|
| Status |
Public on Oct 06, 2023 |
| Title |
ControlM_IL21 |
| Sample type |
SRA |
| |
|
| Source name |
IL21 stimulated control CD4+ T-cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Peripheral blood
age: 30 years
genotype: Healthy donor
stimulation: IL21
Sex: female
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 IL21 stimulated control CD4+ T-cells
R05
|
| 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 |
SAMN26796890 |
| SRA |
SRX14506037 |
