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Sample GSM2226902

Query DataSets for GSM2226902

Status

Public on Feb 04, 2022

Title

Infected (deltaE) - 4dpi - Rep3

Sample type

SRA

Source name

Infected (deltaE)_4dpi_lung

Organism

Mus musculus

Characteristics

strain: BALB/c OlaHsd
age: 16-week-old
gender: female
infected with: rSARS-CoV-ΔE
time point: 4dpi
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

E4E

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