|
Status |
Public on Jun 10, 2014 |
Title |
Marmoset_24_infected_day6_lesion_2_run_3 |
Sample type |
SRA |
|
|
Source name |
Lung, animal 24, day 6, lesion 2
|
Organism |
Callithrix jacchus |
Characteristics |
tissue: lung animal number: 24 treatment: Middle East respiratory syndrome coronavirus (MERS-CoV) infection day of infection: 6 lesion number: 2 technical replicate: 3
|
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 MiSeqâ„¢. 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-24-6
|
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).
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|
|
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 |
SAMN02641863 |
SRA |
SRX470492 |