastic leukemia samples 175 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
- GSE18198 Expression profile of human T-ALL cell lines treated with DMSO or SAHM1 12 samples same disease briefing
- GSE268580 Highly multiplexed single cell chromatin regulator and accessibility profiling elucidates chromatin dynamics in human B cell development and oncogenesis, and reveals an adverse prognostic gene expression signature in B lymphoblastic leukemias 15 samples shares accessibility, lymphoblastic, multiplexed, oncogenesis, elucidates, prognostic, chromatin, regulator
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.