|
| Status |
Public on Oct 28, 2016 |
| Title |
WT-4_Tconv (11466x12) |
| Sample type |
SRA |
| |
|
| Source name |
WT splenic GFP- CD3e+ CD8a- CD4+ CD25- T cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wildtype
strain: C57BL/6
time of isolation: 9 weeks post bone marrow transplant
tissue: spleen
cell type: T cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells using the Qiagen miRNeasy Micro Kit (Cat. #: 217084) according to the manufacturer's instructions.
Isolated RNA was utilized for RNA-seq library preparation using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold treatment to eliminate ribosomal RNAs.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: cDKO_Tcov_vs_WT_Tcov.fpkm.txt
|
| Data processing |
Reads were aligned to mm10 chromosome sequence + splice junction sequences using Novoalign (v2.08.03), allowing up to 50 alignments for each read. Splice junctions were created by running USeq (v8.8.8) MakeTranscriptome application using Ensembl transcript annotations.
The resulting alignment file was processed with the USeq (v8.8.8) application SamTranscriptomeParser, which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. SamTranscriptomeParser also converts splice junction alignment coordinates back to genomic space.
USeq's DefinedRegionDifferentialSeq application was used to calculate FPKMs
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files containing FPKMs
|
| |
|
| Submission date |
Oct 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Dion Pioli |
| E-mail(s) |
peter.pioli@usask.ca
|
| Phone |
1-639-994-8478
|
| Organization name |
University of Saskatchewan
|
| Department |
Biochemistry, Microbiology and Immunology
|
| Street address |
107 Wiggins Rd
|
| City |
Saskatoon |
| State/province |
SK |
| ZIP/Postal code |
S7N 5E5 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE74467 |
Snai2 and Snai3 transcriptionally regulate cellular fitness and functionality of T cell lineages through distinct gene programs |
|
| Relations |
| BioSample |
SAMN04225626 |
| SRA |
SRX1397122 |
