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Sample GSM5510265 Query DataSets for GSM5510265
Status Public on Jan 17, 2022
Title XBN
Sample type SRA
 
Source name Zebrafish body skin
Organism Danio rerio
Characteristics model: Acral melanoma model (Caspers with MiniCoopR-eGFP, mitfa:hsCRKL, mitfa:hsGAB2, mitfa:hsTERT, mitfa:Cas9-mCherry;U6-nf1a-gRNA, mitfa:Cas9-mCherry;U6-nf1b-gRNA)
tissue: Body
cell type: GFP-
Extracted molecule total RNA
Extraction protocol Droplet-based scRNA-seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 (10X Genomics) and Chromium Single Cell 3’ Chip G (10X Genomics). Approximately 10,000 cells were encapsulated per each of the four reactions.
GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles, i5 10 cycles, i7 10 cycles, Read2 90 cycles. Sequencing depth was approximately 40,000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 (10X Genomics).
scRNA-seq (10X genomics)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Acral melanoma model body microenvironment
Data processing Data was processed using R version 4.0.4 and Seurat version 4.0.3 (Hao, Hao et al., 2021). Each of the four reactions were processed separately before merging into a single object.
Cells with fewer than 200 unique genes were filtered out.
Expression data was normalized with SCTransform (Hafemeister and Satija, 2019).
Principal component analysis (Joliffe, 1986) and UMAP dimensionality reduction (McInnes, 2018) were performed using default parameters, with 15 principal components used for UMAP calculations.
Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell-type marker genes as done previously (Baron et al., 2020; Hunter, Moncada et al., 2021).
Genome_build: GRCz10
Supplementary_files_format_and_content: csv file containing counts from all 4 samples
Supplementary_files_format_and_content: Cell ranger output
 
Submission date Aug 09, 2021
Last update date Jan 19, 2022
Contact name Joshua M Weiss
E-mail(s) jmw2015@med.cornell.edu
Organization name Memorial Sloan Kettering Cancer Center
Department Cancer Biology and Genetics
Lab White
Street address 417 E 68th St
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL24995
Series (1)
GSE181748 scRNA-seq of fin and body zebrafish melanocytes
Relations
BioSample SAMN20691352
SRA SRX11692437

Supplementary file Size Download File type/resource
GSM5510265_XBN_barcodes.tsv.gz 25.9 Kb (ftp)(http) TSV
GSM5510265_XBN_genes.tsv.gz 264.6 Kb (ftp)(http) TSV
GSM5510265_XBN_matrix.mtx.gz 11.0 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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