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Status |
Public on Nov 05, 2023 |
Title |
GRG_3h_2 |
Sample type |
SRA |
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Source name |
GRG_3h_liver
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Organism |
Trachinotus blochii |
Characteristics |
treatement: GRG_3h tissue: liver age: 3.5-month-old
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Treatment protocol |
After hypoxia challenge for 0 h and 12 h, the liver of three fish at each sampling time points were collected in the control group and hypoxic group, named normoxia_0h, normoxia_12h, hypoxia_0h, hypoxia_12h, respectively. Upon reoxygenation period, after different reoxygenation methods for 3h and 12h,the liver of three fish at each sampling time points were collected in the RRG group and GRG group,named RRG_3h, RRG_12h, GRG_3h, GRG_12h, respectively. First, the experimental fish was anesthetized with MS-222, the spine of the fish was severed and immediately dissected to collect gill tissues. All samples were collected in 2 mL cryotubes and rapidly frozen in liquid nitrogen and stored at -80 °C until total RNA was isolated.
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Growth protocol |
The amount of 500 fish were randomly transferred to three indoor tanks with a circulating water filtration system (each tank has a volume of 3000 L) for one week. During the holding period, the fish were fed once a day, the amount of feed is controlled at 2 % of the total weight of the 500 fish. What's more, the water qualities were monitored twice a day and maintained as follows: temperature (27.1-29.3 ℃), pH (8.0), and ammonia (0.6), dissolved oxygenation (6.59 - 7.05 mg/L).
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Extracted molecule |
polyA RNA |
Extraction protocol |
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. 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 2500 |
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Data processing |
The de novo assembly was performed on cleaned reads using Trinity (Grabherr et al., 2011). Before assembly, raw reads were trimmed by removing adaptor sequences and ambiguous nucleotides. Reads with quality scores less than 20 and length below 30 bp were all trimmed. The resulting high-quality sequences were used in subsequent assembly. Briefly, the raw reads were assembled into the unique sequences of transcripts in Inchworm via greedy K-mer extension (k-mer 25). After mapping of reads to Inchworm contig bundles, Chrysalis incorporated reads into de Bruijn graphs. Butterfly then processed the individual graphs in parallel, reporting full-length transcripts and paralogous genes. After assembly, the open reading frame (ORF) of each unisequence was predicted by using Trinity software. Unisequences were used for BLAST search and annotation against the NR, NT, STRING (http://string-db.org/) (Franceschini et al., 2013), COG (http://www.ncbi.nlm.nih.gov/COG/), KEGG (http://www.genome.jp/kegg/) databases using an E-value cut-off of 10-5 (Camacho et al., 2009). Functional annotation by gene ontology (GO, http://www.geneontology.org) terms was analysed by using BLAST2GO software (NCBI) (Conesa et al., 2005). Supplementary_files_format_and_content: Identified mRNAs in each library with count reads and normalized data
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Submission date |
Nov 05, 2021 |
Last update date |
Nov 05, 2023 |
Contact name |
tian jiang |
Organization name |
Hainan University
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Street address |
58 of Ren min Road
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City |
Haikou |
ZIP/Postal code |
570228 |
Country |
China |
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Platform ID |
GPL29522 |
Series (1) |
GSE188265 |
Effects of different reoxygenation methods after acute hypoxic stress on the metabolic remodeling of golden pompano (Trachinotus blochii) |
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Relations |
BioSample |
SAMN22929293 |
SRA |
SRX13004539 |
Supplementary file |
Size |
Download |
File type/resource |
GSM5673513_GRG_3h_2.txt.gz |
34.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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