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Transcript Profiling of Soybean Seed Compartments Using Laser Capture Microdissection Coupled With RNA-Seq

ABSTRACT: We used laser capture microdissection (LCM) to capture soybean seed compartments and profiled the transcriptomes of several compartments using next-generation sequencing. We profiled the transcriptomes of the embryo-proper and the suspensor region from globular stage embryos and the seed coat parenchyma layer of early maturation stage seeds using the Illumina GAIIx system. Illumina sequencing of transcripts from laser-captured embryo proper and suspensor of globular stage embryo and seed coat parenchyma layer of the early maturation stage seed.

ORGANISM(S): Glycine max

SUBMITTER: Brandon Le

PROVIDER: E-GEOD-29162 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcript Profiling of Soybean Seed Compartments Using Laser Capture Microdissection Coupled With RNA-Seq

Project description:We used laser capture microdissection (LCM) to capture soybean seed compartments and profiled the transcriptomes of several compartments using next-generation sequencing. We profiled the transcriptomes of the embryo-proper and the suspensor region from globular stage embryos and the seed coat parenchyma layer of early maturation stage seeds using the Illumina GAIIx system.

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Project description:Seeds are comprised of three major parts of distinct parental origin: the seed coat, embryo, and endosperm. The maternally-derived seed coat is important for nurturing and protecting the seeds during development. By contrast, the embryo and the endosperm are derived from a double fertilization event, where one sperm fertilizes the egg to form the diploid zygote and the other sperm fertilizes the central cell to form the triploid endosperm. Each seed part undergoes distinct developmental programs during seed development. What methylation changes occur in the different seed parts, if any, remains unknown. To uncover the possible role of DNA methylation in different parts of the seed, we characterized the methylome of three major parts of cotyledon stage seeds, the seed coat, embryonic cotyledons, and embryonic axis, using Illumina sequencing. Illumina sequencing of bisulfite-converted genomic DNA from three parts of soybean cotyledon stage seeds: seed coat (COT-SC), embryonic cotyledons (COT-COT), and embryonic axis (COT-AX).

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