|
| Status |
Public on Nov 25, 2024 |
| Title |
Scyliorhinus canicula retina, female, 11.0 cm |
| Sample type |
SRA |
| |
|
| Source name |
Retina
|
| Organism |
Scyliorhinus canicula |
| Characteristics |
tissue: Retina
|
| Growth protocol |
Animals were kindly provided by the Aquarium Finisterrae (A Coruña, Spain) and kept in artificial seawater tanks under standard conditions of temperature (15-16 °C), pH (7.5-8.5) and salinity (35 g/L). All procedures were performed in accordance with European and Spanish guidelines for animal experimentation.
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Animals were deeply anaesthetised with 0.5% tricaine methanesulfonate in seawater. The animals were removed from water and the retinas were dissected out under a stereomicroscope. Retinas were immediately frozen in liquid nitrogen, and kept at -80 °C until further processing.
Retina nuclei were extracted following a published protocol (Krishnaswami et al. 2016, Nat. Protoc. https://doi.org/10.1038/nprot.2016.015) with small modifications. Briefly, the frozen retinas were homogenised using a micropestle in 400 µL ice-cold homogenisation buffer. The homogenates were triturated gently using a p1000 tip for 10 times, incubated on ice for 5 min and then centrifuged at 100 g for 1 min at 4 °C. The supernatant was transferred into another 1.5 mL Eppendorf tube and centrifuged at 400 g for 4 min at 4 °C to collect nuclei. The nuclei were washed twice in 400 µL homogenisation buffer and strained using a 40 µm Flowmi strainer (Sigma) during the second wash step to remove nuclei aggregates. The final nuclei pellet was resuspended in 30-50 µL Nuclei Buffer (10x Genomics). To estimate the nuclei concentration, nuclei aliquots were diluted in PBS with Hoechst and PI DNA dyes and counted on Countless II FL Automated Cell Counter (Thermo Fisher Scientific). Around 15,000 nuclei were used as input for the snRNA-seq experiment. The Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (PN-1000121, PN-1000120, and PN-1000213) were used to make snRNA-seq libraries. Libraries were quantified on a Qubit Fluorometer (Thermo Fisher Scientific) and quality checked on a Fragment Analyzer (Agilent). Libraries were sequenced on NextSeq550 (Illumina; 28 cycles for Read 1, 56 cycles for Read 2, 8 cycles for i7 index).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Genome indexing and library mapping was performed with STAR (v2.7.10a).
Assembly: sScyCan1.1
Supplementary files format and content: Tab-separated values file for barcodes
Supplementary files format and content: Tab-separated values file for features
Supplementary files format and content: Matrix file
|
| |
|
| Submission date |
Nov 20, 2024 |
| Last update date |
Nov 25, 2024 |
| Contact name |
Nicolás Vidal-Vázquez |
| E-mail(s) |
nicolas.vidal.vazquez@usc.es
|
| Organization name |
Universidade de Santiago de Compostela
|
| Department |
Departamento de Bioloxía Funcional
|
| Lab |
NEURODEVO Group
|
| Street address |
Av. Lope Gómez de Marzoa s/n
|
| City |
Santiago de Compostela |
| State/province |
A Coruña |
| ZIP/Postal code |
15782 |
| Country |
Spain |
| |
|
| Platform ID |
GPL35117 |
| Series (1) |
| GSE282457 |
A single-nucleus RNA sequencing atlas of the postnatal retina of the shark Scyliorhinus canicula |
|
| Relations |
| BioSample |
SAMN39112973 |
| SRA |
SRX23021408 |
