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Sample GSM5961773 Query DataSets for GSM5961773
Status Public on Oct 06, 2023
Title H332L_IL10
Sample type SRA
 
Source name IL10 stimulated STAT3-LoF (H332L) CD4+ T-cells
Organism Homo sapiens
Characteristics tissue: Peripheral blood
age: 18 years
genotype: STAT3-H332L
stimulation: IL10
Sex: male
cell type: Purified CD4+ T-cells
Treatment protocol CD4+ T-cells derived from the long-term T cell cultures described above were isolated by MACS separation and stimulated or not, for one hour, with IL-10 or IL-21 for activating the STAT3 pathway in T-cells
Growth protocol Patient and control PBMCs were stimulated with irradiated allogeneic PBMCs as feeder cells, PHA (2.5 µg/ml, Remel) and IL-2 in IMDM medium, and split every 2–4 d. A second stimulation round was performed 21 days after the first stimulation.
Extracted molecule polyA RNA
Extraction protocol The total RNA was extracted from 3 million CD4+ T-cells by using QIAGEN RNA extraction kit according to the manufacturer instructions.
Library preparation and paired-end, unstranded, 150 bp sequencing. NEBNext RNA First Strand Synthesis Module; NEBNext Ultra Directional Second Strand Synthesis Module
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description The gene expression profile of IL10 stimulated STAT3-LoF (H332L) CD4+ T-cells
R24
Data processing Illumina adapter clipping with cutadapt v3.4
Quality trimming with trimmomatic v0.39, mode MAXINFO, target read length 75, strictness 0.5
Transcript quantification with salmon v1.5.2, with gcBias correction, with seqBias correction
Generation of a gene count matrix with tximport v1.20.0, countsFromAbundace = lengthScaledTPM
Minimum expression filtering, normalization and batch correction with edgeR v3.34.1, via filterByExpr, calcNormFactors, cpm functions
Assembly: GRCh38, Ensembl release 97
Supplementary files format and content: Tab-delimited text file with isoform identifiers, raw counts and transcripts per million as output by salmon (“quant.sf.txt” file)
Supplementary files format and content: Tab-delimited text file with raw gene counts for each gene per sample
Supplementary files format and content: Tab-delimited text file with normalized gene counts for each gene per sample (counts per million, TMM normalized)
 
Submission date Mar 18, 2022
Last update date Oct 06, 2023
Contact name Senthilkumar Ramamoorthy
E-mail(s) senthilkumar.ramamoorthy@uniklinik-freiburg.de
Phone +49 761 270-46 670
Organization name UNIVERSITAETSKLINIKUM FREIBURG
Street address Mathildenstraße 1
City Freiburg
ZIP/Postal code 79106
Country Germany
 
Platform ID GPL24676
Series (1)
GSE198963 The gene expression profile of CD4 T-cells with STAT3 gain-of-function and loss-of-function mutations
Relations
BioSample SAMN26796871
SRA SRX14506050

Supplementary file Size Download File type/resource
GSM5961773_R24_quant.sf.txt.gz 3.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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