|
| Status |
Public on Sep 24, 2020 |
| Title |
MDM-0H-M3 |
| Sample type |
SRA |
| |
|
| Source name |
MDMs stimulated with M. intracellulare
|
| 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 |
SAMN16245621 |
| SRA |
SRX9177142 |
