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Status |
Public on Dec 30, 2021 |
Title |
Uninfected 2 - 20wpi |
Sample type |
SRA |
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Source name |
Whole blood
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Organism |
Bos taurus |
Characteristics |
cell type: Whole blood cell population strain: Holstein treatment: Uninfected at 20 weeks postinfection
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Treatment protocol |
Aerosol infection of calves was performed by nebulization of virulent M. bovis strain 10–7428
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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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
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Submission date |
Dec 23, 2021 |
Last update date |
Dec 30, 2021 |
Contact name |
Hazem Abdelaal |
E-mail(s) |
hfmahmoud@wisc.edu
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Phone |
6082635036
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Organization name |
University of Wisconsin-Madison
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Street address |
1656 Linden Dr.
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City |
Madison |
State/province |
WI |
ZIP/Postal code |
53706 |
Country |
USA |
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Platform ID |
GPL15749 |
Series (1) |
GSE192537 |
Transcriptional Profiling of Early and Late Phases of Bovine Tuberculosis |
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Relations |
BioSample |
SAMN24366021 |
SRA |
SRX13496439 |
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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