|
| Status |
Public on Apr 16, 2019 |
| Title |
CP29 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Bos taurus |
| Characteristics |
breed: Polish-HF
age: 9-months
tissue: liver
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation from bovine liver tissues of three cattle breeds were harvested using Trizol reagent. Illumina TruSeq mRNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
young bull
fpkm calculated using cufflinks
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UMD cattle genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
fpkm calculated using cufflinks
Genome_build: UMD Bos Taurus plus y-chromosome
Supplementary_files_format_and_content: tab-delimited text files with option of excel file format, include RPKM values for each Sample ...
|
| |
|
| Submission date |
May 09, 2018 |
| Last update date |
Apr 16, 2019 |
| Contact name |
CHANDRA SHEKHAR PAREEK |
| E-mail(s) |
pareekcs@umk.pl
|
| Phone |
+48-605-161800
|
| Organization name |
Nicolaus Copernicus University
|
| Department |
Centre for Modern Interdisciplinary Technologies
|
| Lab |
Division of Functional Genomics in Biological and Biomedical Research
|
| Street address |
ul. Wilenska 4
|
| City |
Torun |
| State/province |
Kuj. Pom. |
| ZIP/Postal code |
87-100 |
| Country |
Poland |
| |
|
| Platform ID |
GPL24980 |
| Series (1) |
| GSE114233 |
Bovine liver gene expression database of Polish-HF, Polish-Red and Hereford cattle breeds. |
|
| Relations |
| BioSample |
SAMN05930870 |
| SRA |
SRX1590611 |
