Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Identification of Peopod2 (PPD2) target genes through GSyellow-based ChIP-seq in Arabidopsis thaliana PSB-D cell cultures.

ABSTRACT: Genome-wide target genes of PPD2 were identified through ChIP-seq on Arabidopsis cell cultures. For ChIP-seq, PPD2 was fused to the GSyellow TAP tag and expressed from the 35S promoter. The p35S:PPD2-GSyellow construct was transformed into Arabidopsis thaliana PSB-D cell culture. ChIP was performed using anti-GFP antibody (abcam290).

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Plant Systems Biology data submission

PROVIDER: E-MTAB-6513 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

GS<sup>yellow</sup>, a Multifaceted Tag for Functional Protein Analysis in Monocot and Dicot Plants.

Besbrugge Nienke N Van Leene Jelle J Eeckhout Dominique D Cannoot Bernard B Kulkarni Shubhada R SR De Winne Nancy N Persiau Geert G Van De Slijke Eveline E Bontinck Michiel M Aesaert Stijn S Impens Francis F Gevaert Kris K Van Damme Daniel D Van Lijsebettens Mieke M Inzé Dirk D Vandepoele Klaas K Nelissen Hilde H De Jaeger Geert G

Plant physiology 20180420 2

The ability to tag proteins has boosted the emergence of generic molecular methods for protein functional analysis. Fluorescent protein tags are used to visualize protein localization, and affinity tags enable the mapping of molecular interactions by, for example, tandem affinity purification or chromatin immunoprecipitation. To apply these widely used molecular techniques on a single transgenic plant line, we developed a multifunctional tandem affinity purification tag, named GS<sup>yellow</sup ...[more]

PMID: 29678859

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Project description:Background & Aims: The metastatic process is complex and remains a major obstacle in the management of colorectal cancer (CRC). To gain a better insight into the biologic events driving the metastatic process we investigated genomic aberrations in a large cohort of matched CRC primaries and distant metastases from various sites. Methods: In total, 62 primary colorectal cancers, 62 matched normal specimens, and 68 matched metastases (from liver, lung, ovary, omentum, and distant lymph nodes) were analyzed by high resolution array comparative genomic hybridization (array CGH) for DNA copy number changes. Findings were validated using a publicly available dataset consisting of 21 primary tumors and matched liver metastases. Fluorescence in situ hybridization (FISH) was used to confirm some of the DNA copy number changes observed. Results: Overall patterns of DNA copy number aberrations were highly similar between primary tumors and their metastases, confirming clonality. Additional copy number aberrations in metastasis are rare and rather than recurrent they were sporadic for individual patients. The only recurrent differences between primary tumors and their metastases were two chromosomal regions, 6q21 and 8q24.21 encompassing the MYC oncogene, that coamplified in three metastases of two patients (3.2%). FISH analysis confirmed the high level co-amplification in the metastasis, which were not detected in their primary tumors. Conclusions: Primary CRC and their metastases show highly similar patterns of DNA copy number changes, additional copy number aberrations in metastasis are rare and recurrences exceptional. These observations are consistent with the hypothesis that the metastatic potential is predestined early in the development of the primary tumor. In total, 62 primary colorectal cancers, 62 matched normal specimens, and 68 matched metastases (liver, lung, ovarian, omentum and distant lymph nodes) were analyzed by high resolution array comparative genomic hybridization (array CGH).

Dataset Information

Identification of Peopod2 (PPD2) target genes through GSyellow-based ChIP-seq in Arabidopsis thaliana PSB-D cell cultures.

Publications

GS<sup>yellow</sup>, a Multifaceted Tag for Functional Protein Analysis in Monocot and Dicot Plants.

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