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Sample GSM4800003 Query DataSets for GSM4800003
Status Public on Sep 24, 2020
Title MDM-24H-C2
Sample type SRA
 
Source name Control MDMs
Organism Canis lupus familiaris
Characteristics breed: beagle
tissue: whole blood
cell type: monocyte-derived macrophages
age: 14month
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.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
canFam3
tab-delimited text files include read count values for each Sample
Genome_build: canFam3
Supplementary_files_format_and_content: abundance measurement
 
Submission date Sep 23, 2020
Last update date Sep 24, 2020
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)
GSE158425 Global gene networks of canine monocyte-derived macrophages infected with Mycobacterium intracellulare
Relations
BioSample SAMN16245615
SRA SRX9177148

Supplementary file Size Download File type/resource
GSM4800003_24H-C2.txt.gz 7.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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