|
| Status |
Public on May 21, 2019 |
| Title |
CG_3 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Cyprinus carpio |
| Characteristics |
group: control group
tissue: liver
developmental stage: 1-year-old
|
| Treatment protocol |
Sampled after fasting for two days, the fish were anesthetized with MS-222. Their livers were collected from three groups in each five fish and immediately snap-frozen in liquid nitrogen, stored at -80℃ until use.
|
| Growth protocol |
The experimental procedures used in this study were approved by the Institutional Animal Care and Use Committee of Sichuan Agricultural University. Ninety fish were randomly divided into three tanks (30 fish in each). For cool and heat stress, all fish were subjected to a stepped cooling regime of 1℃/h for a maximum of 7℃/day and warming by the same regime. The fish were cooled from 17℃ to 5℃ and acclimated at 5℃ was named low temperature group (LTG), the other fish were warmed from 17℃ to 30℃ and acclimated at 30℃ was named high temperature group (HTG), and control group (CG) was maintained at 17℃. The fish were sampled after acclimated 18 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was harvested using Trizol-LS reagent.
The integrity of total RNA was determined by theAgilent 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit with suitable RNA samples having an RNA integrity number > 6.5. Approximately, 15 μg of small RNA-enriched total RNA was prepared for high-throughput sequencing. For each library, small RNA ranging from 15 to 35 nt was purified by 15% Tris-bora-EDTA polyacrylamide gel electrophoresis, and 3´ and 5´ adaptors were ligated with unique small RNA fractions. The modified small RNA was then reverse-transcribed and amplified by reverse transcription-PCR. Finally, the enriched cDNA was sequenced on a Illumina HiSeq 2500 according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
microRNA derived from liver tissue of control (LTG) fish
|
| Data processing |
Initial sequence was subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences) and the output was called clean data. Filtered sequences then were mapped to pig reference genome with stringent criteria (0 mismatch in the first 18bp).
For each sample, counts were first normalized by the total count of mappable reads which is denoted as reads per million (RPM).
Genome_build: Genome database:Cyprinus carpio:common carp genome (assembly GCF_000951615.1); miRbase release 21
Supplementary_files_format_and_content: Identified miRNAs in each library with count reads and normalized data
|
| |
|
| Submission date |
May 21, 2018 |
| Last update date |
May 21, 2019 |
| Contact name |
JunLong Sun |
| E-mail(s) |
1988sunjunlong@sina.com
|
| Organization name |
Hainan University
|
| Street address |
No.58 Renmin Avenue, Haikou City, Hainan Province
|
| City |
Haikou |
| State/province |
Hainan |
| ZIP/Postal code |
570228 |
| Country |
China |
| |
|
| Platform ID |
GPL20956 |
| Series (1) |
| GSE114714 |
Analysis of miRNA-seq in the liver of common carp (Cyprinus carpio L.) in response to different environmental temperatures |
|
| Relations |
| BioSample |
SAMN09231972 |
| SRA |
SRX4107465 |
