|
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 |