Effects of overexpression of PTPN21 on gene expression of Jurkat cells
RNA-seq (gene expression) · human · 12 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
- 12 samples: 3 × NC vs 3 × OE vs 3 × VC vs 3 × OEVCGroups 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
- PTPN21 inhibits cell apoptosis of acute lymphoblastic leukemia induced by chemotherapeutic agents via GADD45A and JNK signaling pathwayPloS one · 2025
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 GSE253979_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 PRJNA1068044 and SRA study SRP485442. 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.
- GSM8031391 NC1 NC
- GSM8031392 NC2 NC
- GSM8031393 NC3 NC
- GSM8031394 OE1 OE
- GSM8031395 OE2 OE
- GSM8031396 OE3 OE
- GSM8031397 VCR1 VC
- GSM8031398 VCR2 VC
- GSM8031399 VCR3 VC
- GSM8031400 OEVCR1 OEVC
- GSM8031401 OEVCR2 OEVC
- GSM8031402 OEVCR3 OEVC
- 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 jurkat
- 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
- 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
- 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
- GSE18198 Expression profile of human T-ALL cell lines treated with DMSO or SAHM1 12 samples same disease briefing
- GSE160298 The chromatin accessibility landscape of T-Cell Acute Lymphoblastic Leukemia 80 samples same disease briefing
- GSE281957 Effects of overexpression of GFP-TDP-43, GFP-TDP-43(86-414) or GFP in human H4 cells, in the presence or absence of the EIF2B activator DNL343. 47 samples shares overexpression
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.