Dataset Information

The genome of the seagrass Zostera marina

ABSTRACT: This dataset contains the transcriptome sequence of Zostera marina as produced by Illumina sequencing. Four tissues were sequenced, female flower in late and early stages of development, the male flower, the root and leaf tissue. Full transcriptome sequencing of four tissues, including female flower at two time points in development

ORGANISM(S): Zostera Marina

TISSUE(S): Male Flower Tissue, Female Flower Tissue, Late Flower Development, Leaf Tissue, Root Tissue, Female Flower Tissue, Early Flower Development

SUBMITTER: Janina Brakel Thorsten Reusch Till Bayer Jeanine L Olsen Yves Van de Peer

PROVIDER: E-GEOD-67579 | ArrayExpress | 2016-01-16

SECONDARY ACCESSION(S): GSE67579SRP056873PRJNA280336

REPOSITORIES: GEO, ArrayExpress, ENA

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Dataset's files

Source:

			Action	DRS
	E-GEOD-67579.additional.1.zip	Other
	E-GEOD-67579.idf.txt	Idf
	E-GEOD-67579.sdrf.txt	Txt

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Project description:This experiment contains the RNA-Seq samples only. Formalin-fixed, paraffin-embedded (FFPE) tissues are an invaluable resource for clinical research. However, nucleic acids extracted from FFPE tissues are fragmented and chemically modified making them challenging to use in molecular studies. We analysed 23 fresh-frozen (FF), 35 FFPE and 38 paired FF/FFPE specimens, representing six different human tissue types (bladder, prostate and colon carcinoma; liver and colon normal tissue; reactive tonsil) in order to examine the potential use of FFPE samples in next-generation sequencing (NGS) based retrospective and prospective clinical studies. Two methods for DNA and three methods for RNA extraction from FFPE tissues were compared and were found to affect nucleic acid quantity and quality. DNA and RNA from selected FFPE and paired FF/FFPE specimens were used for exome and transcriptome analysis. Preparations of DNA Exome-Seq libraries was more challenging (29.5 % success) than that of RNA-Seq libraries, presumably because of modifications to FFPE tissue-derived DNA. Libraries could still be prepared from RNA isolated from two-decade old FFPE tissues. Data were analysed using the CLC Bio Genomics Workbench and revealed systematic differences between FF and FFPE tissue-derived nucleic acid libraries. In spite of this, pairwise analysis of DNA Exome-Seq data showed concordance for 70-80 % of variants in FF and FFPE samples stored for fewer than three years. RNA-Seq data showed high correlation of expression profiles in FF/FFPE pairs (Pearson Correlations of 0.90 +/- 0.05), irrespective of storage time (up to 244 months) and tissue type. A common set of 1,494 genes was identified with expression profiles that were significantly different between paired FF and FFPE samples irrespective of tissue type. Our results are promising and suggest that NGS can be used to study FFPE specimens in both prospective and retrospective archive-based studies in which FF specimens are not available.

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The genome of the seagrass Zostera marina

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