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Sample GSM3905787 Query DataSets for GSM3905787
Status Public on Jun 27, 2019
Title PBMCs, 12HM1
Sample type SRA
 
Source name canine peripheral blood mononuclear cells
Organism Canis lupus familiaris
Characteristics tissue: whole blood
cell type: PBMC
age: 10 months old
infection: M. avium hominissuis strain 104
time: 12h
Extracted molecule total RNA
Extraction protocol total RNA was extracted from the cells using the RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instruction.
the construction of library was performed using QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) according to the manufacturer's instructions. In brief, each 500ng total RNA were prepared and an oligo dT primer containing an Illumina compatible sequence at its 5 end was hybridized to the RNA and reverse transcri ption was performed. After degradation of the RNA template, second strand synthesis was initiated by a random primer containing an Illumina compatible linker sequence at its 5 end. T he double stranded library was purified by using magnetic beads to remove all reaction components. The library was amplified to add the complete adapter sequences required for cluster generation. The finished library is purified from PCR components. High throughput sequencing was performed as single end 75 sequencing using Next Seq 500 (Illumina, Inc., USA).
QuantSeq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing QuantSeq 3' mRNA Seq reads were aligned using Bowtie2 (Langmead and Salzberg, 2012).
Bowtie2 indices were either generated from genome assembly sequence or the representative transcript sequences for aligning to the genome and transcriptome.
The alignment file was used for assembling transcripts, estimating their abundances and detecting differential expression of genes.
Differentially expressed gene were determined based on counts from unique and multiple alignments using coverage in Bedtools (Quinlan AR, 2010).
The RC (Read Count) data were processed based on quantile normalization method using EdgeR within R (R development Core Team, 2016) using Bioconductor (Gentleman et al., 2004).
Genome_build: canFam3
Supplementary_files_format_and_content: abundance measurement
 
Submission date Jun 26, 2019
Last update date Jun 30, 2019
Contact name Suji Kim
E-mail(s) sujiksj43@gmail.com
Organization name Seoul National University
Department Veterinary Medicine
Lab Infectious Disease
Street address 1, Gwanak-ro
City Seoul
State/province Gwanak-gu
ZIP/Postal code ASI/KR/KS013
Country South Korea
 
Platform ID GPL21400
Series (1)
GSE133326 Global gene networks in canine peripheral blood mononuclear cells infected with Mycobacterium avium subsp.hominissuis
Relations
BioSample SAMN12139345
SRA SRX6367512

Supplementary file Size Download File type/resource
GSM3905787_12h-12M1.txt.gz 152.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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