|
| Status |
Public on Feb 20, 2021 |
| Title |
ABLW204 |
| Sample type |
SRA |
| |
|
| Source name |
whole-organism
|
| Organism |
Nematostella vectensis |
| Characteristics |
tissue: Whole body
age: Adult
treatment: Antibiotics + Pseudoalteromonas spiralis
|
| Treatment protocol |
Animals were exposed to all conditions for 7 days. For antibiotic removed condition, the antibiotics were removed 3 days prior to extraction.
|
| 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 |
S118
ABLW204
Replicate 4
genome Putnam et al. (2007)
allcountsFINAL.txt
|
| 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: allcountsFINAL.txt: Tab-delimited table of counts per gene for each sample.
|
| |
|
| Submission date |
Feb 19, 2021 |
| Last update date |
Feb 20, 2021 |
| Contact name |
Adam Reitzel |
| E-mail(s) |
adam.reitzel@uncc.edu
|
| Organization name |
University of North Carolina Charlotte
|
| Department |
Biological Sciences
|
| Street address |
9201 University City Blvd
|
| City |
Charlotte |
| State/province |
NC |
| ZIP/Postal code |
28223 |
| Country |
USA |
| |
|
| Platform ID |
GPL23802 |
| Series (1) |
| GSE167114 |
Impact of antibiotics, cell-free supernatant, LPS, and live cells on Nematostella vectensis gene expression |
|
| Relations |
| BioSample |
SAMN18000171 |
| SRA |
SRX10134068 |
