|
| Status |
Public on Dec 23, 2010 |
| Title |
Degenerative |
| Sample type |
SRA |
| |
|
| Source name |
IVF degenerative embryos (d8)
|
| Organism |
Bos taurus |
| Characteristics |
tissue: IVF embryos
|
| Treatment protocol |
Morphological evaluation of bovine embryos
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from pools of 20 embryos using Ambion's RNaqueous Micro kit according to the manufacturer's instructions. After extraction, total RNA was linearly amplified using Ambion's MessageAmp II. 50ng of the amplified RNA (aRNA) was subjected to Illumina's library preparation protocol for RNA-Seq. For Degenerative: library insert size (excluding primer) = 120 and standard deviation = 20.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Bovine IVF degenerative embryos
|
| Data processing |
For RNA-Seq read counts, we first aligned reads to the genome using Tophat v1.0.13. We then extracted uniquely mapped reads and count the number of reads mapped to non-overlapping exons of Ensembl Genes (release 57) using BEDtools. For paired end reads, we counted fragments while for single end reads, we counted reads. The read counts were then quantile normalized using the 'limma' package in R.
|
| |
|
| Submission date |
Nov 02, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Wen Huang |
| E-mail(s) |
whuang24@wisc.edu
|
| Organization name |
University of Wisconsin - Madison
|
| Department |
Department of Dairy Science
|
| Lab |
Hasan Khatib
|
| Street address |
1675 Observatory Dr. Room 634
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL11153 |
| Series (1) |
| GSE25082 |
Comparison of the bovine embryonic transcriptomes using RNA-Seq |
|
| Relations |
| SRA |
SRX031056 |
| SRA |
SRX031058 |
| BioSample |
SAMN00120238 |
