|
| Status |
Public on Jun 10, 2014 |
| Title |
Marmoset_23_infected_day4_lesion_2_run_2 |
| Sample type |
SRA |
| |
|
| Source name |
Lung, animal 23, day 4, lesion 2
|
| Organism |
Callithrix jacchus |
| Characteristics |
tissue: lung
animal number: 23
treatment: Middle East respiratory syndrome coronavirus (MERS-CoV) infection
day of infection: 4
lesion number: 2
technical replicate: 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We started with 250ul Trizol homogenate from lung and used the Qiagen miRNA kit to extract the RNA.
For Total RNA-seq analysis, approximately 2.5 ug micrograms of total RNA from each sample was submitted. In brief, ribosomal RNAs (rRNAs) were depleted using the RiboZero Human/Mouse/Rat Isolation Kit . The 50 nt single-end sequencing was done using an Illumina MiSeq™.
Libraries were TruSeq Stranded Total RNA and clustering was Illumina version 2 MiSeq reagents.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
CoV-23-4
|
| Data processing |
Reads were aligned to the Marmoset reference genome using the gapped aligner software STAR and Ht-seq (Callithrix_jacchus.C_jacchus3.2.1.74), MERS genome (GenBank accession no. K02013).
Genome_build: Callithrix jacchus-3.2, MERS-virus (GenBank JX869059)
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values for each animal using Htseq and the GTF provided from ENSEMBL (Callithrix_jacchus.C_jacchus3.2.1.74).
|
| |
|
| Submission date |
Feb 13, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Katze |
| E-mail(s) |
data@viromics.washington.edu
|
| Organization name |
University of Washington
|
| Department |
Microbiology
|
| Lab |
Michael G. Katze, Ph.D
|
| Street address |
Rosen Building 960 Republican St.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-4325 |
| Country |
USA |
| |
|
| Platform ID |
GPL18020 |
| Series (1) |
| GSE55023 |
Transcriptional responses of Middle East respiratory syndrome coronavirus (MERS-CoV) in marmosets |
|
| Relations |
| BioSample |
SAMN02641894 |
| SRA |
SRX470483 |
