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Sample GSM5394145 Query DataSets for GSM5394145
Status Public on Jun 21, 2024
Title B_1000_p1
Sample type SRA
 
Source name Primordial germ cells
Organism Oryzias latipes
Characteristics cell type: PGC
treatment: 1000 μg/L
replicate: replicate_1
Treatment protocol The (KCIO4) solutions were prepared (0, 10, 100 and 1000 μg/L) and stored at 4 °C in dark. Fertilized eggs were incubated in a 10 ml exposure solution, which was replaced daily with working solution. Upon hatching, Fry was transferred to Petri dishes containing 30ml of exposure solution, which was replaced daily. Exposure lasted until the 15-dpf (days post fertilization).
Growth protocol The olvas-GFP medaka fish was used in the present study. Fish were raised in 38-liter tanks with constant aeration and water flow of about 76 liters/day. The water temperature was maintained at 25 ± 1 °C under a light: dark cycle of 14 h: 10 h.
Extracted molecule total RNA
Extraction protocol Primordial germ cells (PGCs) were isolated according to the method developed by Wang and Bhandari (2020). Genomic DNA and total RNA were extracted using ZR-Duet™ DNA/RNA MiniPrep kit (Zymo Research, Irvine, U.S.A.).
RNA sequencing libraries were prepared with NEBNext® UltraTM II RNA Library Prep Kit for Illumina accordingly to the manufacturer’s instructional manual. For each sample, 500ng total RNA was used.
RNAseq libraries were sequenced on the Illumina platform using the 150 bp pair-end sequencing strategy.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Sequencing reads from each sample were mapped to medaka reference transcripts (Ensembl version 95) using HISAT2 software with default parameters. Only uniquely mapped reads were used for subsequent analysis. Cufflinks software (http://cole-trapnell-lab.github.io/cufflinks/, University of Washington) was used to conduct differentially expressed gene (DEG) analysis on the raw count data.
Genome_build: ASM223467v1.95
Supplementary_files_format_and_content: FPKM
 
Submission date Jun 21, 2021
Last update date Jun 21, 2024
Contact name Ramji Kumar Bhandari
E-mail(s) rkbhanda@uncg.edu
Organization name University of North Carolina Greensboro
Department Biology
Lab Bhandari Laboratory
Street address 321 McIver St
City Greensboro
State/province NC
ZIP/Postal code 27412
Country USA
 
Platform ID GPL25587
Series (1)
GSE178587 Effects of Potassium Perchlorate on Developing Medaka Primordial Germ Cells
Relations
BioSample SAMN19798122
SRA SRX11189253

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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