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Sample GSM6534018

Query DataSets for GSM6534018

Status

Public on Sep 04, 2022

Title

nextseq_replicate1, scRNAseq

Sample type

SRA

Source name

optic lobe

Organism

Octopus bimaculoides

Characteristics

tissue: optic lobe

Extracted molecule

total RNA

Extraction protocol

O. bimaculoides optic lobes were dissected on ice in Leibovitz-15 medium (Gibco) supplemented with 400mM NaCl, 10mM KCl, 15mM Hepes, 200 U/mL penicillin, and 0.2 mg/mL streptomycin. Single cell dissociation was performed by incubating tissue in papain (1 mg/ml; Worthington Biochemical Co) plus 1% DNase (10mg/ml in HBSS) in supplemented L-15 medium for 10 min at RT. The cells/tissue were gently pipetted up and down several times to dissociate large chunks. The cells/tissue were incubated for another 10 min at RT, pipetted up and down several times, and quenched in wash solution containing 2.5M glucose, 5mM Hepes, and 5% FBS in CMFSS (12mM Hepes, 435mM NaCl, 10.7mM KCl, 21mM Na2HPO4, 16.6mM glucose). Dissociated cells were passed through a 40 μM cell strainer (Fisherbrand), washed again, and resuspended in L-15 medium. A final sample cell concentration of 2000 cells per microliter, as determined on a BioRad TC20 cell counter, was used for cDNA library preparation. Dissociated samples were prepared in tandem, on the same day.
Sample preparation for two biological replicates was performed by the University of Oregon Genomics and Cell Characterization core facility (https://gc3f.uoregon.edu/). Dissociated cells were run on a 10X Chromium platform using 10x v.3 chemistry targeting 10,000 cells. The resulting cDNA libraries were amplified with 11 cycles of PCR and sequenced on either an Illumina Hi-seq or an Illumina Next-seq.

Library strategy

RNA-Seq

Library source

transcriptomic single cell

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Description

used scRNAseq to determine the cell types of the octopus visual system. Used nextseq to sequence our first biological replicate
1_barcodes.tsv.gz
1_genes.tsv.gz
1_matrix.mtx.gz

Data processing

The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: o_bimaculoides_hifi_v1.0.0
Supplementary files format and content: Tab-separated values files and matrix files

Submission date

Sep 01, 2022

Last update date

Sep 28, 2022

Contact name

Cristopher Niell

E-mail(s)

cniell@uoregon.edu

Organization name

University of Oregon

Street address

1565 E 13th st