|
| Status |
Public on Sep 16, 2013 |
| Title |
9599_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
F0 sperm
|
| Organism |
Sus scrofa |
| Characteristics |
gender: male
diet: standard diet supplemented with methylating micronutrients
cell type: sperm cell
|
| Treatment protocol |
F0 boars received either a standard diet or a standard diet supplemented with methylating micronutrients from one to ten months of age. The supplemented diet contained additional methionine, choline, betaine, vitamin B6, B12 and folate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol followed DNase treatment and chlorofom and penol extraction and RNA precipitation
Sperm RNA was directly used for library construction following illumina’s protocol TrueSeq RNA Sample Preparation v2 Guide
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
suppl_diet 3
|
| Data processing |
The quality of the sequence reads was assessed using fastQC version 0.9
Ribosomal RNA contaminations were removed by mapping the 100bp single end reads to a collection of ribosomal RNA sequences using bowtie2 with standard parameters
Genome_build: The reads were mapped to the Sus scrofa genome assembly Ssc10.2/Ssr3 (http://hgdownload.cse.ucsc.edu/goldenPath/susScr3/bigZips/susScr3.fa.gz) using TopHat2 with default parameters
Supplementary_files_format_and_content: fold change data
|
| |
|
| Submission date |
Jul 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin H Braunschweig |
| E-mail(s) |
martin.braunschweig@vetsuisse.unibe.ch
|
| Phone |
031 631 22 23
|
| Organization name |
University of Bern
|
| Department |
Vetsuisse Faculty
|
| Lab |
Institute of Genetics
|
| Street address |
Bremgartenstrasse 109A
|
| City |
Berne |
| State/province |
Berne |
| ZIP/Postal code |
3001 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL11429 |
| Series (2) |
| GSE48777 |
In search of epigenetic marks in testes and sperm cells of differentially fed boars [RNA-Seq] |
| GSE48778 |
In search of epigenetic marks in testes and sperm cells of differentially fed boars |
|
| Relations |
| SRA |
SRX320118 |
| BioSample |
SAMN02230672 |
