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Sample GSM2471370 Query DataSets for GSM2471370
Status Public on Jan 30, 2023
Title AA_CD8_Tofa_300nM_D3_KT_19
Sample type SRA
 
Source name peripheral blood CD8+ T-cells, Tofacitinib
Organism Homo sapiens
Characteristics disease state: healthy
cell type: CD8+ T-cells
treatment: Tofacitinib
concentration: 300nM
timepoint: 40hrs
donor: D3
Treatment protocol CD8+ T-cells were stimulated in vitro with plate bound anti-CD3 (OKT3) in complete media in the presence or absence of different JAK inhibitors; tofacitinib, ruxolitinib and a selective JAK1 inhibitor at 300 nM. Soluble anti-CD28 were added to the CD8+ cultures to facilitate co-stimulation. After 40h, supernatants were harvested for mediator analysis and the cells were washed and resuspended in RLT buffer (Qiagen) for RNA isolation.
Growth protocol Human Peripheral Blood Mononuclear Cells (PBMCs) were isolated by Sepmate technique (Stemcell Technologies) from heparinized venous blood from healthy volunteers. Primary human CD8+ T-cells were further isolated using a negative selection kit according to protocol (Miltenyi Biotech).
Extracted molecule total RNA
Extraction protocol RNeasy Mini kit with on-column DNA digestion (QIAGEN, Hilden, Germany) and eluted in 50 ul RNase-free water.
RNA was diluted to 5ng/ul and used as input to create RNA libraries using TruSeq Stranded mRNA kit (Illumina, CA, USA) following standard instructions. Libraries were validated on the BioAnalyzer (Agilent, CA, USA) using DNA1000 chip and the concentration was determined using Quant-iT dsDNA High Sensitivity assay kit on the Qubit fluorometer (Thermo Fisher, MA, USA). Sample libraries were pooled in equimolar concentrations and diluted and denatured according to Illumina guidelines. The pool was then sequenced using a High Output 2 x 76 bp kit on an Illumina NextSeq500.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description AA_CD8_Tofa_300nM_D3_KT_19_S11
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt
Data processing Base calling was done by bcl2fastq from Illumina.
Reads were mapped with HiSat2 (2.0.4).
Counts were generated with featurecounts (1.4.4).
TPMs were generated using Sailfish (0.10.1).
All processing was wrapped together with bcbio 0.9.9.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: combined.counts.txt: Tab-delimited text file includes counts.
Supplementary_files_format_and_content: combined.gene.sf.tpm.txt: Tab-delimited text file includes TPMs.
 
Submission date Jan 27, 2017
Last update date Jan 30, 2023
Contact name Elisabeth Israelsson
E-mail(s) elisabeth.israelsson@astrazeneca.com
Organization name AstraZeneca, IMED RIA
Department Translational Biology
Street address Pepparedsleden 1
City Molndal
ZIP/Postal code SE-431 83
Country Sweden
 
Platform ID GPL18573
Series (2)
GSE94235 Selective Janus kinase 1 inhibition resolves inflammation and restores hair growth offering a viable treatment option for alopecia areata
GSE94237 JAK inhibition in human CD8+ T-cells and C3H/HeJ Mice with Alopecia Areata In Vivo
Relations
BioSample SAMN06277343
SRA SRX2524196

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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