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| Status |
Public on May 01, 2024 |
| Title |
T-cells of healthy donors, control, 72h stimulation, donor 3 [Ctrl.K379] |
| Sample type |
SRA |
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| Source name |
peripheral blood
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| Organism |
Homo sapiens |
| Characteristics |
disease state: healthy donor
tissue: peripheral blood
cell type: primary T-cells
treatment: untreated
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| Treatment protocol |
T-cells were incubated for 72 h with activating anti-CD2/CD3/CD28 microbeads in a 1:2 bead-to-cell ratio (Miltenyi Biotec). 10 µM H2O2 (Sigma-Aldrich, St. Louis, MO, USA) was added twice per day.
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| Growth protocol |
purified human T-cells were cultured in RPMI 1640 (Thermo Fischer, Waltham, MA, USA) supplemented with GlutaMAX, P/S and 10% FCS
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the innuPREP DNA/RNA Mini Kit (Analytik Jena AG, Jena, Germany); on column DNAse digestion was used to remove genomic DNA contamination (RNAse-Free DNase Set, Qiagen, Venlo, Netherlands). RNA was diluted in RNase free H2O to a maximum concentration of 200 ng/μl.
RNAseq was performed by Eurofins/GATC Biotech (INVIEW NGS transcriptome explore). Library preparation: Strand specific cDNA library; Purification of poly-A containing mRNA molecules, mRNA fragmentation, random primed cDNA synthesis (strand specific), adapter ligation and adapter specific PCR amplification.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
read length: 2 x 150 bp
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| Data processing |
Adapters were clipped by trim_galore
Sequence reads were mapped by STAR aligner
Counting with featureCounts
Analysed using edgeR, normallized with TMM method
Supplementary files format and content: GRCh38
Supplementary files format and content: Tab-delimited normalized cpm
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| Submission date |
May 25, 2022 |
| Last update date |
May 01, 2024 |
| Contact name |
Chunguang Liang |
| E-mail(s) |
liang@biozentrum.uni-wuerzburg.de
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| Phone |
09313184561
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| Organization name |
Biozentrum
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| Department |
Bioinformatics
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| Lab |
Dr. Chunguang Liang
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| Street address |
Bioinformatik, Biozentrum, Uni Würzburg, Am Hubland
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| City |
Würzburg 97074 |
| State/province |
Bayern |
| ZIP/Postal code |
97074 |
| Country |
Germany |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE204781 |
Accumulating Oxidative DNA Damage in Reconstituting T-cells is Associated with Disease Relapse and Inferior Survival Following Allo-SCT [RNAseq in vitro] |
| GSE204783 |
Accumulating Oxidative DNA Damage in Reconstituting T-cells is Associated with Disease Relapse and Inferior Survival Following Allo-SCT |
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| Relations |
| BioSample |
SAMN28657037 |
| SRA |
SRX15450096 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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