|
| Status |
Public on Jun 21, 2023 |
| Title |
ND1 |
| Sample type |
SRA |
| |
|
| Source name |
physa
|
| Organism |
Nematostella vectensis |
| Characteristics |
tissue: physa
genotype: genome Putnam et al. (2007)
state: active asexual repro.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from all samples using the RNAqueous kit (Ambion) according to the manufacturer’s protocol. Briefly, after pipetting off and discarding RNAlater from each sample, whole animals were lysed by pipetting in lysis buffer for < 2 min, washed 2–3 times, and eluted on a column. Genomic DNA was removed using DNA-free kit (Invitrogen), and RNA was assessed using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific).
Sequencing libraries were prepared using TruSeq Stranded mRNA Preparation Kit(Illumina) following the manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
active pinching replicate 1
|
| Data processing |
Illumina bcl2fastq2 v2.18 was used to generate fastq files
Reads were aligned to UCSC genome Nvec200 with STAR aligner (version 2.7.3a), using Ensembl 99 gene models.
TPM and RPKM are calculated using RSEM v1.3.0
Raw Read counts are calculted using STAR (version 2.7.3.a)
Assembly: UCSC genome Nvec200 (https://simrbase.stowers.org/jb_pub/?data=data%2Fstarlet_pub&tracks=NV2g_genes&NV2t_transcripts=&loc=chr15%3A5620252..5627144&highlight)
Supplementary files format and content: tab-delimited text file includes raw count values for each Sample
|
| |
|
| Submission date |
Jan 26, 2023 |
| Last update date |
Jun 21, 2023 |
| Contact name |
Andrew Joseph Price |
| E-mail(s) |
APrice@stowers.org
|
| Organization name |
Stowers Institute for Medical Research
|
| Department |
Computational Biology
|
| Street address |
1000 E. 50th Street
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL23029 |
| Series (1) |
| GSE223794 |
Environmental and molecular regulation of asexual reproduction in the cnidarian Nematostella vectensis |
|
| Relations |
| BioSample |
SAMN32929997 |
| SRA |
SRX19188970 |
