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Sample GSM2226908 Query DataSets for GSM2226908
Status Public on Feb 04, 2022
Title Infected (Wild Type) - 2dpi - Rep2
Sample type SRA
 
Source name Infected (Wild Type)_2dpi_lung
Organism Mus musculus
Characteristics strain: BALB/c OlaHsd
age: 16-week-old
gender: female
infected with: rSARS-CoV wild type
time point: 2dpi
tissue: lung
molecule subtype: small RNAs
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 isolated (mirVana miRNA Isolation Kit, Ambion) from mouse lungs were 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 W2C
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 mouse genome sequence (GRCm38) or 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).
Small RNA loci definition: A unified list of candidate regions (small RNA loci) was created by collapsing coverage data of all 16 samples on a single combined coverage track where, for each nucleotide, the maximum individual coverage was recorded. In this track, continuous genomic regions with a combined coverage of 2 or more nucleotides and with a summit of at least 10 nt were considered. By this way, a set of 5208 genomic features was defined with an average size of 36 nt. Features overlapping with known mmu-miRNAs from miRBase v.20 (Kozomara and Griffiths-Jones, 2014) were annotated. By this way, 593 out of 2035 (29%) of all miRBase v.20 mmu-miRNAs were detected.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include raw read count values for all samples
 
Submission date Jul 06, 2016
Last update date Feb 04, 2022
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)
GSE84081 Contribution of host an viral small non-coding RNAs to SARS-CoV lung pathology
Relations
Reanalyzed by GSM2409481
BioSample SAMN05362778
SRA SRX1899218

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

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