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| Status |
Public on Aug 05, 2023 |
| Title |
Ts12L-3 |
| Sample type |
SRA |
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| Source name |
liver tissues
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| Organism |
Oncorhynchus mykiss |
| Characteristics |
tissue: liver tissues
treatment: acute hypoxia
phenotype: wild-type
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| Extracted molecule |
total RNA |
| Extraction protocol |
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Oncorhynchus mykiss Omyk_1.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Aug 01, 2023 |
| Last update date |
Aug 05, 2023 |
| Contact name |
Jinqiang Huang |
| E-mail(s) |
huangjq@gsau.edu.cn
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| Phone |
18893812894
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| Organization name |
Gansu Agricultural University
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| Street address |
Yintanlu stress
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| City |
Lanzhou |
| ZIP/Postal code |
730070 |
| Country |
China |
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| Platform ID |
GPL24430 |
| Series (1) |
| GSE239806 |
Combined application of whole transcriptome sequencing and ceRNA theory: lncRNA LOC110519952 participates in glucose transport under hypoxia stress in rainbow trout (Oncorhynchus mykiss) by regulating novel-m0023-5p/glut1a axis |
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| Relations |
| BioSample |
SAMN36792383 |
| SRA |
SRX21215030 |
| 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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