|
| Status |
Public on Jun 03, 2021 |
| Title |
c-di-GMP polyp 1 |
| Sample type |
SRA |
| |
|
| Source name |
whole polyps
|
| Organism |
Nematostella vectensis |
| Characteristics |
treatment: c-di-GMP
|
| Treatment protocol |
Polyps were treated with 500μM CDNs for 24 hours; embryos with treated with 100μM 2'3'-cGAMP for 4 hours.
|
| Growth protocol |
Animals were maintained at room temperature in 1/3x sea water
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For polyps, total RNA was extracted using Qiagen RNeasy Mini kits according to the manufacturer’s protocol. Embryos were homogenized in Trizol (Thermo Fisher Scientific) and RNA was extracted according to the manufacturer’s protocol
For polyps, libraries were prepared using WaferGen PrepX library prep kits with oligo dT beads for mRNA enrichment according to the manufacturer’s protocol. For embryos, libraries were prepared as follows: oligo dT beads from the KAPA mRNA Capture Kit (KK8581) were used for mRNA enrichment; fragmentation, adapter ligation and cDNA synthesis were performed using the KAPA RNA HyperPrep kit (KK8540); libraries were pooled evenly by molarity and sequenced to generate 25M read pairs per sample
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
polyps_normalized_counts.txt
|
| Data processing |
fastq read quality was assessed using FastQC (v0.11.9)
Reads were pseudoaligned to the N. vectensis transcriptome (NCBI: GCF_000209225.1) and quantified using kallisto (v0.46.1)
Normalized read counts were generated using DESeq2
Genome_build: NCBI Nematostella vectensis Annotation Release 100 (Assembly Accesssion GCF_000209225.1)
Supplementary_files_format_and_content: tab delimited txt files with normalized read counts for each sample and each gene
|
| |
|
| Submission date |
Jun 02, 2021 |
| Last update date |
Jun 03, 2021 |
| Contact name |
Shally Rebecca Margolis |
| Organization name |
UC Berkeley
|
| Department |
Molecular and Cell Biology
|
| Lab |
Russell Vance
|
| Street address |
415 Life Sciences
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL29855 |
| Series (1) |
| GSE175984 |
Cyclic dinucleotide stimulation of Nematostella vectensis |
|
| Relations |
| BioSample |
SAMN19494017 |
| SRA |
SRX11048975 |
