|
| Status |
Public on Apr 29, 2020 |
| Title |
24h_PBMC_T2_3 |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral Blood Mononuclear Cells
|
| Organism |
Bos taurus |
| Characteristics |
cell type: in vivo driven
treatment: 24 h infection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNeasy Mini kit (Qiagen, Germany). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
TruSeq Stranded mRNA Sample Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Low quality reads were filtered according to the following criteria; reads contain more than 10% of skipped bases (marked as ‘N’s), reads contain more than 40% of bases whose quality scores are less than 20 and reads of which average quality scores of each read is less than 20.
Filtered reads were mapped to the reference genome related to the species using the aligner TopHat v2.0.12
Gene expression level was measured with Cufflinks v2.1.1
Differential expression analysis was performed by Cuffdiff
Genome_build: UMD3.1
Supplementary_files_format_and_content: Text files include FPKM values for each Sample
|
| |
|
| Submission date |
Apr 28, 2020 |
| Last update date |
Apr 29, 2020 |
| Contact name |
Hong-Tae Park |
| E-mail(s) |
twinstar23@snu.ac.kr
|
| Organization name |
Seoul National University
|
| Lab |
Infectious diseases
|
| Street address |
1, Gwanak-ro
|
| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL26012 |
| Series (1) |
| GSE149494 |
Analysis of global gene expressions in initial infection of Mycobacterium avium subsp. paratuberculosis using epithelial cells-peripheral blood mononuclear cells culture passage model. |
|
| Relations |
| BioSample |
SAMN14752970 |
| SRA |
SRX8188669 |
