Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of Arabidopsis replum cells at two development time points using cells obtained from laser capture microdissection of tape-transferred paraffin sections to promote recovery of structurally intact RNA

ABSTRACT: RNA prepared from specialized replum cells within siliques provided targets for profiling the Arabidopsis genome during replum cell development.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Coralie Lashbrook

PROVIDER: E-MEXP-1451 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Laser capture microdissection of plant cells from tape-transferred paraffin sections promotes recovery of structurally intact RNA for global gene profiling.

Cai Suqin S Lashbrook Coralie C CC

The Plant journal : for cell and molecular biology 20061004 4

Laser capture microdissection and related technologies permit the harvest of individual cells and cell types. Isolation of either nucleic acids or proteins from laser-captured cells supports such downstream applications as the construction of cell-specific cDNA libraries and the profiling of expressed genes and proteins. The success of these endeavors is dependent upon the yield, purity and structural integrity of the macromolecules derived from harvested cells. Here, we report protocols that pr ...[more]

PMID: 17026538

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Project description:Background A unique feature of fish is that new muscle fibres continue to be produced throughout much of the life cycle; a process termed muscle hyperplasia. In trout, this process begins in the late embryo stage and occurs in both a discrete, continuous layer at the surface of the primary myotome (stratified hyperplasia) and between existing muscle fibres throughout the myotome (mosaic hyperplasia). In post-larval stages, muscle hyperplasia is only of the mosaic type and persists until 40% of the maximum body length is reached. To characterise the genetic basis of myotube neoformation in trout, we combined laser capture microdissection and microarray analysis to compare the gene expression profile of hyperplastic areas of the late embryo myotome with that of adult myotomal muscle which displays only limited muscle hyperplasia. Results. Gene expression was analysed using Agilent trout oligo microarrays. Our analysis identified more than 6800 transcripts that were significantly up-regulated in the superficial hyperplastic zones of the late embryonic myotome compared to adult myotomal muscle. In addition to Pax3, Pax7 and the fundamental myogenic basic helix-loop-helix regulators, we identified a large set of up-regulated transcriptional factors, including Myc paralogs, members of Hes family and many homeobox-containing transcriptional regulators. Other cell-autonomous regulators overexpressed in hyperplastic zones included a large set of cell surface proteins belonging to the Ig superfamily. Among the secreted molecules found to be overexpressed in hyperplastic area, we noted growth factors as well as signalling molecules. A novel finding in our study is that many genes that regulate planar cell polarity (PCP) were overexpressed in superficial hyperplastic zones, suggesting that the PCP pathway is involved in the oriented elongation of the neofibres. Our microarray results were validated by in situ hybridisation of transcripts overexpressed in laser captured growth zones. Conclusion. The results obtained in this study provide a valuable resource for further analysis of novel genes potentially involved in hyperplastic muscle growth in fish. Ultimately, this study could yield insights into particular genes, pathways or cellular processes that may potentially regulate muscle regeneration in other vertebrates. To characterise the genetic basis of myotube neoformation in trout, we combined laser capture microdissection and microarray analysis to compare the gene expression profile of hyperplastic areas of the late embryo myotome (peripheral and deep domains) with that of adult myotomal muscle which displays only limited muscle hyperplasia.

Dataset Information

Transcription profiling of Arabidopsis replum cells at two development time points using cells obtained from laser capture microdissection of tape-transferred paraffin sections to promote recovery of structurally intact RNA

Publications

Laser capture microdissection of plant cells from tape-transferred paraffin sections promotes recovery of structurally intact RNA for global gene profiling.

Similar Datasets

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