|
| Status |
Public on Dec 16, 2013 |
| Title |
Treated biological replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Olfactory sensory neuron
|
| Organism |
Danio rerio |
| Characteristics |
tansgenic line: OMP-Gal4 transgenic zebrafish
cell sorting: GFP (+)
agent: 100 µM gallein
|
| Treatment protocol |
At 16-20 hours post fertilization (hpf), embryos were treated with 100 µM gallein or DMSO (control). Fresh embryo media with the appropriate drug treatment was replaced every 24 hours. Heads of 5 days post fertilization embryos were dissected and dissociated with trypsin and collagenase and sorted for GFP fluorescence; cells were collected in 1ml of Trizol and stored at -80oC
|
| Growth protocol |
OMP-Gal4;UAS-GCaMP1.6 transgenic zebrafish embryos were collected upon fertilization and raised in embryo media at 28oC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using Trizol reagent & DNase treated. Poly(A)+ RNA was enriched from total RNA using oligo(dT)25 magnetic beads (Life Technologies, cat#61006).
The libraries were prepared using PrepX SPIA RNA-Seq (cat#400030) and ILM DNA Library kits (cat#400044) according to the manufacturer’s (IntegenX, Inc.) protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Reads were mapped to a custom reference, defined as the union of the Zv9 reference zebrafish genome downloaded from Ensembl v. 67 and the ERCC spike-in sequences, using TopHat (v. 2.0.4, supplying the Ensembl GTF annotation through the -G option)
Gene-level read counts were generated using the htseq-count python script in the "union" mode and Ensembl (v. 67) gene annotation
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files contain gene-level read counts for each sample
|
| |
|
| Submission date |
Dec 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Davide Risso |
| Organization name |
University of Padova
|
| Street address |
Via C. Battisti, 241
|
| City |
Padova |
| ZIP/Postal code |
35121 |
| Country |
Italy |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE53334 |
Silencing of odorant receptor gene expression by G protein βγ signaling ensures the expression of one odorant receptor per olfactory sensory neuron |
|
| Relations |
| BioSample |
SAMN02444389 |
| SRA |
SRX392057 |
