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| Status |
Public on Jan 08, 2018 |
| Title |
8647.03 |
| Sample type |
SRA |
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| Source name |
Mammary gland
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| Organism |
Bos taurus |
| Characteristics |
tissue: Mammary gland
breed: Holstein
subject id: 8647
treatment: CL
time: Day 3
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA). RNA concentration was determined on Qubit® 2.0 Fluorometer (ThermoFisher, Invitrogen, Grand Island, NY), and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).
Libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, USA). Sequencing libraries were created from 500 ng samples and sequenced with Illumina’s NextSeq 500 at the University of Florida Biotechnology Center.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
The quality of the sequencing reads was evaluated using FastQC software, and if necessary, sequencing reads were trimmed using the software Trim Galore (version: 0.4.1)
Reads were mapped to the reference genome (bosTau7) using the software package Tophat (version: 2.0.13).
Mapping sequencing reads: a maximum of 2 mismatches were allowed and reads that mapped equally well to more than 40 genomic locations were discarded.
Cufflinks (v2.2.1) was used to reconstruct transcript models from alignments.
The tool cuffmerge (Cufflinks v2.2.1) was used for merging together each of the assemblies with the reference mouse annotation file in order to combine novel isoforms with known isoforms.
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty).
Genome_build: Cow genome assembly: UMD3.1
Supplementary_files_format_and_content: Tab-delimited text files including locus, number of mapped reads, and gene name
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| Submission date |
Jan 07, 2018 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Francisco Peñagaricano |
| E-mail(s) |
fpenagarican@wisc.edu
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| Organization name |
University of Wisconsin-Madison
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| Department |
Animal and Dairy Sciences
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| Street address |
1675 Observatory Drive
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| City |
Madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53706 |
| Country |
USA |
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| Platform ID |
GPL23055 |
| Series (1) |
| GSE108840 |
Deciphering the mammary gland transcriptome during the dry period in dairy cows under heat stress |
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| Relations |
| BioSample |
SAMN08323653 |
| SRA |
SRX3539597 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2914223_8647.03.counts.txt.gz |
189.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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