NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5093809 Query DataSets for GSM5093809
Status Public on Feb 20, 2021
Title NTLW203
Sample type SRA
 
Source name whole-organism
Organism Nematostella vectensis
Characteristics tissue: Whole body
age: Adult
treatment: No antibiotic + 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 S113
NTLW203
Replicate 3
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 SAMN17999915
SRA SRX10134031

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap