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Series GSE132304 Query DataSets for GSE132304
Status Public on Aug 21, 2019
Title Tissue-specific transcriptomes reveal gene expression trajectories in two maturing skin epithelial layers in zebrafish embryos
Organism Danio rerio
Experiment type Expression profiling by high throughput sequencing
Summary We purified (FACS) and profiled (RNA-Seq) zebrafish embryo skin cells vs. nonskin cells at three early developmental stages. At two of the stages, we further purified and profiled two distinct epithelial layers of the skin: the periderm and basal cells. Our comprehensive expression analysis provides the first reported transcriptomes of these two cell types, reveals gene expression dynamics in space and time, and identifies common and distinct features of epithelial maturation in the two layers. Given the conserved nature of skin development, we believe our study to be of interest to those studying skin in other vertebrates.
Overall design At each of 20 SS, 52 hpf, and 72 hpf, we used krt4:dsRed transgenic zebrafish embryos and FACS to prepare and run two RNA-Seq conditions: all skin vs. nonskin1, with two replicates for each condition. At each of 52 hpf and 72 hpf, we used krt4:dsRed;krt5:GFP transenic zebrafish embryos and FACS to prepare and run three RNA-Seq conditions: periderm vs. basal cells vs. nonskin2, with two replicates for each condition, except 52 hpf nonskin2 has only one replicate.
Web link
Contributor(s) Cokus SJ, Wang F, Sagasti A
Citation(s) 31431477
NIH grant(s)
Grant ID Grant title Affiliation Name
R21 EY024400 The morphogenesis of actin-based structures in mucosal epithelia UNIVERSITY OF CALIFORNIA LOS ANGELES Alvaro Sagasti
R01 GM122901 Cytoskeletal control of microridge morphogenesis on mucosal epithelial cells of the zebrafish skin UNIVERSITY OF CALIFORNIA LOS ANGELES Alvaro Sagasti
R01 AR064582 Peripheral Territory Establishment By Zebrafish Somatosensory Neurons UNIVERSITY OF CALIFORNIA LOS ANGELES Alvaro Sagasti
Submission date Jun 06, 2019
Last update date Aug 24, 2019
Contact name Shawn J. Cokus
Organization name UCLA
Street address UCLA, 3000 Terasaki Life Sciences Building, 610 Charles Young Drive East
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
Platforms (2)
GPL14875 Illumina HiSeq 2000 (Danio rerio)
GPL18413 Illumina HiSeq 2500 (Danio rerio)
Samples (23)
GSM3855890 20 SS, nonskin1, replicate A
GSM3855891 20 SS, nonskin1, replicate B
GSM3855892 20 SS, all skin, replicate A
BioProject PRJNA547573
SRA SRP200656

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE132304_RAW.tar 6.9 Gb (http)(custom) TAR (of TAR)
GSE132304_ZFishSkin-MASTER-WORKBOOK-20190605.xlsx 251.9 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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