|
| Status |
Public on Aug 31, 2019 |
| Title |
2.WT CD4+ CD90.1+ T cells (replicate 2) |
| Sample type |
SRA |
| |
|
| Source name |
CD4+ CD90.1+ T cells from GvHD-induced mice on d4, wildtyp
|
| Organism |
Mus musculus |
| Characteristics |
disease model: Allogenic hematopoietic stem cell transplantation (allo-HSCT)
strain background: C57BL/6
genotype/variation: wild type
cell type: CD4+ CD90.1+ T cells
|
| Growth protocol |
Allogenic hematopoietic stem cell transplantation (allo-HSCT): BALB/c host mice (H-2d CD90.2+) were conditioned by myeloablative total body irradiation (TBI) at a dose of 8.0 Gy using a Faxitron CP-160 X-ray system and injected retroorbitally with sex- and age-matched 5x10^6 B6 BM cells (H-2b CD90.2+) plus 1.2x10^6 B6 T cells (H-2b CD90.1+) within 2 hours after irradiation. Mice were treated with antibiotic drinking water (Baytril, Bayer) after allo-HSCT to prevent unspecific infections. CD4+ CD90.1+ T cells were enriched from spleen single cell suspension by flow cytometry using Zombie Aqua™ Fixable Viability Kit, anti-CD90.1 (OX-7) and anti-CD4 (RM4-5) at day 4 of allo-HSCT.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells enriched by flow cytometry were directly collected in RNA extraction buffer
Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Pico chip on Agilent's bioanalyzer. Barcoded mRNA seq libraries were prepared from 10 ng total RNA using a NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual. All quality controls were done using Invitrogen’s Qubit HS assay and fragment size was determined on Agilent’s 2100 Bioanalyzer HS DNA assay.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
WT 2
|
| Data processing |
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v7.5.1 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome.
Genome_build: GRCm38
Supplementary_files_format_and_content: RPKM
|
| |
|
| Submission date |
Aug 31, 2018 |
| Last update date |
Sep 01, 2019 |
| Contact name |
Stefan Klein-Hessling |
| E-mail(s) |
stefan.klein-hessling@mail.uni-wuerzburg.de
|
| Phone |
+49 931 3181179
|
| Organization name |
University of Würzburg
|
| Department |
Institute of Pathology
|
| Lab |
Molecular Pathology
|
| Street address |
Josef-Schneider-Str. 2
|
| City |
Würzburg |
| ZIP/Postal code |
97072 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE119313 |
Lack of NFATc1 SUMOylation protects from inflammatory diseases |
|
| Relations |
| BioSample |
SAMN09940809 |
| SRA |
SRX4628614 |
