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| Status |
Public on May 19, 2020 |
| Title |
14 dpf retina rep |
| Sample type |
SRA |
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| Source name |
Retina
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| Organism |
Danio rerio |
| Characteristics |
strain: AB
genotype: wildtype
tissue: CMZ
developmental stage: 14 dpf
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Nov 19, 2018 |
| Last update date |
May 19, 2020 |
| Contact name |
Baijie Xu |
| E-mail(s) |
xbjie123@sina.com
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| Organization name |
Institute of Neuroscience, CAS
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| Lab |
Lab of Stem Cell and Neurogenesis
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| Street address |
320 Yue Yang Road
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| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platform ID |
GPL24995 |
| Series (1) |
| GSE122680 |
Unifying Developmental Programs for Embryonic and Post-Embryonic Neurogenesis in the Zebrafish Retina |
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| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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