|
| Status |
Public on Dec 27, 2020 |
| Title |
B. orientalis embryo, 9hr, 100 ug/mL heavy diesel particulate matter treatment, rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Bombina orientalis |
| Characteristics |
treatment: PM100 treatment
incubation_time: 9hr
biological_replicate: rep2
|
| Treatment protocol |
Xenopus laevis and Bombina orientalis embryos were washed using appropriate sterilized grown solution to remove mucus particles remained on epithelium. After washing, embryos were incubated in 100ug/ml heavy diesel particulate matter (PM) for 3 hours or 9 hours. Incubated embryos were lysed for further analysis.
|
| Growth protocol |
Xenopus laevis and Bombina orientalis adult females were ovulated using 380 units of human chorionic gonadotropin (HCG) a day before. For B. orientalis, an adult male was also ovulated using 280 units of HCG a day before for natural mating. For X. laevis egg fertilization, a testicle was dissected from an adult male, ground, and sprayed on the squeezed X. laevis eggs. To remove the jelly layer, a 3% cysteine pH 7.9 solution was used for X. laevis embryos and a 3% cysteine pH 9.5 solution for B. orientalis embryos. Fertilized X. laevis embryos were grown in 1/3× MMR and fertilized. B. orientalis embryos were grown in sterilized water until used.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Thermo Fisher, 15596018) according to manufacturer’s protocol. To eliminate DNA, samples were purified using PCI/Ethanol purification and lithium chloride methods.
Library preparation were performed using a TruSeq stranded mRNA sample prep kit (Illumina, 20020595).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Clena up the adpater sequences with trimmomatic (0.39)
Map the reads to the cDNA references using kallisto (0.44.0)
Normalize with txtimport and limma
Call the differentially expressed genes with limma
Genome_build: Bombina_orientalis.a2020_08.cdna.fa.gz
Genome_build: XENLA_XB201901_tx_annot.fa.gz
Supplementary_files_format_and_content: Default output of kallisto (0.44.0)
|
| |
|
| Submission date |
Dec 26, 2020 |
| Last update date |
Dec 27, 2020 |
| Contact name |
Taejoon Kwon |
| E-mail(s) |
tkwon@unist.ac.kr
|
| Organization name |
Ulsan National Institute of Science and Technology
|
| Department |
Department of Biomedical Engineering
|
| Street address |
50 Unist-gil
|
| City |
Ulsan |
| ZIP/Postal code |
44919 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL26992 |
| Series (1) |
| GSE163875 |
Alpha-tocopherol exerts protective function against the mucotoxicity of particulate matter in amphibian and human goblet cells |
|
| Relations |
| BioSample |
SAMN17164137 |
| SRA |
SRX9736357 |
