|
| Status |
Public on Aug 20, 2020 |
| Title |
ER-F1-2000-5 |
| Sample type |
SRA |
| |
|
| Source name |
stage 35, whole embryo
|
| Organism |
Fundulus heteroclitus |
| Characteristics |
developmental stage: embryo, stage 35, 10 days post fertilization
population: Elizabeth River
pcb_dosage: 2000
generation: F1
|
| Treatment protocol |
on the day of fertilization, embryos were exposed to PCB-126 or DMSO at dosage given in "Characteristics" field, in ng/L
|
| Growth protocol |
embryos derived from F1 or F2 generation lab reared fish.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
at 10 days post-fertilization, embryos were homogenized and total RNA was extracted using Trizol
NEB Next Ultra RNA kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
adapter and quality trimmed using Trimmomatic
aligned to reference using bwa mem
quantified using featureCounts (subread package)
Genome_build: GCF_000826765.1
Supplementary_files_format_and_content: tab-delimited text. Fundulus heteroclitus GeneID is column 1, raw count of fragments mapping to gene feature is column 7
|
| |
|
| Submission date |
Aug 19, 2020 |
| Last update date |
Aug 20, 2020 |
| Contact name |
Noah M Reid |
| E-mail(s) |
noah.reid@gmail.com
|
| Organization name |
University of Connecticut
|
| Department |
Ecology and Evolutionary Biology
|
| Street address |
67 North Eagleville Road
|
| City |
Storrs |
| State/province |
CT |
| ZIP/Postal code |
06269 |
| Country |
USA |
| |
|
| Platform ID |
GPL29035 |
| Series (1) |
| GSE156460 |
Transcriptional response to embryonic PCB exposure in 8 killifish populations |
|
| Relations |
| BioSample |
SAMN15856646 |
| SRA |
SRX8969425 |
