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Sample GSM4890089 Query DataSets for GSM4890089
Status Public on Nov 01, 2023
Title CM2
Sample type SRA
 
Source name Testis tissue
Organism Oreochromis niloticus
Characteristics tissue: Testis 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 Testis 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) qiangj@ffrc.cn
Organization name Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences
Street address 9 Shanshi East road
City Wuxi
State/province Jiangsu
ZIP/Postal code 214081
Country China
 
Platform ID GPL29385
Series (1)
GSE161135 Antisense RNA technology induces the loss of function of steroidogenic factor 1 leading to abortion of tilapia
Relations
BioSample SAMN16710329
SRA SRX9463292

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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