TNF-mediated cell death: an actionable target for immunotherapy in T-ALL
RNA-seq (gene expression) · human · 50 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Topic
- Acute lymphoblastic leukemiaThis series is part of our curated briefing on it.
- Samples
- 50 samples: 13 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.
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 GSE266348_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1106795 and SRA study SRP505184. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 32 samples.
How we read this: 13 replicated groups read from 50 sample titles; they account for 32 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.
- GSM8245373 UPNT1077, Thymo, H0 UPNT1077, Thymo, H
- GSM8245374 UPNT1077, Thymo, H1 UPNT1077, Thymo, H
- GSM8245375 UPNT1077, Thymo, H4 UPNT1077, Thymo, H
- GSM8245376 UPNT1077, Thymo, H24 UPNT1077, Thymo, H
- GSM8245377 UPNT474, Thymo, H0 UPNT474, Thymo, H
- GSM8245378 UPNT474, Thymo, H1 UPNT474, Thymo, H
- GSM8245379 UPNT474, Thymo, H4 UPNT474, Thymo, H
- GSM8245380 UPNT474, Thymo, H24 UPNT474, Thymo, H
- GSM8245381 UPNT1012, Thymo, H0 UPNT1012, Thymo, H
- GSM8245382 UPNT1012, Thymo, H1 UPNT1012, Thymo, H
- GSM8245383 UPNT1012, Thymo, H4 UPNT1012, Thymo, H
- GSM8245384 UPNT1012, Thymo, H24 UPNT1012, Thymo, H
- GSM8245405 UPNT1077, CT
- GSM8245406 UPNT1077, Thymo
- GSM8245407 UPNT525, CT
- GSM8245408 UPNT525, Thymo
- GSM8245409 Jurkat, CT
- GSM8245410 Jurkat, Thymo
- GSM8245411 UPNT474, CT
- GSM8245412 UPNT474, Thymo
- GSM8245413 UPNT380, CT, run1 UPNT380, CT,
- GSM8245414 UPNT380, Thymo, run1 UPNT380, Thymo,
- GSM8245415 UPNT420, CT, run1 UPNT420, CT,
- GSM8245416 UPNT420, Thymo, run1 UPNT420, Thymo,
- GSM8245417 UPNT534, CT
- GSM8245418 UPNT534, Thymo
- GSM8245419 UPNT1095, CT
- GSM8245420 UPNT1095, Thymo
- GSM8245421 RPMI, HO, rep2 RPMI, HO,
- GSM8245422 RPMI, HO, rep1 RPMI, HO,
- GSM8245423 RPMI, H1, CT, rep2 RPMI, H1, CT,
- GSM8245424 RPMI, H1, CT, rep1 RPMI, H1, CT,
- GSM8245425 RPMI, H1, Thymo, rep2 RPMI, H1, Thymo,
- GSM8245426 RPMI, H1, Thymo, rep1 RPMI, H1, Thymo,
- GSM8245427 ALL-SIL, H0, rep2 ALL-SIL, H0,
- GSM8245428 ALL-SIL, H0, rep1 ALL-SIL, H0,
- GSM8245429 ALL-SIL, H1, CT, rep2 ALL-SIL, H1, CT,
- GSM8245430 ALL-SIL, H1, CT, rep1 ALL-SIL, H1, CT,
- GSM8245431 ALL-SIL, H1, Thymo, rep2 ALL-SIL, H1, Thymo,
- GSM8245432 ALL-SIL, H1, Thymo, rep1 ALL-SIL, H1, Thymo,
+ 10 more — browse all 50 samples with per-sample file links →
- 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 t-all
- GSE18198 Expression profile of human T-ALL cell lines treated with DMSO or SAHM1 12 samples same disease briefing · shares t-all
- 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
- GSE160298 The chromatin accessibility landscape of T-Cell Acute Lymphoblastic Leukemia 80 samples same disease briefing
- GSE13425 Expression data from ALL patients included in the set used to construct a classification signature (COALL cohort) 190 samples same disease briefing
- GSE12995 Expression data for diagnosis acute lymphoblastic leukemia samples 175 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
- GSE266346 TNF-mediated cell death: an actionable target for immunotherapy in T-ALL [2] 38 samples shares t-all, immunotherapy, tnf-mediated, actionable, target, death
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.