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Sample GSM1922772 Query DataSets for GSM1922772
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

Supplementary file Size Download File type/resource
GSM1922772_WT3_M1lo.txt.gz 170.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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