run_metadata: 56605
This data as json
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| 56605 | SRR11031290 | SRX7683557 | SRS6110537 | SRP247442 | PRJNA605021 | Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2 | GSE144827 | Transcriptome Analysis | This dataset consists of single cell RNA seq 10X data of neuromast cells from zebrafish larvae. Posterior lateral line neuromast cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs and from Tg[Etkrt4:EGFPsqgw57A] larvae expressing EGFP in supporting cells. Overall design: A single cell RNA seq experiment of isolated neuromast cells from zebrafish larvae was performed using 10X Genomics technology to generate single cell transcriptomic profiles of supporting cells and hair cells. | pubmed:32109392 | hair cells | GSM4298909 | source name:zebrafish neuromast cells|genotype:Tg[myo6b:actb1 EGFP]|source tissue:neuromast|developmental day:7 dpf | hair cells | The 10X Genomics core computational software Cellranger v.2.1.1 was used for alignment and processing of next generation sequencing reads of the scRNA seq data as recommended https://support.10xgenomics.com/single cell gene expression/software/overview/welcome. Genome build: GRCz11 Supplementary files format and content: Raw UMI count matrix feature x cell barcode from 10X Genomics single cell RNAseq experiments. gzipped files contains count matrix in market matrix format cell barcodes as tab delimited text file and feature names as tab delimited text file. | zebrafish neuromast cells | none | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. Single cell libraries were generated using the ChromiumTM Single cell 3`library and gel bead kit v2 PN #120237 from 10x Genomics. Libraries were sequenced on the HiSeq4000 Illumina with 150bp paired end sequencing. RNA Seq 10X Genomics | Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution. | genotype:Tg[myo6b:actb1 EGFP]|source tissue:neuromast|developmental day:7 dpf | GSM4298909 | GSM4298909: hair cells; Danio rerio; RNA Seq | GSM4298909 | 1 | Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. Single cell libraries were generated using the ChromiumTM Single cell 3`library and gel bead kit v2 PN #120237 from 10x Genomics. Libraries were sequenced on the HiSeq4000 Illumina with 150bp paired end sequencing. RNA Seq 10X Genomics | GEO Accession:GSM4298909 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP247442 | hair_cells_R2.fastq.gz hair_cells_R1.fastq.gz | fastq fastq | 89474157378.0 | 505503714.0 | GSM4298909 r1 | 0:26 1:151 | A:25071099481;C:19794086212;G:19845960995;T:24749018204;N:13992486 | 26 | 151 | 25071099481 | 19794086212 | 19845960995 | 24749018204 | 13992486 | SRX7683557 | SRS6110537 | SRA1038640 | GEO | Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München | 2 | 0.00294 | 0.9352 | 0.00072 | 0.07461 | 0.99358 | 0.81487 | 0.46744 | 0.43177 | 26 | 151 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2020-02-05 | Larval | Larval | Lateral Line | Sensory System |