|
| Status |
Public on May 19, 2015 |
| Title |
KO_cTEC_3 |
| Sample type |
SRA |
| |
|
| Source name |
Thymic epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Aire KO
cell type: cTEC
strain: B6.129S2-Airetm1.1Doi/J
tissue: Thymus
age: 6-8 week old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Thymi were isolated and stromal cell enrichment was performed. Briefly, thymi were mecanically disrupted, digested and thymic stromal cells were sorted by multicolour flow cytometry.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA 1.8.2
Sequenced reads were trimmed for adaptor sequence and mapped to the reference genome using CASAVA 1.8.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.
|
| |
|
| Submission date |
Feb 04, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Charles St-Pierre |
| E-mail(s) |
charles.stpierre78@gmail.com
|
| Organization name |
Montreal University
|
| Department |
Institute for Research in Immunology and Cancer
|
| Lab |
Immunobiology - Claude Perreault
|
| Street address |
2950, Chemin de Polytechnique
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H3T 1J4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE65617 |
Differential features of Aire-induced and Aire-independent promiscuous gene expression in thymic epithelial cells |
|
| Relations |
| BioSample |
SAMN03329003 |
| SRA |
SRX864935 |
