Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-Seq of Drosophila tim promoter/enhancer mutants around the clock

ABSTRACT: RNA-Seq of Drosophila tim promoter/enhancer mutants around the clock

PROVIDER: PRJNA1080522 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

RNA-Seq of Drosophila tim promoter/enhancer mutants around the clock

Project description:The contribution of cis-regulatory elements to Drosophila circadian gene expression is poorly understood. We generated a series of CRISPR-mediated deletions within the regulatory regions of the circadian gene timeless (tim) and characterized them through multiple high-throughput sequencing experiments. We isolated heads from wild-type and mutant flies around the clock and performed RNA-Seq on them to determine the effects of regulatory element deletions on circadian gene expression.

2024-02-28 | GSE259245 | GEO

ChIP-Seq of V5-Clk in wildtype and tim promoter mutant Drosophila heads around the clock

Project description:To address the contribution of transcriptional regulation to Drosophila clock gene expression and to behavior, we generated a series of CRISPR-mediated deletions within two regions of the circadian gene timeless (tim), an intronic E box region and an upstream E box region that are both recognized by the key transcription factor Clock (Clk) and its heterodimeric partner Cycle. The upstream deletions but not an intronic deletion dramatically impact tim expression in fly heads; the biggest upstream deletion reduces peak RNA levels and tim RNA cycling amplitude to about 15% of normal, and there are similar effects on tim protein (TIM). The cycling amplitude of other clock genes is also strongly reduced, in these cases due to increases in trough levels. To examine the effect of promoter E-box deletions on Clk binding, we performed Clk-ChIP around the clock in wild-type and 126 mutant flies.

2024-02-28 | GSE259247 | GEO

ChIP-Seq of V5-Clk in wildtype and tim promoter mutant Drosophila heads around the clock

Project description:ChIP-Seq of V5-Clk in wildtype and tim promoter mutant Drosophila heads around the clock

| PRJNA1080521 | ENA

A transcriptomic taxonomy of Drosophila circadian neurons around the clock

Project description:A transcriptomic taxonomy of Drosophila circadian neurons around the clock

| PRJNA661535 | ENA

Oscillating and stable promoter-enhancer loops underlie core- and clock-controlled gene expression rhythms in mouse liver

Project description:The circadian clock dynamically rewires promoter-enhancer loops in tissues to drive robust daily rhythms in gene transcription and locomoter activity.

2020-12-18 | GSE139195 | GEO

Circadian gene expression profile of pancreatic islets from C57BL6 mice fed on rodent chow diet collected at 4hr intervals around the clock

Project description:Comparison of pancreatic islet transcriptome at 4hr intervals around the clock helps to identify genes that are cycling under the control of the circadian clock. We used Agilent microarrays to analyze pancreatic islet transcriptome at different time points across the circadian cycle.

2016-09-01 | GSE80692 | GEO

CLOCKWORK ORANGE promotes CLOCK-CYCLE activation via the Drosophila ortholog of CLOCK INTERACING PROTEIN, CIRCADIAN (ChIP-Seq)

Project description:CWO reinforces PER-TIM repression of core clock gene transcription by antagonizing CLK-CYC binding to E-boxes, but also functions to promote CLK-CYC transcription of core clock genes. To determine the relationship between CWO and CLK-CYC binding across the genome, we identified CWO and CLK binding sites via ChIP-seq.

2021-07-23 | GSE165042 | GEO

Proteome analysis of Arabidopsis thaliana circadian clock mutants

Project description:The circadian clock is comprised of proteins that form negative feedback loops, which regulate the timing of global gene expression in a coordinated 24 hour cycle. As a result, the plant circadian clock is responsible for regulating numerous physiological processes central to growth and survival. To date, most plant circadian clock studies have relied on diurnal transcriptome changes to elucidate molecular connections between the circadian clock and observable phenotypes in wild-type plants. Here, we have combined high-throughput RNA-sequencing and mass spectrometry to comparatively characterize the lhycca1, prr7prr9, gi and toc1 circadian clock mutant rosette transcriptome and proteome at the end-of-day and end-of-night.

2018-01-02 | PXD004763 | Pride

microRNA expression in Tim-3 knockdown RAW264.7 cell

Project description:RAW264.7 cell was stably transfected with Tim-3 siRNA(SI) or negative control(NC) and were analyzed for microRNA expression Differerently expressed microRNA in Tim-3 knockdown RAW264.7 cells were summarized and were used for further analysis RAW264.7 cells stably transfected with Tim-3 siRNA(SI) or negative control(NC) and were used to collect microRNA without any other treatment

2016-01-14 | E-GEOD-76839 | biostudies-arrayexpress

A transcriptomic taxonomy of Drosophila circadian neurons around the clock

Project description:Many different functions are regulated by circadian rhythms, including those orchestrated by discrete clock neurons within animal brains. To comprehensively characterize and assign cell identity to the 75 pairs of Drosophila circadian neurons, we optimized a single cell RNA sequencing method and assayed clock neuron gene expression at different times of day. The data identify at least 17 clock neuron categories with striking spatial regulation of gene expression. Transcription factor regulation is prominent and likely contributes to the robust circadian oscillation of many transcripts, including those that encode cell-surface proteins previously shown to be important for cell recognition and synapse formation during development. The many other clock-regulated genes also constitute an important resource for future mechanistic and functional studies between clock neurons and/or for temporal signaling to circuits elsewhere in the fly brain.

2021-01-12 | GSE157504 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data