About ZebrafishCircaDB

Circadian clocks regulate several biochemical processes in different body tissues in living animals (e.g., sleep-wake cycle, blood pressure, body temperature, etc.). The role of malfunctioning circadian rhythm for a variety of diseases (e.g. Porphyria) is actively being investigated. We, at the Circadian Clocks Center, are interested in uncovering novel mechanisms of circadian oscillations in zebrafish. Our research focuses on the collection, measurements and investigation of experimental observations (e.g. RNASeq, microarray data) to assess rhythmicity in the zebrafish genome.

Our datasets are continuously being expanded to understand the rhythmicity in different zebrafish tissue types (e.g. ovary, liver, brain, testes). We have collected experimental time course data for a variety of zebrafish lines (WT, Per2 knockout, etc.). We are also interested in applying bioinformatics utilities (e.g. MetaCycle) to bring novel insights by highlighting the role of marker genes in regulating the circadian clocks.

Data type	Dataset
Zebrafish miRNA (WT)	miRNA differential expression
Zebrafish lncRNA (WT)	LncRNA differential expression
Zebrafish mRNA (WT)	mRNA differential expression
Zebrafish miRNA (MT, Per2 knockout)	miRNA differential expression
Zebrafish lncRNA (MT, Per2 knockout)	LncRNA differential expression
Zebrafish mRNA (MT, Per2 knockout)	mRNA differential expression
Zebrafish miRNA (MT, Per1b knockout)	miRNA differential expression
Zebrafish lncRNA (MT, Per1b knockout)	LncRNA differential expression
Zebrafish mRNA (MT, Per1b knockout)	mRNA differential expression

Zebrafish Circadian Clocks Datasets

Data type	Dataset	Remarks
Zebrafish melanocytes 48 hour Li 2017	GSE37332	Li et al., PLoS Comput Biol, 2013
Zebrafish Liver 48 hour Boyle 2017	GSE87659	Boyle et al., PLoS One, 2017
WT and Per2 Knockout Count	LncRNA_exp	LncRNA identify
Zebrafish WT vs Per2 knockout 120hpf	WT-CT0-120h--Per2-CT0-120hpf.	LncRNA differential expression
Zebrafish WT vs Per2 knockout 124hpf	WT-CT4-124h--Per2-CT4-124hpf	LncRNA differential expression
Zebrafish WT vs Per2 knockout 128hpf	WT-CT8-128h--Per2-CT8-128hpf	LncRNA differential expression
Zebrafish WT vs Per2 knockout 132hpf	WT-CT12-132h--Per2-CT12-132hpf	LncRNA differential expression
Zebrafish WT vs Per2 knockout 136hpf	WT-CT16-136h--Per2-CT16-136hpf	LncRNA differential expression
Zebrafish WT vs Per2 knockout 140hpf	WT-CT20-140h--Per2-CT20-140hpf	LncRNA differential expression
Zebrafish Per2 knockout : CT0 vs CT4	Per2-CT0-120hpf--Per2-CT4-124hpf	LncRNA differential expression
Zebrafish Per2 knockout : CT0 vs CT8	Per2-CT0-120hpf--Per2-CT8-128hpf	LncRNA differential expression
Zebrafish Per2 knockout : CT0 vs CT12	Per2-CT0-120hpf--Per2-CT12-132hpf	LncRNA differential expression
Zebrafish Per2 knockout : CT0 vs CT16	Per2-CT0-120hpf--Per2-CT16-136hpf	LncRNA differential expression
Zebrafish Per2 knockout : CT0 vs CT20	Per2-CT0-120hpf--Per2-CT20-140hpf	LncRNA differential expression