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Sample GSM5114142

Query DataSets for GSM5114142

Status

Public on Oct 19, 2021

Title

Lung_2

Sample type

SRA

Source name

unfractionated lung tissue

Organism

Mus musculus

Characteristics

tissue: lung
strain: BALB/cJ
treatment: OVA/OM-85
Sex: Male
bal eosinophils (percent): 0.5
ahr slope (z-score): -0.879181504134179

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

AD02

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