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Sample GSM4890095

Query DataSets for GSM4890095

Status

Public on Nov 01, 2023

Title

CF2

Sample type

SRA

Source name

Ovarian tissue

Organism

Oreochromis niloticus

Characteristics

tissue: Ovarian tissue
genotype: control

Treatment protocol

Introduction of antisense RNA fragments: First, 1.5 mL solution for promoting the opening of fertilization hole (each liter of water contained 6 g of sodium chloride, 0.1 g of potassium chloride, 0.1 g of calcium chloride, and 0.1 g of sodium bicarbonate, 0.1 g of sodium dihydrogen phosphate and 1.2 g of glucose) was added respectively into the stainless steel basin where the eggs were placed. The opening time of the egg fertilization hole could be prolonged and the antisense RNA fragments could be fully introduced by using the chemical solution that obtained above. Then 0.8 mL of transfection reagent was added. The stainless steel basin was gently shaken for 15 min to make the antisense RNA fragment enter the eggs through the fertilization hole. In negative control group, 0.8 mL of transfection reagent containing blank plasmid was added according to the above operation. In control group, 0.8 mL of transfection reagent containing ultrapure water was added according to the above operation.

Growth protocol

The newly-hatched larvae were placed and fed in a small water circulating system for 30 days, then the feeding larvae were transferred to a large water circulating system for culturing. The culture cycle was a 150-day period. The fish were stopped feeding for 1 day before the end of the experiment, and then the body shape of the fish, sexual organs, and gonads were photographed. The blood was drawn from tail vein to extract serum for hormone determination, and gonadal weight was weighed. At the same time, gonadal tissues were selected for HE staining, related gene quantification and protein level determination.

Extracted molecule

total RNA

Extraction protocol

Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

Ovarian tissue of tilapia during sexual maturity

Data processing

Using the Illumina paired-end RNA-seq approach
we aligned reads of all samples to the reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Genome_build: http://asia.ensembl.org/Oreochromis_niloticus/Info/Index
Supplementary_files_format_and_content: xls include FPKM values for each Sample

Submission date

Nov 09, 2020

Last update date

Nov 01, 2023

Contact name

Jun Qiang

E-mail(s)

[email protected]

Organization name

Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences

Street address

9 Shanshi East road