Project description:Viral siRNA generated from antiviral RNA silencing machinery was profiled using small RNA sequencing from Phalaenopsis orchid mixed infected with CymMV and ORSV
Project description:Proteomics data from a combind transcriptome/proteome study of three sexually deceptive orchids of the genus Ophrys. Data are from labella of mature, unpollinated flowers of (1) Ophrys exaltata subsp. archipelagi, (2) O. sphegodes, and (3) O. garganica. Proteomics data were searched against SwissProt and TAIR databases and further against organism-specific databases obtained from transcriptome sequencing (454, Sanger ESTs and Solexa data). Thirteen trypsinised gel slices per sample were subjected to electrospray ionisation-based LC-MS/MS analysis with a 2D linear ion trap Finnigan LTQ (Thermo Electron Corporation) equipped with an Ultimate Nano HPLC System (Dionex Corporation). Mass spectra were searched against SwissProt and Arabidopsis TAIR9 protein databases to identify peptides. Additionally, spectra were searched against protein databases created from the Ophrys reference transcriptome obtained in this study. Stringent criteria were used for the assignment of spectra to peptides (95% peptide identification probability) in Scaffold 3.3 (Proteome Software Inc., USA). In order to maximise the utility of proteomics data for uncovering proteins predicted by the orchid transcriptome, a minimum of one unique peptide was used for protein identification, while using two different stringency levels for the probabilistic assignment of peptides to proteins (99% for highest quality, HQ; 90% to maximise protein discovery, PD, in the absence of a fully sequenced genome). Concerning the sequencing and transcriptomics results: Three normalised cDNA libraries were constructed from three different Ophrys species, O. exaltata, O. garganica, and O. sphegodes. These libraries were 454 pyrosequenced and all the high quality reads generated in this study are available in the Sequence Read Archive (SRA) of the National Centre for Biotechnology Information (NCBI) with the accession number SRA060767. Additional sequencing of O. sphegodes flower labella yielded 1.7 Mbp of Sanger (dbEST library LIBEST_028084; dbEST IDs 77978749-77979571; GenBank accessions JZ163765-JZ164587) and 2.5 Gbp of Illumina Solexa (SRA060767) data.
Project description:We investigated the biological effects of ZEA exposure on donkey granulosa cells by using RNA-seq analysis. ZEA at 10 and 30 μM were administered to granulosa cells within 72 hours of in vitro culture. ZEA at 10 μM significantly altered the tumorigenesis associated genes in donkey granulosa cells. Exposure to 10 and 30 μM ZEA treatment significantly reduced mRNA expression of PTEN, TGFβ, ATM, and CDK2 genes, particularly, the ZEA treatment significantly increased the expression of PI3K and AKT genes. Furthermore, immunofluorescence, RT-qPCR, and Western blot analysis verified the gene expression of ZEA-exposed granulosa cells. Collectively, these results demonstrated the deleterious effect of ZEA exposure on the induction of ovarian cancer related genes via the PTEN/PI3K/AKT signaling pathway in donkey granulosa cells in vitro.
Project description:We performed four small RNA sequencing for identification and characterization of microRNAs in Phalaenopsis aphrodite subsp. formosana. By comparing the low temperature-treated group with treated group, we concluded four miRNAs - miR156, miR162, miR528 and miR535 - as low temperature-induced miRNAs. In addition, tissue-specific expression of these miRNAs was investigated. The files contain the miRNAs analysis results in each group. Examination of low temperature-treated leaves and two other organs of Phalaenopsis orchid
