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Sample GSM5114143 Query DataSets for GSM5114143
Status Public on Oct 19, 2021
Title Lung_3
Sample type SRA
 
Source name unfractionated lung tissue
Organism Mus musculus
Characteristics tissue: lung
strain: BALB/cJ
treatment: PBS
Sex: Male
bal eosinophils (percent): 0
ahr slope (z-score): -1.07375668836124
Treatment protocol Balb/c mice (7-8 weeks old) were sensitized intra-peritoneally (i.p.) with OVA (chicken egg white albumin, Sigma: 20 ug) + Alum (Imject Alum, Thermo Fisher: 50 ul) at day 0 and 14 and challenged i.n. with OVA (50 ug) 6 at day 28 and 38. OM-85 (1 mg in 0.9% saline/treatment x 14 treatments) was administered i.n, 25 ul/nostril, under light anesthesia (1-5% isoflurane) every 2-3 days from day 0. Control mice received PBS at the time of sensitization, challenge and treatment. Unfractionated lung tissue was collected at day 39 and processed for RNA-sequencing.
Extracted molecule polyA RNA
Extraction protocol total RNA was isolated using RNeasy mini kits (Qiagen) and mRNA capture (polyA enrichment) was achieved using oligo(dT)25 Dynabeads (ThermoFisher)
cDNA libraries were constructed using KAPA Biosystems kits (Roche)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description AD03
Data processing Adapter sequences were trimmed from RNA-seq reads (fastq files) and only reads >25bp long were included in the analysis
Reads were mapped to the BALB/cJ genome (version mm10) using STAR and genomic coordinates were shifted to the standard mm10 genome using MARGE
HOMER was used to select uniquely aligning reads and to generate gene counts. A maximum of 3 clones/read was included to minimize bias due to PCR amplification.
Expression data were estimated for 24,538 genes and were filtered to include only genes with at least one read in 20% of the samples, which retained a total of 19,613 genes.
RUVSeq was used to estimate latent factors of unwanted variation (3 RUVs) that were included as covariates in differential expression analysis.
Differential expression analysis was performed using DESeq2 and differentially expressed genes were defined as having an FDR-adjusted P-value <0.05 and a |log2 fold change| >0.5.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text file including normalized counts (rlog transformation) for each sample
 
Submission date Feb 27, 2021
Last update date Oct 19, 2021
Contact name Donata Vercelli
Organization name University of Arizona
Street address 1657 E. Helen St.
City Tucson
State/province Arizona
ZIP/Postal code 85721
Country USA
 
Platform ID GPL21103
Series (1)
GSE167867 Intranasal administration of OM-85, a bacterial lysate, alters lung transcriptional profiles and protects against experimental asthma
Relations
BioSample SAMN18083163
SRA SRX10184378

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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