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Sample GSM3428890

Query DataSets for GSM3428890

Status

Public on May 01, 2019

Title

RNA_Tfh_rep2

Sample type

SRA

Source name

CD4positiveCD44hiCD62LlowCXCR5hiPD1hiCXCR3negativeYFPnegative

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