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| Status |
Public on Jun 01, 2020 |
| Title |
48h2 |
| Sample type |
SRA |
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| Source name |
intestine tissue
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| Organism |
Apostichopus japonicus |
| Characteristics |
treatment: heat stress
time point: 48h
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| Treatment protocol |
heat stress under 26ºC
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| Growth protocol |
sea cucumber (100-120g)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of each individua was extracted using Trizol RNA isolation reagent (Invitrogen) following the manufacturer’s instructions.
RNA molecules ranging from 18 to 30 nt were encriched by polyacrylamide gel electrophoresis (PAGE). Adapters were added repectively in 3’- and 5’ - end of RNAs.The ligation products were reverse-transcribed by PCR amplification. The PCR products in the size of 140~160 bp were encriched to generate the cDNA library. The library products were then sequenced via HiSeq.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
BGISEQ-500 |
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| Data processing |
Adapters sequences and low-quality reads were removed. Other RNAs, including rRNA, tRNA, snRNA, snoRNA, piRNA, repeats, exon and intron sequences, were removed.
The expression levels of miRNA were calculated by summing the read counts which were aligned with the temporary miRNA database with ≤ 2 mismatches.
Temporary miRNA database were constituted of miRNAs with the highest expression for each mature miRNA family. The potentially novel miRNAs were predicted via MIREAP.
Supplementary_files_format_and_content: Two "xlsx" files include the analysis about differential expression of miRNAs in Control, HS 6h and HS 48h group.Two "fa" files include the sequences of known and novle miRNAs by our sequencing.
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| Submission date |
May 30, 2018 |
| Last update date |
Jun 01, 2020 |
| Contact name |
Dongxue Xu |
| E-mail(s) |
dongxuexu1989@126.com
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| Organization name |
Qingdao Agricultural University
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| Street address |
Changcheng road No.700
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| City |
Qingdao |
| ZIP/Postal code |
266109 |
| Country |
China |
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| Platform ID |
GPL23583 |
| Series (1) |
| GSE115076 |
Understanding microRNAs regulation in heat shock response in the sea cucumber Apostichopus japonicus |
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| Relations |
| BioSample |
SAMN09280966 |
| SRA |
SRX4140090 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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