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Sample GSM3445023 Query DataSets for GSM3445023
Status Public on Oct 20, 2021
Title WT4
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Spleen
genotype: Wild type
age: > 18 months
Treatment protocol NA
Growth protocol NA
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from splenocytes of tumor developing plck-GAPDH mice and wt mice using the RNA extraction kit (Qiagen, Valencia, CA, USA) according to manufacturer’s instructions.
Truseq Stranded Total RNA
Libraries were generated from 500ng of total RNAs using Truseq Stranded Total RNA kit (Illumina). Libraries were then quantified with Qubit and pooled. 4nM of this pool were loaded on a High Output Flowcell and sequenced on a NextSeq500 platform (Illumina) with 2x75bp paired-end chemistry.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Mapping with STAR_2.4.0a versus mm10 folowing Encode RNA-seq options "--outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignMatesGapMax 1000000 --outReadsUnmapped Fastx --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMultimapNmax 20". Raw count table was generated with featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M -C" options.
Raw count table was generated with featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M -C" options.
RNAseq data were quantified using RSEM sofware 1.2.25 (Li and Dewey, 2011) with bowtie2-2.2.6 and m38 as reference genome.
Genome_build: mm10
 
Submission date Oct 24, 2018
Last update date Oct 20, 2021
Contact name Kevin Lebrigand
Organization name IPMC/CNRS
Lab Functional Genomics Platform of Nice-Sophia-Antipolis, France.
Street address 660 route des lucioles
City Valbonne - Sophia-Antipolis
ZIP/Postal code 06560
Country France
 
Platform ID GPL19057
Series (2)
GSE121747 Identification of a T cell lymphoma in plkcGAPDH transgénic mice (RNA-Seq)
GSE121748 Identification of a T cell lymphoma in plkcGAPDH transgenic mice
Relations
SRA SRX4932751
BioSample SAMN10319496

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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