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| Status |
Public on Aug 30, 2018 |
| Title |
C9223 |
| Sample type |
SRA |
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| Source name |
Mammary gland
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| Organism |
Bos taurus |
| Characteristics |
tissue: Mammary gland
breed: Holstein
treatment: ID: 9223 TRT: CL
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from mammary tissue using the RNeasy Plus Universal Mini Kit (Qiagen, Valencia, CA) and RNA concentration was determined using a NanoDrop instrument (ND-2000, ThermoFisher Scientific, Waltham, MA). RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).
RNA-Seq library was constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) following manufacturer’s recommendations. Libraries were sequenced on the Illumina HiSeq3000 platform at the University of Florida Biotechnology Center.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
The quality of the sequencing reads was evaluated using FastQC software.
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.
The number of reads that mapped to each annotated gene in the bovine GTF file 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 gene Ensembl ID and number of mapped reads.
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| Submission date |
Aug 29, 2018 |
| Last update date |
Aug 30, 2018 |
| Contact name |
Francisco Peñagaricano |
| E-mail(s) |
[email protected]
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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 |
GPL21659 |
| Series (1) |
| GSE119216 |
In utero heat stress alters the offspring epigenome |
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| Relations |
| BioSample |
SAMN09934706 |
| SRA |
SRX4623476 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3361082_C9223.counts.txt.gz |
102.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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