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Sample GSM4095387 Query DataSets for GSM4095387
Status Public on Sep 26, 2019
Title Sample 25_TH2
Sample type SRA
 
Source name TH2
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: OTII Tg IL-4BacTg x OTII Tg
age: 8 weeks
tissue: spleen
cell type: CD4+hCD2+
Extracted molecule total RNA
Extraction protocol Spleen were removed, stained TH cells were sorted using flow cytometer, and RNA was harvested using Trizol reagent. NEB Next Ultra RNA Library Prep Kit (Cat#E7530) for Sample1-8 or Lexogen 3'mRNA-seq library prep kit (Cat#015) for Sample9-30 was used with 10 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard NEB Ultra protocols or Lexogen 3'QuantSeq protocols
Sample1-Sample8, RNA-Seq; Sample9-Sample30, 3'QuantSeq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description S16155
Data processing Illumina Casava1.7 software used for basecalling.
Sample1-8; Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole mouse genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Sample9-30; Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole mouse genome using STAR 2.7.0c (command --runThreadN 60 --outSAMtype BAM SortedByCoordinate) Genome: mm10 GRCm38.p6 ENSEMBL GTF: GRCm38.97 ENSEMBL
Sample1-8; featurecounts v1.6.0 (command: -M -O -t exon -g gene_id -a) GTF: mm9 ENSEMBL release 67
Sample9-30; featurecounts v1.6.0 (command: -M -O -t exon -g gene_id -a) GTF: GRCm38.97 ENSEMBL
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for genes
 
Submission date Sep 25, 2019
Last update date Sep 26, 2019
Contact name Kosuke Miyauchi
E-mail(s) kosuke.miyauchi@riken.jp
Organization name RIKEN Center for Integrative Medical Sciences
Street address 1-7-22 Suehiro-sho
City Yokohama
State/province Kanagawa
ZIP/Postal code 230-0045
Country Japan
 
Platform ID GPL18480
Series (1)
GSE137970 Next Generation Sequencing Facilitates Quantitative Analysis of TFH2 cell Transcriptomes
Relations
BioSample SAMN12838965
SRA SRX6902635

Supplementary file Size Download File type/resource
GSM4095387_S16155.txt.gz 240.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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