|
| Status |
Public on Jun 30, 2016 |
| Title |
WT 1 |
| Sample type |
SRA |
| |
|
| Source name |
H2-Db+GP33-41+ CD8+ T cell
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen
cell population: CD8+ T cell
lcmv cl 13 infection: 9 days post-infection
genotype/variation: Wildtype
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sorted WT or PSGL-1 KO CD8+ T cells were washed, pelleted, and frozen in RLT +BME Buffer (Quiagen RNeasy Micro Kit Cat. no. 74004). Total RNA extraction was completed using Quiagen Kit following manufactuer's instructions.
1ug of Total subjected to Ribo depletion to remove rRNA and then Multiplexed library was constructed using Illumina's Truseq Stranded Total RNA LT Kit Cat # RS-122-2201
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Base-calling software is Real-Time Analysis (RTA) version 1.18.64 (http://support.illumina.com/sequencing/sequencing_software/real-time_analysis_rta.html)
To remove the least reliable data from the analysis results, which is often derived from overlapping clusters, raw data are filtered to remove any reads that do not meet the overall quality as measured by the Illumina chastity filter. The chastity of a base call is calculated as the ratio of the brightest intensity divided by the sum of the brightest and second brightest intensities (chastity = brightest intensity/(brightest intensity + second brightest intensity)).
Clusters passing filter are represented by PF in analysis reports. Clusters pass filter if no more than one base call in the first 25 cycles has a chastity of < 0.6.
|
| |
|
| Submission date |
Apr 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Linda M Bradley |
| E-mail(s) |
lbradley@sbmri.org
|
| Phone |
858-646-3100
|
| Organization name |
Sanford Burnham Prebys Discovery Institute
|
| Department |
Inflammatory Diseases
|
| Lab |
Linda Bradley
|
| Street address |
10901 N. Torrey Pines Rd.
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE80113 |
Transcriptome analysis of virus-specific H2-Db-GP33-41+CD8+ T cells from WT or PSGL-1 KO mouse spleens at day 9 post LCMV Cl 13 infection |
|
| Relations |
| BioSample |
SAMN04632008 |
| SRA |
SRX1689018 |
