Project description:In this study, we use DNA affinity purification sequencing to identiy genome-wide binding of LFY transcription factor, a master regulator of flower development in Arabidopsis. We generated two sets of data, one using genomic DNA from plant tissue, thus retain DNA methylation, as probe for DNA affinity purification (DAP-seq dataset), and the other using PCR amplified genomic DNA (without DNA methylation; AmpDAP-seq dataset).
Project description:In this study, we performed deep sequencing and bioinformatics analyses of tea plant leaves to identify and characterize known and novel miRNAs. A total of 26,876,261 raw reads were produced from 2 libraries. We detected 422 known miRNAs belonging to 125 families, and 68 putative novel miRNAs.
Project description:The role of on-CG methylation in seed development and dormancy remains unknown. There are four genes in charge of non-CG methylation in Arabidopsis: drm1, drm2, cmt2 and cmt3. The majority of non-CG methylation in vegetative tissues, leaf, is gone in homozygous ddcc mutant line (Hume et al., 2014). To uncover the possible role of non-CG DNA methylation in seed development and dormancy, we characterized the methylome of ddcc mutant in Arabidopsis dry seed using Illumina sequencing. Meanwhile, vegetative tissue, leaves from 3 week plant with ddcc mutant and from wild type, and dry seed from wild type plant were used as control. Illumina sequencing of bisulfite-converted genomic DNA from dry seed and 3-week-plant leaves of ddcc mutant and wild type.
Project description:Solexa sequencing technology was used to perform high throughput sequencing of the small RNA library from the cold treatment of tea leaves. Subsequently, aligning these sequencing date with plant known miRNAs, we characterized 112 C. sinensis conserved miRNAs. In addition, 215 potential candidate miRNAs were found; among them, 131 candidates with star sequence were chosen as novel miRNAs. There are both congruously and differently regulated miRNAs, and line-specific miRNAs were identified by microarray-based hybridization in response to cold stress. The miRNA chip included 3228 miRNA probes corresponding to miRNA transcripts listed in Sanger miRBase release 19.0 and 283 novel miRNAs probes founding in tea plant. In the study presented here, two tea plant cultivars, ‘Yingshuang’ (YS, a cold-tolerant tea plant cultivar) and ‘Baiye 1’ (BY, a cold-sensitive tea plant cultivar), were kept at 4°C for 4,12, 24 h, respectively, and 28°C for as control. These samples were used to acquire expression profiles of a total of 3,511 unique genes, leading to the successful construction of supervised
Project description:Solexa sequencing technology was used to perform high throughput sequencing of the small RNA library from the cold treatment of tea leaves. Subsequently, aligning these sequencing date with plant known miRNAs, we characterized 112 C. sinensis conserved miRNAs. In addition, 215 potential candidate miRNAs were found; among them, 131 candidates with star sequence were chosen as novel miRNAs. There are both congruously and differently regulated miRNAs, and line-specific miRNAs were identified by microarray-based hybridization in response to cold stress. The miRNA chip included 3228 miRNA probes corresponding to miRNA transcripts listed in Sanger miRBase release 19.0 and 283 novel miRNAs probes founding in tea plant.
Project description:Genome-Wide Screening of Genomic Alterations and Transcriptional Modulation in Non-Smoking Female Lung Cancer in Taiwan Sixty-one pairs of cancer and normal lung tissue specimens from non-smoking females were collected at National Taiwan University Hospital and Taichung Veterans General Hospital. The selection criteria of clinical specimens depend on pathology report, physical examination and cigarette-smoking history. Surgical lung tissue specimens were immediately snap-frozen in liquid N2 and stored at -80 °C. Surgical specimens would be further processed for RNA and DNA extraction. Only those samples passed quality controls were processed for gene expression profiling analysis and single nucleotide polymorphism (SNP) analysis respectively.
