|
| Status |
Public on Jun 06, 2019 |
| Title |
LDT2A [S151] |
| Sample type |
SRA |
| |
|
| Source name |
light:dark_time point 2_whole organism
|
| Organism |
Nematostella vectensis |
| Characteristics |
genome: Putnam et al. (2007)
light: dark cycling timepoint: light:dark, time point 2, replicate A
age: adult
|
| Treatment protocol |
Animals were experimentally exposed to either light:dark (LD) or dark:dark (DD) conditions for 1 month, then sampled every 4 hours for 1 day (24 hours), then in the LD treatment, the light cycle was removed and animals were continually sampled from both LD and DD for 2 more days (44 more hours)
|
| Growth protocol |
Animals were maintained as described in Hand et al. (1994)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole-organism RNA was extracted from animals (that were preserved in RNAlater and 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 |
LDT2A_S151_L005
|
| 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_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 |
Jun 05, 2019 |
| Last update date |
Jun 06, 2019 |
| 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) |
| GSE132202 |
Transcriptional remodeling upon light removal in a model cnidarian: losses and gains in gene expression |
|
| Relations |
| BioSample |
SAMN11960072 |
| SRA |
SRX5973827 |
