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Chromatin Immunoprecipitation of TRA-1 in C. elegans and C. briggsae

ABSTRACT: The goal of this study is to identify and characterize sites in the C. elegans genome bound by the transcription factor TRA-1.

ORGANISM(S): Caenorhabditis elegans Caenorhabditis briggsae

PROVIDER: GSE48917 | GEO | 2013/11/04

SECONDARY ACCESSION(S): PRJNA212403

REPOSITORIES: GEO

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Chromatin Immunoprecipitation of TRA-1 in C. elegans and C. briggsae

Project description:The goal of this study is to identify and characterize sites in the C. elegans genome bound by the transcription factor TRA-1. TRA-1 ChIP-seq was performed in the following stages of animals in duplicate: 1) L2 stage of C. elegans wild-type N2 strain; 2) L3 stage of C. elegans wild-type N2 strain; 3) young adult stage of C. elegans glp-4(bn2) mutant; 4) young adult stage of C. elegans spe-11(hc77) mutant; 5) L3 stage of C. briggsae wild-type AF16 strain. As a negative control, TRA-1 ChIP-seq was also performed in C. elegans L3 stage with tra-1(e1834) homozygous and heterozygous mutation. Input DNA was also sequenced in each condition.

2013-11-04 | E-GEOD-48917 | biostudies-arrayexpress

Chromatin Immunoprecipitation of TRA-1 in C. elegans and C. briggsae

Project description:Chromatin Immunoprecipitation of TRA-1 in C. elegans and C. briggsae

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Tra-Dgr

Project description:Tra-Dgr Raw sequence reads

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Project description:This SuperSeries is composed of the following subset Series: GSE15233: C. briggsae developmental timecourse GSE15234: C. elegans developmental timecourse Refer to individual Series

2009-08-31 | E-GEOD-15551 | biostudies-arrayexpress

Chromatin immunoprecipitation of C. elegans intestine

Project description:For each experiment (as described in Pauli et al. 2006): Channel 1: whole worm lysate from strain SD1084 carrying transgene Pges-1::FLAG::PAB-1 Channel 2: mRNA immunoprecipitated from strain SD1084 carrying transgene Pges-1::FLAG::PAB-1 mRNA was amplified and hybridized to C. elegans DNA arrays from the Stuart Kim lab

2006-01-04 | E-SMDB-3592 | biostudies-arrayexpress

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Project description:Brachypodium sylvaticum Tra-1 Resequencing

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Transcriptome Analysis of Tra Catfish (Pangasianodon hypophthalmus) Early Development Provides Novel Insights for the Terrestrial Adaptation

Project description:Channel catfish (Ictalurus punctatus) and tra catfish (Pangasianodon hypophthalmus) both belong to the order Siluriformes. Channel catfish does not possess an air-breathing organ (ABO), and thus cannot breathe in the air, while tra catfish is a facultative air-breather and use the swim bladder as its air-breathing organ, which provides for aerial breathing in low oxygen conditions. Tra and channel catfish serve as a great comparative model for studying the transition of life from water to terrestrial living, as well as for understanding genes that are crucial for development of the swim bladder and the function of air-breathing in tra catfish. We selected seven developmental stages in tra catfish for RNA-Seq analysis based on their transition to a stage that could live at 0 ppm oxygen. More than 587 million sequencing clean reads were generated in tra catfish, and a total of 21, 448 unique genes were detected. A comparative genomic analysis was conducted between channel catfish and tra catfish. Gene expression analysis was performed for these tra catfish specific genes. Hypoxia challenge and microtomy experiments collectively suggested that there are critical timepoints for the development of the air-breathing function and swim bladder development stages in tra catfish. Key genes were identified to be the best candidates of genes related to the air-breathing ability in tra catfish. This study provides a large data resource for functional genomic studies in air-breathing function in tra catfish, and sheds light on the adaption of aquatic organisms to the terrestrial environment.

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Gene expression profile of TRA-1-60 population in FL cell line

Project description:Objective and goals: To find a clue for the mechanism of drug resistance in TRA-1-60 positive minor cell populations

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PRG-1 Immunoprecipitation in C. Elegans

Project description:Co-Immunoprecipitation of PRG1 in Caenorhabditis elegans.

2020-09-11 | PXD016838 | Pride

Genome-wide analysis of TRA (tissue restricted antigen)-specific co-expression groups in mouse medullary thymic epithelial cells (mTECs)

Project description:Analysis of gene co-expression patterns in TRA-specific medullary thymic epithelial cell (mTEC) subsets. The whole genome gene signatures of purified mTEC subsets respectively positive for the TRAs Gp2, Pdpn, Cea1, Gad1, Ins2, Tspan8 were compared to their corresponding TRA-negative mTEC subset control. Results provide the enriched and depleted gene expressions in the different subsets.

2015-10-28 | GSE69435 | GEO

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