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Sample GSM1283046 Query DataSets for GSM1283046
Status Public on Dec 31, 2015
Title NKT-3_5
Sample type SRA
 
Source name NKT stage-3
Organism Mus musculus
Characteristics cell type: thymocyte
strain: C57BL/6
age: 6-to-8 wk old
Growth protocol DN1eP thymocytes were cultured for 10 days on OP9/Dll-1 stromal monolayer in the presence of mouse IL-2 (5 ng/ml) and mouse IL-7 (5 ng/ml), both from R&D, in a complete RPMI1640 culture medium supplemented with 10% FCS.
Extracted molecule total RNA
Extraction protocol Thymocyted were highly purified using standard methods, including MACS sorting followed by FACS sorting, and RNA was prepared using RNeasy Micro Plus kit containing gDNA eliminator columns. RNA was analyzed for quantity and quality using Agilent Bioanalyzer 2100 equipment. and around 10-to-100 ng of total RNA was used with SMARTer Ultra Low Input RNA for Illumina Sequencing kit (Clontech) or Illumina TruSeq RNA Sample Prep Kit v2 for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1000
 
Description Surface Valpha14Jalpha18 TCR positive
Data processing Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
RNA-seq reads were aligned to mm9 genome using tophat2 (version 2.0.6) with default parameters.
Aligned reads were assigned to genes and counted using cufflinks version 2.1.1) with default parameters and annotation file of mouse Entrez genes.
Genome_build: mm9 (NCBI version 37.2)
Supplementary_files_format_and_content: FPKM (cufflinks output, tab-separated values)
 
Submission date Dec 09, 2013
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 GPL15103
Series (1)
GSE53150 RNAseq analysis of mature thymic NKT cells and immature thymic DN1eP cells
Relations
BioSample SAMN02439432
SRA SRX389419

Supplementary file Size Download File type/resource
GSM1283046_NKT-3_5.csv.gz 730.9 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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