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Sample GSM3449417 Query DataSets for GSM3449417
Status Public on Jan 23, 2019
Title PLN DC of GF Rag KO mice injected with naïve CD4 T cells
Sample type SRA
 
Source name dendritic cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: peripheral lymph node (PLN)
Extracted molecule total RNA
Extraction protocol PLN or SPL DCs were purified with flow cytometory sorting and RNA was harvested with trizol. Illumina TruSeq RNA sample prep kit was used with 1ug of total RNA for the construction of sequencing libararies.
RNA libraries were prepared for sequencing using standard Illumina protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
 
Description JAEUYI_S2
Data processing Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to mouse reference transcriptome build mm10 (M10, GRCm38.p4) from GENCODE (http://www.gencodegenes.org/mouse_releases/10.html)
Fragments Per Kilobase Million (FPKM) were calculated by RSEM with default parameters.
Differentially expressed genes were identified by edgeR-3.16.5 [49] given absolute fold change > 2 and FDR < 10-3
Genome_build: mm10
Supplementary_files_format_and_content: differential gene expression comparsion with FPKM value
 
Submission date Oct 26, 2018
Last update date Jan 23, 2019
Contact name Jaeu Yi
E-mail(s) discount73@gmail.com
Organization name POSTECH
Street address Cheongamro77
City Pohang
ZIP/Postal code 37673
Country South Korea
 
Platform ID GPL16417
Series (1)
GSE121882 Unregulated APC activation by T cells breaks self-tolerance
Relations
BioSample SAMN10331478
SRA SRX4941343

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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