|
Status |
Public on Feb 20, 2021 |
Title |
ABLA61 |
Sample type |
SRA |
|
|
Source name |
whole-organism
|
Organism |
Nematostella vectensis |
Characteristics |
tissue: Whole body age: Adult treatment: Antibiotics + Vibrio alginolyticus
|
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 |
S83 ABLA61 Replicate 1 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 |
SAMN18000267 |
SRA |
SRX10134061 |