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Sample GSM5750803 Query DataSets for GSM5750803
Status Public on Dec 30, 2021
Title Uninfected 2 - 20wpi
Sample type SRA
 
Source name Whole blood
Organism Bos taurus
Characteristics cell type: Whole blood cell population
strain: Holstein
treatment: Uninfected at 20 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
Street address 1656 Linden Dr.
City Madison
State/province WI
ZIP/Postal code 53706
Country USA
 
Platform ID GPL15749
Series (1)
GSE192537 Transcriptional Profiling of Early and Late Phases of Bovine Tuberculosis
Relations
BioSample SAMN24366021
SRA SRX13496439

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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