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Sample GSM1921180 Query DataSets for GSM1921180
Status Public on Oct 28, 2016
Title cDKO-3_Tconv (11466x15)
Sample type SRA
 
Source name cDKO splenic GFP- CD3e+ CD8a- CD4+ CD25- T cells
Organism Mus musculus
Characteristics genotype: cDKO
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 SAMN04225629
SRA SRX1397125

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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