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A novel gain-of-function phosphorylation site modulates PTPN22 inhibition of TCR signaling

GSE264373 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2024/07/17 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 24 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)
Samples
24 samples: 8 conditions, mostly in triplicateGroups 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
A novel gain-of-function phosphorylation site modulates PTPN22 inhibition of TCR signalingThe Journal of biological chemistry · 2024
Summary (written by the submitters)
Protein Tyrosine Phosphatase Non-receptor type 22 (PTPN22) is encoded by a major autoimmunity gene and is a known inhibitor of T cell receptor (TCR) signaling and drug target for cancer immunotherapy. However, little is known about PTPN22 post-translational regulation. Here we characterize a phosphorylation site at Ser325 situated C-terminal to the catalytic domain of PTPN22, and its roles in altering protein function.
Read the full summary ↓
Signaling through the major TCR-dependent pathway under PTPN22 control was enhanced by CRISPR/Cas9 mediated suppression of Ser325 phosphorylation and inhibited by mimicking it via glutamic acid substitution. Next-generation sequencing (NGS) revealed it differentially regulates the expression of chemokines and T cell activation pathways. In conclusion, this study explores the function of a novel phosphorylation site of PTPN22 that is involved in complex regulation of TCR signaling .
Published in
A novel gain-of-function phosphorylation site modulates PTPN22 inhibition of TCR signaling
Zhuang C, Yang S, Gonzalez CG et al. · The Journal of biological chemistry 2024 · PMID 38777143 · doi:10.1016/j.jbc.2024.107393
This dataset
Open GSE264373 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE264373_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1102292 and SRA study SRP502779. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38777143) ↗
Study design
8 conditions, mostly in triplicate
S325A counterpart WT, Nonstimulated, biol ×3 S325A mutant, Nonstimulated, biol ×3 S325E counterpart WT, Nonstimulated, biol ×3 S325E mutant, Nonstimulated, biol ×3 S325A counterpart WT, CD3/CD28 stimulated, bi… ×3 S325A mutant, CD3/CD28 stimulated, biol ×3 S325E conterpart WT, CD3/CD28 stimulated, biol ×3 S325E mutant, CD3/CD28 stimulated, biol ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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.

Samples in this study
Datasets on a similar topic

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