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Sample GSM8526825

Query DataSets for GSM8526825

Status

Public on Sep 24, 2024

Title

Liver from normal fish, 3 days of recovery, rep2

Sample type

SRA

Source name

Liver

Organism

Micropterus salmoides

Characteristics

tissue: Liver
time point: After 3 days of recovery

Treatment protocol

For transportation, 125 fish were put into a 54 cm × 38 cm × 32 cm plastic box filled with 30 L water. The boxes were put into the trunk of a car and 500 fish assigned into 4 boxes were transported each time. During transportation, the water was continuously aerated using a rechargeable inflation pump. After 4 hours of transportation, the fish in each box were transferred into an indoor plastic aquarium (diameter 100 cm, height 125 cm, filled with 600 L water) for recovery. The aquaria were supplied with recycled water and the room temperature was controlled at 28 °C using an air conditioner. The fish were checked every 12 hour and the dead ones were removed and counted. The fish were not fed during the experiment.

Growth protocol

Largemouth bass fingerlings (body weight 11.99 ± 4.34 g, standard length 10.32 ± 3.02 cm) were obtained from a breeding farm in Daye, China. Before transportation, the fish were raised in a 5 m × 3 m × 1 m concrete pond and fed with a commercial extruded feed to satiation twice daily.

Extracted molecule

total RNA

Extraction protocol

Total RNA of the tissue samples was extracted using the TRIzol™ Reagent from Thermo Fisher Scientific (Waltham, MA, USA).
For library construction, 1 mg of DNase I-treated total RNA of each sample was used for sequencing library construction. The NEBNext® rRNA Depletion Kit was used for rRNA depletion. The RNAs were purified by using the Agencourt RNAClean XP Beads from Beckman Coulter. RNA fragmentation, first strand and second strand cDNA synthesis and double-stranded cDNA end repair were performed using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of the NEBNext Multiplex Oligos for Illumina. Finally, the Q5 Hot Start HiFi PCR Master Mix (NEB) was used for PCR enrichment of the adaptor-ligated DNA. Concentration and quality of the libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

R3d-NO-L#2

Data processing

The raw reads were preprocessed using fastp (v0.23.2) with default parameters to trim the adaptors and filter the low quality reads.
The clean read pairs were mapped to the reference transcriptome sequences of LMB (NCBI accession: GCF_014851395.1, accessed on October 3, 2023) using salmon (v1.10.0) with default settings.
Gene transcriptional abundance (transcript per million, TPM) was calculated using the R package tximport (v1.26.1).
Assembly: GCF_014851395.1
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

Submission date

Sep 20, 2024

Last update date

Sep 24, 2024

Contact name

Yong Long

E-mail(s)

longyong@ihb.ac.cn

Organization name

Institute of Hydrobiology, Chinese Academy of Sciences

Street address

No. 7 Donghu South Rd.