|
| Status |
Public on Sep 07, 2022 |
| Title |
Octopus Adult Arm Left 1 Tip [OB9] |
| Sample type |
SRA |
| |
|
| Source name |
Adult arm tip, collected till 1.5 cm from the arm tip
|
| Organism |
Octopus bimaculoides |
| Characteristics |
Sex: Female
developmental stage: Adult
tissue: arm tip
|
| Treatment protocol |
Animals were euthanized by overdose of ethanol and tissues were immediately collected, flash frozen in liquid nitrogen, and stored at -80°C.
|
| Growth protocol |
Animals were catched from wild and manteined in husbandy accordingly to the current policy for the use of cephalopods at Marine Biology Laboratories (MBL, https://www.mbl.edu/policies/files/2018/07/J1.10-CEPH-Policies-Procedures-Jan-1-31-2020-fillable-form.pdf).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For each sample, tissues stored at -80°C were ground in liquid nitrogen using a mortar placed in dry ice. Resulting powder was aliquoted and 15 mg of this powder was used to extract RNA. RNA was extracted using Trizol (Invitrogen) following the manufacturer’s instructions with some modifications. Briefly, during precipitation in isopropanol, 10 µg of Glycoblue (Thermo Fisher Scientific) was added and precipitation was performed overnight at -20°C followed by 1 hour centrifuge at 12000g at 4°C. RNA was resuspended in water . RNA was treated by DNAse I for 30 minutes at 37 °C followed by RNA purification (RapidOut DNA Removal Kit – Thermo Fisher Scientific).
RiboZero was used to remove ribosomal RNA and the remaining sample was used for library preparation according to manufacturer’s instructions (Illumina) from 250 ng of RNA. Libraries were sequenced on NextSeq550 (Illumina) to obtain 150 bp paired end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads where first assessed for quality using FastQC v0.11.5. Trimmomatic v0.36 was used for quality trimming and adapter sequence removal, with the parameters (ILLUMINACLIP: trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36)
The dataset from hatchling was also processed with Fastp in order to remove poly-G tails and Novaseq/Nextseq specific artifacts. Following the Fastp quality trimming, the reads were assessed again using FastQC
Quality trimmed reads were used to produce psuedoalignments using Kallisto, and quantification was assessed with the --bias flag using the reference O. bimaculoides genome (PRJNA270931) and its corresponding annotation
The resulting transcripts per kilobase per million (TPMs) from the pseudo-counts were used for further downstream analysis
Assembly: PRJNA270931
Supplementary files format and content: .tsv file containing pseudo-counts (TPMs) for each transcript
|
| |
|
| Submission date |
Sep 07, 2022 |
| Last update date |
Nov 29, 2022 |
| Contact name |
Kirsten Sadler Edepli |
| E-mail(s) |
kirsten.edepli@nyu.edu
|
| Phone |
971568327587
|
| Organization name |
New York University Abu Dhabi
|
| Department |
Biology
|
| Street address |
PO Box 129188
|
| City |
Abu Dhabi |
| State/province |
Abu Dhabi |
| ZIP/Postal code |
000 |
| Country |
United Arab Emirates |
| |
|
| Platform ID |
GPL30957 |
| Series (1) |
| GSE188925 |
Genome-wide expression profiling of Octopus Arm and Hatchlings |
|
| Relations |
| BioSample |
SAMN30718669 |
| SRA |
SRX17476296 |
