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Sample GSM5750809

Query DataSets for GSM5750809

Status

Public on Dec 30, 2021

Title

Infected 2 - 8wpi

Sample type

SRA

Source name

Whole blood

Organism

Bos taurus

Characteristics

cell type: Whole blood cell population
strain: Holstein
treatment: Infected at 8 weeks postinfection

Treatment protocol

Aerosol infection of calves was performed by nebulization of virulent M. bovis strain 10–7428

Extracted molecule

total RNA

Extraction protocol

RNA was extracted from whole blood samples using the RiboPure RNA purification kit (Ambion) following the manufacturer’s recommendation. TURBO DNA-Free DNase Treatment (Ambion) was used to eliminate residual genomic DNA. RNA quantity and quality were assessed using the RNA Pico Series Chip on the Bioanalyzer 2100 (Agilent). RNA integrity numbers (RINs) . 8 were obtained for all total RNA samples purified.
Libraries were prepared according to Illumina's instructions. RNA extracted from the whole blood of cows at 8 and 20 wpi, or at the same time for the uninfected control group (12 biological replicates per group), was subjected to RNA sequencing at the University of Wisconsin–Madison Biotechnology Center. A total of 1 mg of RNA was used as input for TruSeq RNA Sample Prep Rev.F (March 2014; Illumina). Single-end RNA sequencing was performed on the Illumina HiSeq 2000 sequencer according to manufacturer’s instructions

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Raw RNA-Seq reads were uploaded to CLC Genomics Workbench 8.5 (Qiagen, Redwood City, CA, USA) for processing
Trimmed reads were mapped to the reference genome sequence of Bos taurus (assembly ARS-UCD1.2), and read counts generated against the reference genome annotation tracks were compiled and tabulated
Normalization and differential gene expression analysis in R using the package DESeq2 version 1.16.1 (84). Differentially expressed (DE) transcripts were defined as transcripts with fold changes $62.0, and P value , 0.05 when compared to the naive control group.
DEGs analyses were conducted to search for overrepresented pathways, gene set enrichment, and signaling pathway impact
Network analysis was performed using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING)on the DE transcripts identified in this study
Supplementary_files_format_and_content: Excel file has all samples' genes normalized counts

Submission date

Dec 23, 2021

Last update date

Dec 30, 2021

Contact name

Hazem Abdelaal

E-mail(s)

hfmahmoud@wisc.edu

Phone

6082635036

Organization name

University of Wisconsin-Madison