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Sample GSM3428893 Query DataSets for GSM3428893
Status Public on May 01, 2019
Title RNA_Th1_rep1
Sample type SRA
 
Source name CD4positiveCD44hiCD62LlowCXCR5negativeCXCR3positiveYFPpositive
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Spleen and draining LN
genotype: IFN-gamma-YFP reporter
Treatment protocol IFN-γ-YFP reporter mice were infected by ZIKV with anti-IFNα/β receptor blocking one day before. Spleens and dLNs were harvested 7 dpi
Extracted molecule total RNA
Extraction protocol Three populations from IFN-γ-YFP reporter mice were isolated by cell sorting (IFN-γ-Tfh: CD4+CD44hiCD62LlowCXCR5hiPD-1hiCXCR3-YFP- ,IFN-γ+Tfh: CD4+CD44hiCD62LlowCXCR5hiPD-1hiCXCR3+YFP+, Th1: CD4+CD44hiCD62LlowCXCR5-CXCR3+YFP+ ).
Total RNA were extracted using Trizol(Thermo), and sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were cleaned for trimming adaptor sequence, low-quality sequence (Q<20) from the 3' end, and filtering the reads with the length less than 20.
Cleaned reads were then mapped to mm10 whole genome using HISAT2 (version 2.0.5) with the default parameters for paired-end data.
Fragments Per Kilobase of transcript per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
HTSeq was used to count the reads for each gene. Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using TMM.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Counts and FPKM values for each Sample.
 
Submission date Oct 15, 2018
Last update date May 01, 2019
Contact name Jinyi Tang
E-mail(s) taotao11011011@163.com
Phone 17721241521
Organization name IPS
Lab Wang Haikun
Street address Yueyang road 320
City Shanghai
ZIP/Postal code 200031
Country China
 
Platform ID GPL21273
Series (1)
GSE121250 ZIKV infection induces robust Th1-like Tfh cell and long-term protective antibody responses in immunocompetent mice
Relations
BioSample SAMN10241743
SRA SRX4886154

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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