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| Status |
Public on Jan 11, 2023 |
| Title |
9497_BRD [Re-analysis of GSM4943636] |
| Sample type |
SRA |
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| Source name |
Blood
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| Organism |
Bos taurus |
| Characteristics |
disease status: BRD
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from Tempus tubes using a Preserved Blood RNA Purification Kit (Norgen Biotek Corp.,Thorlord ON, ), and the Nanodrop 1000 (Thermo Scientifc, Willmingotn, DE, USA) and 2200 RNA Screentape Tapestation System (Agilent Technologies Inc, Cedar Creek, TX) were used respectively to quantify and measure the RNA integrity Number for each sample.
All samples had RIN values above 8,0 and were all used for library construction and RNA-seq was performed on the Novaseq platform running 50 samples per lane on 2 lanes.
cDNA libraries were prepared for sequencing for each individual animal from the high-quality RNA using the TruSeq RNA Library Preparation kit v2 (Illumina, San Diego, CA, United States) and the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs Ltd., Whitby, ON, Canada).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Re-analysis of GSM4943636
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| Data processing |
The raw reads were concatenated as there were two files for each read (run on seperate lanes), then trimmed so those samples with quality scores < 20 were filtered, and mapped to bovine genome (ARS-UCD1.2.98;https://bovinegenome.elsiklab.missouri.edu/downloads/ARS-UCD1.2 ) using the STAR software. The number of reads uniquely aligned to each gene was calculated using FeatureCounts.
Assembly: ARS-UCD1.2
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Nov 04, 2022 |
| Last update date |
Jan 11, 2023 |
| Contact name |
Graham Plastow |
| E-mail(s) |
plastow@ualberta.ca
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| Organization name |
University of Alberta
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| Department |
Agricultural, Food & Nutritional Science
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| Lab |
Livestock Gentec
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| Street address |
1400 College Plaza, 8215 - 112 Street
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| City |
Edmonton |
| State/province |
Alberta |
| ZIP/Postal code |
T6G 2C8 |
| Country |
Canada |
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| Platform ID |
GPL23295 |
| Series (1) |
| GSE217317 |
Applying multi-omics data to study the genetic background of bovine respiratory disease infection in feedlot crossbred cattle |
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| Relations |
| Reanalysis of |
GSM4943636 |
| BioSample |
SAMN31611234 |
| SRA |
SRX18174412 |
| 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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