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| Status |
Public on Jul 26, 2024 |
| Title |
Whole blood, ID10_Day0 |
| Sample type |
SRA |
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| Source name |
Whole blood
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| Organism |
Bos taurus |
| Characteristics |
tissue: Whole blood
time point: Day0
treatment: INR
pen: 3
individual id: ID10
disease: No
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| Treatment protocol |
All samples were collected in Tempus blood RNA tubes (Applied Biosystem). Samples were stored per product recommendation.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from Tempus Blood Tubes with Tempus Spin RNA Isolation Kit per product instruction.
RNA libraries were prepared for sequencing using Illumina Stranded mRNA Prep kits, using standard Illumina protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
S005.10.Day0_S5
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| Data processing |
Illumina RTA v3 software was used for basecalling.
Read quality was assessed in FastQC v0.11.9
Read trimming was performed with Trimmomatic v0.39 with parameters for a 4-base pair sliding window and removing read segments below a minimum base quality score of 20, read length of less than 28 bases, leading and trailing basepairs below a quality score of 3, and removal of all Illumina adaptors.
Read mapping and indexing was performed with HISAT2 v2.1.1, using the bovine whole genome assembly ARS-UCD1.3; parameters -p 14 --dta -x GCF_002263795.2_ARS-UCD1.3
Read assembly and quantification was performed with StringTie v2.2.0 with parameters -p 14 -G GCF_002263795.2_ARS-UCD1.3_genomic.gff, followed by stringtie --merge -p 14 -G GCF_002263795.2_ARS-UCD1.3_genomic.gff -o mergefile.gtf, and stringtie -e -p 14 -G mergefile.gtf -o. A read count matrix was generated with prepDE3.py with parameters python prepDE3.py -l 150 -i mergelist.txt. Differential expression analysis was performed with edgeR v3.36.0, glmmSeq v0.2.0, and EBSeq-HMM v1.32.0.
Assembly: GCF_002263795.2
Supplementary files format and content: Comma-delimited text file of raw gene counts for each sample
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| Submission date |
Feb 15, 2023 |
| Last update date |
Jul 26, 2024 |
| Contact name |
Matthew Adam Scott |
| E-mail(s) |
matthewscott@tamu.edu
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| Organization name |
Texas A&M University
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| Department |
Large Animal Clinical Sciences
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| Street address |
3201 Russell Long Blvd
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| City |
Canyon |
| State/province |
TX |
| ZIP/Postal code |
79015 |
| Country |
USA |
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| Platform ID |
GPL26012 |
| Series (1) |
| GSE225397 |
Transcriptome analysis of high-risk cattle supplemented with inorganic or organic Co, Cu, Mn, and Zn |
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| Relations |
| BioSample |
SAMN33316431 |
| SRA |
SRX19384080 |
| 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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