run_metadata: 50661
This data as json
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| 50661 | SRR11812054 | SRX5025779 | SRS4057279 | SRP169565 | PRJNA506002 | Unifying Developmental Programs for Embryonic and Post Embryonic Neurogenesis in the Zebrafish Retina | GSE122680 | Transcriptome Analysis | It provides an opportunity to make the first comparative study of molecular programs used by embryonic and post embryonic neurogenic programs in the vertebrate retina. Overall design: Retinal samples from 4 developmental stages and 1 post embryonic stage | pubmed:32467236 | 48 hpf retina | GSM3478015 | source name:Retina|strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:48 hpf | 48 hpf retina | 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 | Retina | 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 post 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 Chip10x Genomics according to the manufacturer’s protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer’s protocol. | strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:48 hpf | GSM3478015 | GSM3478015: 48 hpf retina; Danio rerio; RNA Seq | GSM3478015 | 1 | 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 post 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 Chip10x Genomics according to the manufacturer's protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer's protocol. | GEO Accession:GSM3478015 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP169565 | intentional duplicate | 48hpf_possorted_genome_bam.bam | 10X Genomics bam file | 27828827400.0 | 185525516.0 | GSM3478015 r11 | 0:150 | A:8568529313;C:5431445717;G:5968188905;T:7860573445;N:90020 | 150 | 8568529313 | 5431445717 | 5968188905 | 7860573445 | 90020 | SRX5025779 | SRS4057279 | SRA812747 | GEO | Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS | 1 | 0.91308 | 0.11004 | 0.82213 | 0.48772 | 150 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2018-11-19 | Hatching | Embryo | Eye | Sensory System |