|
| Status |
Public on Feb 04, 2022 |
| Title |
25_1 |
| 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, 25 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 |
H26643
|
| 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 |
| E-mail(s) |
fraune@hhu.de
|
| 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 |
|
| Relations |
| BioSample |
SAMN18313943 |
| SRA |
SRX10343386 |
