|
| Status |
Public on Feb 14, 2017 |
| Title |
Infected (Wild Type) - 4dpi - Rep1 [W4A] |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c OlaHsd
age: 16-week-old
|
| Treatment protocol |
16-week-old mice were inoculated with rSARS-CoV wt or rSARS-CoV-ΔE in 50 μl of DMEM containing 2% fetal bovine serum (FBS, Biowhittaker). Mice were sacrificed at days 2 and 4 post infection and lung and serum samples were collected.
|
| Growth protocol |
Specific-pathogen-free 8 week-old BALB/c OlaHsd female mice were purchased from Harlan. Mice were maintained for 8 additional weeks in the animal care facility at the National Center of Biotechnology (CNB-CSIC, Madrid).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNAs were isolated (mirVana miRNA Isolation Kit, Ambion) from mouse lungs and analyzed using the Bioanalyzer 2100 expert_Eukaryote Total RNA to determine their integrity.
1 μg of the small RNA fraction was used for library construction (BGI Genomics, Hong-Kong).
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
Infected (Wild Type) - 4dpi - Rep1
W4A
|
| Data processing |
Filtering: Strand-specific, single-end reads longer than 18 nt provided by BGI sequencing company were quality-checked with FASTQCjects/fastqc/). No additional filters were necessary.
Read alignment: Short reads were aligned against SARS-CoV genome, with BWA (Li and Durbin, 2009) allowing up to 1 mismatch and no gaps (bwa aln -n 1 -k 1 -o 0). Only unique hits were considered for posterior steps. SAM alignment files generated by BWA were compressed, sorted and indexed using “view”, “sort” and “index” functions of Samtools package (Li et al., 2009).
Ten peaks were selected by visual inspection of coverage reads for SARS-CoV genome with SeqMonk browser (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk) attending the high-abundance sequences above an uniformily distributed background. In all cases, the consensus mature svRNA sequence was determined by the summit of the peak that was between 18 to 22 nt in length.
Genome_build: SARS-CoV MA15
Supplementary_files_format_and_content: tab-delimited text file including sequence, genome coordinates and raw read count values for ten peaks manually selected.
|
| |
|
| Submission date |
Nov 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Juan Carlos Oliveros |
| Organization name |
CNB, CSIC
|
| Street address |
Darwin 3
|
| City |
Cantoblanco |
| State/province |
Madrid |
| ZIP/Postal code |
28049 |
| Country |
Spain |
| |
|
| Platform ID |
GPL15103 |
| Series (1) |
| GSE90624 |
SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology |
|
| Relations |
| Reanalysis of |
GSM2226910 |
| BioSample |
SAMN06066721 |
| SRA |
SRX2379905 |
