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Title: Transcriptome-wide profiling of Spadetail-regulated genes in early somite progenitors      
dateReleased:
06-27-2016
description:
We integrate zebrafish embryology with photoactivatable caged morpholinos (cMO), the photoactivatable lineage tracer caged fluorescein-dextran (cFD), fluorescence-activated cell-sorting (FACS) and RNA sequencing (RNA-seq) to identify Spadetail-regulated genes in mesodermal cells enriched for early somite progenitors. 1 to 4-cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hours post-fertilization (hpf). Early ventral somite progenitors were then optically targeted with ultraviolet (360 nm) light using a 100-μm diameter circular diaphragm. Embryos were permitted to develop until 9 hpf, dechorionated, and dissociated into single-cells. Fluorescein-positive cells were then isolated by FACS. Five experimental replicates were performed. Sequencing libraries were then prepared from purified cells according to the CEL-Seq protocol (Hashimshony, T et al. Cell Reports. 2012). In short, total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL-seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-70623
refinement:
raw
alternateIdentifiers:
70623
keywords:
functional genomics
dateModified:
07-03-2016
availability:
available
types:
gene expression
name:
Danio rerio
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-70623/E-GEOD-70623.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-70623/E-GEOD-70623.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70623
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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