|
| Status |
Public on Jun 17, 2017 |
| Title |
Junbfl/flCD4cre_RNA_1 |
| Sample type |
SRA |
| |
|
| Source name |
Th17 cells
|
| Organism |
Mus musculus |
| Characteristics |
time point: 48 h
replicate: rep 1
strain: C57Bl/6 (N5 backcross)
|
| Growth protocol |
Naïve CD4+ T cells were sort purified and cultured in Th17 cell polarizing conditions in vitro for 48 hours. Sorted cells were seeded into 12 well plates coated with anti-hamster IgG secondary antibody in IMDM supplemented with 10% FBS, penicillin (10U/ml), streptomycin (10μg/ml, glutamine (2mM), gentamicin (50μg/ml), and β-mercaptoethanol (55μM). For TCR stimulation, cultures were provided anti-CD3ε (0.25μg/ml) and anti-CD28 (1μg/ml). Cultures were also supplemented with anti-IL-4 (2μg/ml) and anti-IFNγ (2μg/ml), in addition to IL-6 (20ng/ml) and TGFβ1 (0.3ng/ml).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified using the Trizol method.
Libraries were prepared from RNA using the Kapa stranded mRNA-Seq kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Junb_counts_normalized.tab
|
| Data processing |
Aligned to mouse genome using Tophat 2.0.13 with parameters “-a 10 -g 20 --no-novel-juncs -G”
Count reads in features from mm10 genome annotation using htseq-count 0.6.1 with options “-s no -m union”
Read counts were normalized and statistical analysis performed using edgeR ver 3.16, default settings
Genome_build: mm10
Supplementary_files_format_and_content: Matrices of raw and filtered / normalized read counts from edgeR in tab-delimited text format
|
| |
|
| Submission date |
May 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Maria Ciofani |
| E-mail(s) |
maria.ciofani@duke.edu
|
| Organization name |
Duke University School of Medicine
|
| Department |
Integrative Immunobiology
|
| Street address |
207 Research Drive, 128 Jones Building
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE98413 |
Role of JunB in Th17 cell effector stability [RNA-seq] |
| GSE98414 |
Role of JunB in Th17 cell effector stability |
|
| Relations |
| BioSample |
SAMN06857859 |
| SRA |
SRX2773932 |
