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Sample GSM5673513 Query DataSets for GSM5673513
Status Public on Nov 05, 2023
Title GRG_3h_2
Sample type SRA
 
Source name GRG_3h_liver
Organism Trachinotus blochii
Characteristics treatement: GRG_3h
tissue: liver
age: 3.5-month-old
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.
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).
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
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
 
Submission date Nov 05, 2021
Last update date Nov 05, 2023
Contact name tian jiang
Organization name Hainan University
Street address 58 of Ren min Road
City Haikou
ZIP/Postal code 570228
Country China
 
Platform ID GPL29522
Series (1)
GSE188265 Effects of different reoxygenation methods after acute hypoxic stress on the metabolic remodeling of golden pompano (Trachinotus blochii)
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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