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Sample GSM2409484 Query DataSets for GSM2409484
Status Public on Feb 14, 2017
Title Infected (Wild Type) - 4dpi - Rep2 [W4C]
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 - Rep2
W4C
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 GSM2226911
BioSample SAMN06066720
SRA SRX2379906

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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