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Status |
Public on Feb 04, 2022 |
Title |
Infected (deltaE) - 2dpi - Rep3 [E2D RNA-seq] |
Sample type |
SRA |
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Source name |
Infected (deltaE)_2dpi_lung
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Organism |
Mus musculus |
Characteristics |
strain: BALB/c OlaHsd age: 16-week-old infected with: rSARS-CoV-ΔE time point: 2dpi tissue: lung
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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.
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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).
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Extracted molecule |
total RNA |
Extraction protocol |
To isolate long and small RNAs separately, one-half of the right lung was homogenized in 2 mL of Lysis/Binding Solution (mirVana miRNA Isolation Kit, Ambion) using a MACS homogenizer (Miltenyi Biotec), according to manufacturer’s protocols. Small and long RNAs were extracted separately from total RNA samples using mirVana miRNA Isolation protocol. .6 µg of the long RNA fraction were treated to eliminate ribosomal RNA (RiboZero rRNA Removal Kit, Epicentre) and libraries were constructed (NEBNext Ultra directional Library prep A, Illumina) and subjected to 100SE sequencing on a Hiseq 2000 sequencer (Illumina, Parque Científico de Madrid, PCM), resulting in 20 million reads per sample.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
E2D_CGTACG
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Data processing |
Raw 100nt strand-specific single-end reads were quality checked with FASTQC. As many samples presented undetermined nucleotides (“N”) and decreased quality after 76th position, all reads from all samples were truncated to the first 75 nucleotides. Truncated (75nt) reads were aligned against mouse genome sequence (GRCm38) with TopHat2 (Kim et al. 2013) allowing intron sizes up to 100.000 nt and using default settings for single-end alignments. Htseq-count function of HTSeq package (Anders et al., 2014) was used for assigning reads to each mouse gene and lncRNA. Genomic feature coordinates were obtained from mouse annotation version GRCm38.76 (ENSEMBL). To evaluate differential expression of features between SARS-CoV-∆E (2dpi) and WildType (2dpi) samples, DESeq2 (Love et al., 2014) was used. Default parameters were used except detection of outlier counts by Cook’s distance that was not applied (cooksCutoff=FALSE). Three biological replicates per sample were included in the analysis and p.values obtained were adjusted by FDR (Benjamini and Hochberg, 1995). Genome_build: GRCm38 Supplementary_files_format_and_content: tab-delimited text file include raw read count values for all samples
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Submission date |
Jul 21, 2021 |
Last update date |
Feb 04, 2022 |
Contact name |
Juan Carlos Oliveros |
Organization name |
CNB, CSIC
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Street address |
Darwin 3
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City |
Cantoblanco |
State/province |
Madrid |
ZIP/Postal code |
28049 |
Country |
Spain |
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Platform ID |
GPL13112 |
Series (1) |
GSE180563 |
Contribution of host miRNA-223-3p to SARS-CoV-induced lung inflammatory pathology |
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Relations |
BioSample |
SAMN20342123 |
SRA |
SRX11515189 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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