|
| Status |
Public on Jun 21, 2024 |
| Title |
B_100_p3 |
| Sample type |
SRA |
| |
|
| Source name |
Primordial germ cells
|
| Organism |
Oryzias latipes |
| Characteristics |
cell type: PGC
treatment: 100 μg/L
replicate: replicate_3
|
| 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 |
SAMN19798123 |
| SRA |
SRX11189252 |
