|
| Status |
Public on Dec 31, 2018 |
| Title |
transported_miRNA seq |
| Sample type |
SRA |
| |
|
| Source name |
duodenum
|
| Organism |
Anas platyrhynchos |
| Characteristics |
stain: Jingjiang duck
tissue: duodenum mucosa damage caused by transportation stress
treated: placed in the transport vehicle and transported 8 hours
|
| Treatment protocol |
Control group ducks and transported group ducks were placed in the newborn poulty carry cases. The transported group were placed in the transport vehicle and transported 8 hours, and the transport took place on ordinary roads and bumpy roads at speeds between 40 and 70 km/hr.Ducks in control group has not been transported.
|
| Growth protocol |
The experiment was carried out using one-day-old female Jingjiang ducks. 20 ducks were divided into two groups and placed under natural conditions of light and temperature.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of each sample was extracted with Trizol (Invitrogen, USA). Using a Novex 15% TBE-Urea gel, 20–30-nt long RNA fragments were isolated and purified from 10 μg of total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
After removing the adaptors, low quality tags and contaminants reads, the clean reads were aligned with the duck genome
The expressions of miRNAs were normalized by Fragments per Kilobase of Transcript per Million Fragments Mapped (FPKM)
Genome_build: BGI_duck_1.0
Supplementary_files_format_and_content: The processed data columns are annotated as: CC.tpm CT.tpm is the "The expressions of miRNAs were normalized by Fragments per Kilobase of Transcript per Million Fragments Mapped (FPKM)". The processed data columns are annotated as: CC.readcount CT.readcount were unnormalized.
|
| |
|
| Submission date |
Oct 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Hao Zhang |
| E-mail(s) |
haozhang_0308@hotmail.com
|
| Phone |
15172520011
|
| Organization name |
Hubei Academy of Agricultural Sciences
|
| Department |
Institute of Animal Husbandry and Veterinary Sciences
|
| Street address |
Nanhu Road 7#
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430064 |
| Country |
China |
| |
|
| Platform ID |
GPL19739 |
| Series (1) |
| GSE104798 |
miRNA profile of duck duodenum mucosa damage caused by transportation stress |
|
| Relations |
| BioSample |
SAMN07768662 |
| SRA |
SRX3268646 |
