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Sample GSM3074018 Query DataSets for GSM3074018
Status Public on Mar 31, 2019
Title wild type DP thymocyte rep 1
Sample type SRA
Source name CD4+CD8+ thymocyte
Organism Mus musculus
Characteristics cell type: thymocyte
strain: C57Bl/6J
age: 4-8 weeks
cell markers: CD4+ and CD8+
Treatment protocol thymocyte and spleen cells were sorted based on CD4, CD8 and TCR beta expression pattern.
Extracted molecule total RNA
Extraction protocol total RNA was isolated using Trizol(ThermoFisher sientific) reagent
SureSelect Strand Specific RNA-Seq LibraryPreparation kit (Agilent Technologies) was used according to the manufacturer’s protocol.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Data processing Basecalls performed using CASAVA version 1.4
RNA-seq reads were alingned to the mm10 genome assembly using Hisat2 with default option
data were processed with Cufflinks ver2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: fpkm_tracking of each gene
Submission date Apr 02, 2018
Last update date Mar 31, 2019
Contact name kiyokazu kakugawa
Phone 81455037045
Organization name Riken
Department IMS
Lab Immune Crosstalk
Street address 1-7-22 Suehiro-cho
City Yokohama
State/province Kanagawa
ZIP/Postal code 2300045
Country Japan
Platform ID GPL18480
Series (1)
GSE112609 RNA-seq data from double positive thymocyte and CD4 or CD8 single positive spleen T cell
BioSample SAMN08833064
SRA SRX3873694

Supplementary file Size Download File type/resource
GSM3074018_S05250_genes.fpkm_tracking.gz 1.2 Mb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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