|
| Status |
Public on Dec 02, 2013 |
| Title |
Sample 4_P14 Dicer+/+ Cre-RV (Ctrl) |
| Sample type |
SRA |
| |
|
| Source name |
P14 Dicer+/+ Cre-RV (Ctrl)
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL6
genotype/variation: P14 Dicer+/+
cell type: In vitro generated CTLs
differentiation time: 6 days
|
| Growth protocol |
Stimulation of purified CD8+ T cells from control (samples 1,2,4,5) or Dicer knockout (samples 3,6) with antiCD3 plus anti-CD28, followed by culture in 100U/ml IL-2 for 6 days; Stimulation of P14 transgenic CD8+ T cells with gp33 (samples 9,11) or gp33 plus CpG (samples 10,12) followed by culture in 100U/ml IL-2 (samples 9,11) or IL-2 plus IL-12 (samples 10,12); Sorting of KLRG1+CD127- and KLRG1-CD127+ cells from spleens of mice 8 days after LCMV-Arm infection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mirVana miRNA isolation kit or Qiagen miRNeasy isolation kit
TruSeq small RNA (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 4; B4ST4_CAAAAG
|
| Data processing |
Cutadapt [http://code.google.com/p/cutadapt/] was used to remove adapter sequences.
Bowtie was used to map all the reads longer than 15 nucleotides to the mm9 genome without allowing mismatches. If a read had multiple mappable positions, then one was selected randomly.
MicroRNA annotations were extracted from the miRBase (mus musculus) database. The number of reads falling into each miRNA locus was quantified using BEDTools. To count a read as a miRNA read we required that it had the correct strand information and resided completely within the annotated miRNA region.
Read counts were normalized based on the total number of million mapped reads and the average miRNA length (0.022 kilobases) and expressed as RPKM values.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample
|
| |
|
| Submission date |
Oct 18, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Tarmo Äijö |
| Organization name |
Flatiron Institute
|
| Department |
Center for Computational Biology
|
| Street address |
162 5th Avenue
|
| City |
New York |
| ZIP/Postal code |
10010 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE51393 |
A microRNA-directed program of cytotoxic CD8+ T cell differentiation |
|
| Relations |
| BioSample |
SAMN02377785 |
| SRA |
SRX365184 |
