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Status |
Public on Jan 17, 2022 |
Title |
XBN |
Sample type |
SRA |
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Source name |
Zebrafish body skin
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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-
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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)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
Acral melanoma model body microenvironment
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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
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Submission date |
Aug 09, 2021 |
Last update date |
Jan 19, 2022 |
Contact name |
Joshua M Weiss |
E-mail(s) |
jmw2015@med.cornell.edu
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Organization name |
Memorial Sloan Kettering Cancer Center
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Department |
Cancer Biology and Genetics
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Lab |
White
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Street address |
417 E 68th St
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City |
New York |
State/province |
NY |
ZIP/Postal code |
10065 |
Country |
USA |
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Platform ID |
GPL24995 |
Series (1) |
GSE181748 |
scRNA-seq of fin and body zebrafish melanocytes |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
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