|
Status |
Public on Oct 30, 2016 |
Title |
WT 3 M1lo |
Sample type |
SRA |
|
|
Source name |
Thymus T Cells
|
Organism |
Mus musculus |
Characteristics |
mhc class i phenotype: Low genotype: Wildtype mouse: Wildtype 3 cell type: CD69+ MHC I low
|
Extracted molecule |
total RNA |
Extraction protocol |
Sorted cells were preserved in RNAlater (ThermoFisher Scientific) and frozen at -80°C, then RNA was isolated with RNeasyPlus Mini kit (Qiagen) mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Indexed sample libraries were sequenced using the 75 cycle high output kit v2 chemistry for the Illumina NextSeq 500 sequencing instrument Reads were aligned to the mouse genome by Rsubread version 1.18.0 Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation Genome_build: mm10 (NCBI build 38.1) Supplementary_files_format_and_content: tab-delimited text files were written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene
|
|
|
Submission date |
Oct 30, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Gordon K Smyth |
E-mail(s) |
smyth@wehi.edu.au
|
Phone |
(+61 3) 9345 2326
|
Fax |
(+61 3) 9347 0852
|
URL |
http://www.wehi.edu.au
|
Organization name |
Walter and Eliza Hall Institute of Medical Research
|
Department |
Bioinformatics
|
Lab |
Smyth
|
Street address |
1G Royal Pde
|
City |
Parkville |
State/province |
Vic |
ZIP/Postal code |
3052 |
Country |
Australia |
|
|
Platform ID |
GPL19057 |
Series (1) |
GSE74552 |
Transcriptional profiling of post-positive selection thymocytes from HOIL- and SHARPIN-deficient mice |
|
Relations |
BioSample |
SAMN04227712 |
SRA |
SRX1404463 |