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| Status |
Public on Jul 05, 2022 |
| Title |
liver, OO3 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Larimichthys crocea |
| Characteristics |
tissue: Liver
treatment: OO
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using TRIzol reagent (Invitrogen, United States USA) according to the manufacturer’s protocol. The quantity and quality of total RNA were determined by using the NanoDrop 2000 (Thermo Fisher Scientific, USA) and the Agilent 2100 Bioanaylzer (Agilent Technologies, USA, respectively. Ribosomal RNA of the 12 RNA samples was removed using the Ribo-Zero™ rRNA Removal Kit (Epicentre, USA).
RNA libraries were prepared for sequencing using BGISEQ500
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Data processing |
The sequencing data was filtered with SOAPnuke (v1.5.2) by Removing reads containing sequencing adapter
Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database built by BGI (Beijing Genomic Institute in ShenZhen), in which known and novel, coding and noncoding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12).
Genome_build: L_crocea_2.0
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample
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| Submission date |
Oct 15, 2021 |
| Last update date |
Jul 05, 2022 |
| Contact name |
xiufei cao |
| E-mail(s) |
caoxiufei@stu.ouc.edu.cn
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| Organization name |
ocean university of china
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| Street address |
Wenhai Road
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| City |
Qingdao |
| ZIP/Postal code |
266003 |
| Country |
China |
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| Platform ID |
GPL30869 |
| Series (1) |
| GSE186012 |
lncRNAs expression in the liver of large yellow croaker fed with fish oil, soybean oil, olive oil, and palm oil diets |
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| Relations |
| BioSample |
SAMN22330265 |
| SRA |
SRX12634106 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5628898_OO3.gene.FPKM.txt.gz |
504.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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