|
| Status |
Public on Aug 02, 2012 |
| Title |
60hpf-TCDD-2 |
| Sample type |
SRA |
| |
|
| Source name |
Embryos
|
| Organism |
Danio rerio |
| Characteristics |
strain: TL wild type
tissue: embryos
time: 60 hpf
treatment: TCDD
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNA libraries were prepared using the small RNA expression kit (SREK) protocol (Applied Biosystems, Foster City, CA). Sequencing was done on a SOLiD V3 system (Applied Biosystems).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Data processing |
CLC Bio Genomics Work bench version 4.7 was used
Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16.
Remaining reads were mapped to other non-coding RNAs downloaded from ncRNA.org
Statistical analysis was done using edgeR, a bioconductor package (R project)
Genome_build: miRBase version 16
Supplementary_files_format_and_content: tab-delimited text files
|
| |
|
| Submission date |
Aug 01, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Neelakanteswar Aluru |
| E-mail(s) |
naluru@whoi.edu
|
| Phone |
508-289-3607
|
| Organization name |
Woods Hole Oceanographic Institution
|
| Department |
Biology
|
| Lab |
Aluru Lab
|
| Street address |
45 Water Street
|
| City |
Woods Hole |
| State/province |
MA |
| ZIP/Postal code |
02543 |
| Country |
USA |
| |
|
| Platform ID |
GPL10658 |
| Series (2) |
| GSE39808 |
MicroRNA expression profiling after short-term exposure to TCDD in zebrafish embryos [miRNA-Seq data] |
| GSE39809 |
MicroRNA expression profiling after short-term exposure to TCDD in zebrafish embryos |
|
| Relations |
| SRA |
SRX172597 |
| BioSample |
SAMN01096349 |
