GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM5172625 Query DataSets for GSM5172625
Status Public on Feb 04, 2022
Title 20_3
Sample type SRA
Source name host tissue
Organism Nematostella vectensis
Characteristics strain: F1 offspring of CH2XCH6 (Kimura et al., 2003)
tissue: mesenteric body portion
life stage: adult
treatment: 16 per 1000, 20 C
Growth protocol polyps cultured in 16‰ arificial sea water, at either 15, 20 or 25°C
Extracted molecule total RNA
Extraction protocol Total RNA and DNA extraction protocol from Qiagen "AllPrep DNA/RNA/miRNA Universal Kit"
TruSeq stranded mRNA (incl. p-A enrichment)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Description H26648
Data processing Sequencing reads were trimmed for adaptor and low-quality bases using Trimmomatic v.0.38
Trimmed reads were mapped to Nematostella vectensis genome using hisat2 v2.1.0
Mapped reads were used for genome guided assemblies using StringTie v2.0 and Scallop v0.10.4. These assemblies were merged using TACO, which was then used to improve the ensembl gene model
FeatureCounts was used to to generate read counts for each gene in each sample
Genome_build: Nemetostella vectensis (Ensembl Metazoa database release 40,)
Supplementary_files_format_and_content: gene model in gff3 format
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Submission date Mar 15, 2021
Last update date Feb 04, 2022
Contact name Sebastian Fraune
Phone 49 211 81 14991
Organization name Heinrich-Heine-University
Department Institute for Zoology and Organismic Interactions
Lab AG Fraune
Street address Universitätsstr. 1, Building: 26.24, Floor/Room: 02.114
City Düsseldorf
State/province North Rhine-Westphalia
ZIP/Postal code 40225
Country Germany
Platform ID GPL29855
Series (1)
GSE168938 Microbiome mediated plasticity promotes thermal adaptation in Nematostella vectensis
BioSample SAMN18313938
SRA SRX10343391

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