|
| Status |
Public on Sep 09, 2020 |
| Title |
3859: ctrl_8h_stim |
| Sample type |
SRA |
| |
|
| Source name |
Naive CD4+ T cells
|
| Organism |
Mus musculus |
| Characteristics |
genetic background: C57BL/6J
mouseid: 5
genotype/variation: Control
tissue: Naive CD4+ T cells
|
| Treatment protocol |
Naive T cells were stimulated with 1 ug/ml of anti-CD3 and anti-CD28 antibodies
|
| Growth protocol |
Naive CD4+ T cells were isolated directly, stimulation and control were cultured in IMDM medium supplemented with 10% FCS, 1% Pen/Strep, 1% L-glutamine, 5mM HEPES, 0.5 mM sodium pyruvate and 55µM β-mercaptoethanol
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spleen was manually homogenized and naive CD4+ T cells were FACS sorted as CD3+CD4+CD25-CD62L+CD44-
According to the manufacturer´s instructions in the Tru-Seq RNA library preparation kit v2, 10 ng of RNA was converted into cDNA libraries
75 bp single-end run was performed on a HiSeq2000
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
base calling and de-multipexing using CASAVA version 1.8
Alignment with HiSat2 version 2.1.0 and SAMtools version 1.4 using the default parameters
Quantification with Partek Genomics Suite V6.6
reads mapped to each transcript against the RefSeq mm10 annotation download on October 2018
Normalization using DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include DeSeq2 rlog counts for each Sample.
|
| |
|
| Submission date |
Jul 05, 2019 |
| Last update date |
Sep 09, 2020 |
| Contact name |
Joachim Schultze |
| E-mail(s) |
j.schultze@uni-bonn.de
|
| Organization name |
LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)
|
| Department |
Genomics and Immunoregulation
|
| Street address |
Carl-Troll-Strasse 31
|
| City |
Bonn |
| State/province |
NRW |
| ZIP/Postal code |
53115 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE133863 |
Creld1-deficient CD4+ T cells under homeostatic condition and CD3/CD28 stimulation |
| GSE153238 |
Creld1-deficient CD4+ T cells |
|
| Relations |
| BioSample |
SAMN12219568 |
| SRA |
SRX6408121 |
