Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Sequencing for Transcriptomes Analysis for LAG-1 time course by auxin treatment.

ABSTRACT: Purpose: Ultilize Next Generation Sequencing to identify genes that are activated or repressed by LAG-1 (following auxin treatment to specifically deplete LAG-1 in C. elegans germline). The list of genes generated from RNA-seq identify primary and secondary targets of LAG-1 in C. elegans germline stem cells. Methods: RNA isolated from hand dissected C. elegans germline tumor (one day old adult animals) were used for RNA-seq library. Results: two genes (lst-1 and sygl-1) were identified as primary target for LAG-1 (2 hours auxin treatment); five additional genes are identified as secondary targets of LAG-1 based on their RNA accumulation depend on primary targets lst-1 and sygl-1 activity (4 hours auxin treatment). 94 genes are identified to be activated by LAG-1 (48 hours auxin treatment) from 4 biological replicates with the following criteria: gene counts per million greater than 2.0; fold of change greater than 2.0; false discovery rate (FDR) <0.05. Conclusions: lst-1 and sygl-1, two previously reported genes, are identified as primary transcriptional target for LAG-1 in C. elegans germline stem cells.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE144227 | GEO | 2020/02/17

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Next Generation Sequencing for Transcriptomes Analysis in GLP-1 Notch receptor ON and OFF genetic background

Project description:Purpose: Ultilize the Next Generation Sequencing to determine the genes that are activated or repressed by GLP-1 Notch receptor in C. elegans germline. The list of genes generated from RNA-seq were intersected with the LAG-1 germline ChIP-seq data to identify direct transcriptional targets of the GLP-1/LAG-1 transcriptional complex in C. elegans germline stem cells. Methods: RNA isolated from hand dissected C. elegans germline tumor (one day old adult animals) are used for RNA-seq library. Results: 94 genes were identified as activated by GLP-1 Notch receptor from 5 biological replicates with the following criteria: gene counts per million greater than 2.0; fold of change greater than 2.0; false discovery rate (FDR) <0.05. Conclusions: lst-1 and sygl-1, two previously reported genes, were identified as direct transcriptional target for GLP-1/LAG-1 in C. elegans germline stem cells.

2020-02-17 | GSE144229 | GEO

Genome-wide maps of chromatin state for LAG-1 in germline

Project description:We report the application of conventional ChIP-seq analysis for LAG-1 chromatin state in germline. We identified 137 genes putatively regulated by LAG-1 that's overlapped by three independent biological replicates. These genes included previously known targets lst-1, sygl-1, and mir-61/250.

2020-02-17 | GSE144223 | GEO

Genome-wide maps of chromatin state for LAG-1 in whole animals

Project description:We report the application of conventional ChIP-seq analysis for LAG-1 chromatin state in whole animals. We identified 76 genes putatively regulated by LAG-1 that's overlapped by two independent antibodies (FLAG ab and GFP ab). These genes including previously known targets lst-1, sygl-1, and mir-61/250, supporting the success of the assay.

2020-02-17 | GSE144225 | GEO

Regulation of germline gene expression in C. elegans germline stem cells.

Project description:ChIP-Seq study to understand regulation of germline stem cell gene expression by immunoprecipitation of stem-cell factor Notch and associated transcriptional cofactor LAG-1 in C. elegans.

2019-07-01 | GSE70426 | GEO

Using Auxin-inducible-degradation System to Interrogate Tissue-specific Transcriptional Programs of HSF-1 in Reproduction and Heat Shock Response. [Germline - Timecourse]

Project description:To understand the roles of HSF-1 and its regulation in reproduction and heat shock response in a tissue-specific manner, we coupled tissue-specific HSF-1 depletion in C. elegans by auxin-inducible degron (AID) with genome-wide transcriptional analyses in whole animals. We used ChIP-seq to analyze the occupancy of HSF-1 (tagged with AID::GFP) and RNA Pol II in young adult (YA) animals grown at 20°C or upon heat shock (HS) at 34°C for 30 min following an acute depletion of HSF-1 by AID for 2 hours either in the somatic or in the germline cells. Depletion by AID was performed by transferring worms expressing the E3 ligase TIR1 and carrying AID insertion to endogenous HSF-1 (JTL611 or JTL621) to NGM plates containing 1mM auxin (indole- 3-acetic acid, Sigma). The mock treatment was done by transferring worms to plates only containing the vehicle ethanol (EtOH). In parallel, we used RNA-seq to analyze the heat shock respnse upon depletion of HSF-1 in the soma or the germline for 2 hours. In addition, we also analyzed the transcriptomic changes by RNA-seq upon tissue-specific depletion of HSF-1 initiated at young adult stage for different length of time. In all RNA-seq analyses, we included the strains that only express TIR1 but do not have degron insertion at HSF-1 (CA1200 and CA1199) to control for the effects of auxin treatment and AID insertion into HSF-1.

2021-07-01 | GSE162066 | GEO

Using Auxin-inducible-degradation System to Interrogate Tissue-specific Transcriptional Programs of HSF-1 in Reproduction and Heat Shock Response. [HS response]

2021-07-01 | GSE162064 | GEO

Using Auxin-inducible-degradation System to Interrogate Tissue-specific Transcriptional Programs of HSF-1 in Reproduction and Heat Shock Response. [ChIP-Seq]

2021-07-01 | GSE162063 | GEO

Novel Peripheral Blood Allergen Stimulation Test for Non-IgE-mediated Gastrointestinal Food Allergies in Neonates and Infants.

Project description:The lymphocyte stimulation test (LST) helps with the diagnosis of non-IgE-mediated gastrointestinal food allergies. However, The LST requires large volumes of fresh peripheral blood and long culture times.The purpose of this study was to develop a novel LST. we obtained whole blood from patients with non-IgE-GI-FAs to cow’s milk and disease control children. And, we stimulated it with α-casein and Pmix, which is a mixture of four milk protein components (α-casein, κ-casein, α-lactalbumin, or β-lactoglobulin for 24 hours. Then we analyzed genome-wide gene expression using microarray and selected up- or down-regulated genes Nine putative marker genes, including those known to be involved in allergic inflammation, such as IL2RA, CCL17 and CISH were specific to patient group after stimulation with α-casein. On the other hand, 232 marker genes were specific to patient group after stimulation with Pmix.

2022-02-01 | GSE171660 | GEO

The impact of cold priming on the alerting phase of light and cold regulation of gene expression in Arabidopsis thaliana

Project description:We analysed the effect of a short 24 hours cold exposure (priming-stimulus) on gene regulation upon the first two hours of a second cold (4°C) stimulus (cold-triggering) and upon the first two hours of excess light exposure (800 µmol photons m-2 s-1, light triggering). The first and the second stress treatment was seperated by 5 days long lag-phase, which is long enough to reset most of the primary stress response. Several early light and early cold responsive genes showed however a altered transcript abundance in plants, which received five days befor the cold priming stimulus. Espicially JA responsive genes showed a common priming regulation within the cold and light exposure.

2021-06-25 | GSE162507 | GEO

Next Generation Sequencing for Transcriptomes Analysis for LAG-1 time course by auxin treatment.

Project description:Next Generation Sequencing for Transcriptomes Analysis for LAG-1 time course by auxin treatment.

| PRJNA603087 | ENA