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Sample GSM3168259 Query DataSets for GSM3168259
Status Public on Sep 27, 2020
Title Ly6Clo macrophages RNA-seq
Sample type SRA
Source name Ly6Clo macrophages
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: infarcted heart
cell type: Ly6Clo macrophages
day of collection: at 3 days after MI
Treatment protocol C57BL/6 J mice were subjected to ligation of the left anterior descending coronary artery.
Extracted molecule total RNA
Extraction protocol Total RNA of Ly6Chi and Ly6Clo macrophage were purified using a ReliaPrep RNA Cell Miniprep System (Promega, Madison, WI).
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Data processing Illumina CASAVA ver 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat.
Then, we got WAD ranking list from BAM files.
Data are normalized by using TCC (an acronym for Tag Count Comparison) of R package (PMID 23837715) , and then differentially expressed genes (DEGs) were analysed by weighted average difference method (WAD) (PMID 18578891).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include WAD ranking for each Sample. G1_rep1 denotes FPKM of Ly6Chi macrophages, G2_rep1 denotes FPKM of Ly6Clo macrophages.
Submission date May 31, 2018
Last update date Sep 27, 2020
Contact name Akihiko Kubota
Phone 81-43-226-2555
Organization name Graduate School of Medicine, Chiba University
Department Department of Cardiovascular Medicine
Street address 1-8-1 Inohana
City Chiba City
State/province Chiba
ZIP/Postal code 260-8670
Country Japan
Platform ID GPL18480
Series (1)
GSE115151 RNA-sequencing analysis of Ly6Chi macrophage and Ly6Clo macrophage harvested from infarcted heart
BioSample SAMN09288608
SRA SRX4147559

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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