|
| 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 |
| E-mail(s) |
akihiko_kubota1@hotmail.com
|
| 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 |
|
| Relations |
| BioSample |
SAMN09288608 |
| SRA |
SRX4147559 |
