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Sample GSM2375317 Query DataSets for GSM2375317
Status Public on Nov 30, 2016
Title cKO DN NKT liver rep1
Sample type SRA
 
Source name liver DN invariant NKT
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: liver
developmental stage: mature invariant NKT cell
Extracted molecule total RNA
Extraction protocol Before FACS staining, DN thymocytes were highly purified by depletion of CD4+ and CD8+ and DP thymocytes with AutoMACS. Then, DN NKT cells were FACS sorted using BD FACS Aria, and RNA was prepared using RNeasy Micro Plus kit containing gDNA eliminator columns (Qiagen). RNA was analyzed for quantity and quality using Agilent Bioanalyzer 2100 or Agilent 2200 TapeStation equipment, and 10 ng of total RNA was used with SMARTer Ultra Low Input RNA Kit v3 for Illumina Sequencing (Clontech) for cDNA synthesis.
Illumina TruSeq RNA Sample Prep Kit v2 (Illumina) or ThruPLEX DNA-seq Kit (RUBICON GENOMICS) were used for the construction of sequencing libraries.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description NKT cells from YFP+ mouse
Data processing Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
Sequences were aligned to mm9 genome using tophat2 (version 2.8.0) with default parameters.
Aligned seqeunces were converted relative expression using cufflinks (version 2.1.1).
Genome_build: mm9
Supplementary_files_format_and_content: plain text containig FPKM (fragments per kilobase exon per million reads) values.
 
Submission date Nov 04, 2016
Last update date May 15, 2019
Contact name Takaho A. Endo
E-mail(s) takaho.endo@riken.jp
Organization name RIKEN
Department IMS
Lab Laboratory for Integrative Genomics
Street address 1-7-22 Suehiro, Tsurumi
City Yokohama
State/province Kanagawa
ZIP/Postal code 230-0045
Country Japan
 
Platform ID GPL18480
Series (1)
GSE89532 RNAseq analysis of thymic CD4-CD8- double-negative (DN) invariant NKT cells from CD4+CD8+ double-positive (DP)-specific Rag2-conditional knock-out mice
Relations
BioSample SAMN05981578
SRA SRX2327419

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

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