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Sample GSM3478019 Query DataSets for GSM3478019
Status Public on May 19, 2020
Title 14 dpf retina rep
Sample type SRA
 
Source name Retina
Organism Danio rerio
Characteristics strain: AB
genotype: wildtype
tissue: CMZ
developmental stage: 14 dpf
Extracted molecule total RNA
Extraction protocol We dissected 24-, 36-, 48-, 72-hpf retinas of wild-type zebrafishes and isolated via papin solution. 14-dpf retinas were dissected from PCNA-GFP transgenic fishes. And after isolation by papin solution, the GFP positive cells which could label the ciliary marginal zone (CMZ) cells were sorted via FACS. These isolated cells filtered by 40μm cell strainer (BD Falcon) were loaded onto the Chromium Single Cell Chip(10x Genomics) according to the manufacturer’s protocol.
Single-cell RNA-seq libraries were generated using the GemCode Single-Cell Instrument and Single Cell 3' Library &Gel Bead kit v2 Chip kit (10x Genomics) following the manufacturer’s protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Single-cell FASTQ sequencing reads (Novogene) aligned to the zebrafish genome (Zv10) were processed and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite (v2.1.0) provided in 10x genomics website (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
To further analyze the data, we used an analysis pipeline provided by the Seurat R package (http://satijalab.org/seurat/).
We substract progenitor cell clusters of 36hpf and 48hpf samples according to the proliferative gene expression.
For post-embryonic samples, we substract the ciliary marginal zone (CMZ) cell clusters based on marker genes' expression.
Genome_build: Zv10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx
 
Submission date Nov 19, 2018
Last update date May 19, 2020
Contact name Baijie Xu
E-mail(s) xbjie123@sina.com
Organization name Institute of Neuroscience, CAS
Lab Lab of Stem Cell and Neurogenesis
Street address 320 Yue Yang Road
City Shanghai
ZIP/Postal code 200031
Country China
 
Platform ID GPL24995
Series (1)
GSE122680 Unifying Developmental Programs for Embryonic and Post-Embryonic Neurogenesis in the Zebrafish Retina
Relations
BioSample SAMN10440904
SRA SRX5025783

Supplementary file Size Download File type/resource
GSM3478019_barcodes.tsv.gz 21.4 Kb (ftp)(http) TSV
GSM3478019_genes.tsv.gz 232.2 Kb (ftp)(http) TSV
GSM3478019_matrix.mtx.gz 22.8 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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