|
| Status |
Public on Jan 23, 2020 |
| Title |
S-T3D_S154 |
| Sample type |
SRA |
| |
|
| Source name |
streptomycin_T3_oral disc/tentacles
|
| Organism |
Nematostella vectensis |
| Characteristics |
developmental stage: adult
treatment: streptomycin
time point: time point 3
tissue: oral disc/tentacles
replicate: replicate D
|
| Treatment protocol |
Animals were exposed to one of three types of trauma (streptomycin, cytochalasin D, or calcium-free KSW) and allowed to recover. Sampling occurred at hourly time points during recovery. For streptomycin, sampling occurred after one hour of recovery following designated exposure times to streptomycin.
|
| Growth protocol |
Animals were maintained as described in Hand et al. (1994)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from oral discs and tentacles (flash frozen in liquid nitrogen/stored at -80) using Ambion RNAqueous extraction kit.
Libraries were prepared as in Meyer et al. (2011)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
S-T3D_S154
|
| Data processing |
Sequenced reads were concatenated and renamed based on sample ID
Each Illumina read was trimmed of the adapter and PCR duplicates were removed
Quality filtering was performed using fastx_toolkit
Transcriptome mapping was performed using Bowtie2
genome Putnam et al. (2007)
Genome_build: https://figshare.com/articles/Nematostella_vectensis_transcriptome_and_gene_models_v2_0/807696
Supplementary_files_format_and_content: tab-delimited table of counts per gene for each sample
|
| |
|
| Submission date |
Jan 22, 2020 |
| Last update date |
Jan 23, 2020 |
| Contact name |
Whitney at Leach |
| Organization name |
University of North Carolina at Charlotte
|
| Department |
Biological Sciences
|
| Lab |
Reitzel
|
| Street address |
9201 University City Blvd.
|
| City |
Charlotte |
| ZIP/Postal code |
28223 |
| Country |
USA |
| |
|
| Platform ID |
GPL23802 |
| Series (1) |
| GSE144080 |
Gene expression during recovery from different forms of trauma in the sea anemone, Nematostella vectensis |
|
| Relations |
| BioSample |
SAMN13901869 |
| SRA |
SRX7619033 |
