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Sample GSM4271631 Query DataSets for GSM4271631
Status Public on Mar 05, 2020
Title TAGTTT: hair_cells_Emx2_mutant_2C6
Sample type SRA
 
Source name zebrafish neuromast hair cells
Organism Danio rerio
Characteristics genotype: Tg[myo6b:actb1-EGFP]_Emx2-mutant
tissue: zebrafish neuromast hair cells
developmental day: 6 days post fertilization
Treatment protocol none
Growth protocol Standardized conditions at 28.5°C in the 0,3 x Danieau’s solution.
Extracted molecule total RNA
Extraction protocol Enzymatic dissociation of larval trunks and isolation of green fluorescent protein-expressing cells by FAC-sorting.
mcSCRB-seq (Bagnoli et al., 2018)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description Libraries were constructed using the mcSCRB-seq protocol (see Bagnoli et al., 2018)
Data processing Fastq reads were processed with the zUMIs pipeline version 0.2.0 (Parekh et al., 2018)
cDNA reads were aligned to the Zebrafish Genome (GRCZ11) with STAR_2.6.0a
Quantification was done with ENSEMBL gene model (GRCz11.94)
Genome_build: Zebrafish: GRCz11, Ensembl 94
Supplementary_files_format_and_content: cell (columns) and gene (rows) -wise UMI expression table
 
Submission date Jan 14, 2020
Last update date Mar 05, 2020
Contact name Hernán López-Schier
E-mail(s) hernan.lopez-schier@helmholtz-muenchen.de
Organization name Helmholtz Zentrum München
Department Research Unit Sensory Biology and Organogenesis
Street address Ingolstaedter Landstr. 1
City Neuherberg
ZIP/Postal code D-85764
Country Germany
 
Platform ID GPL18171
Series (1)
GSE143663 Epithelial planar bipolarity emerges from Notch- mediated asymmetric inhibition of Emx2
Relations
BioSample SAMN13855259
SRA SRX7556432

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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