ABSTRACT: The 3′-tag digital gene expression library construction and Illumina sequencing analysis of Wild Type and SPL-/- ovules with placenta Transcriptomes
Project description:To elucidate the molecular basis underlying early female reproductive development, Here, we used high-throughput tag-sequencing analysis to identify genes preferentially expressed in female meiocytes (FMs) by comparing gene expression profiles from wild type ovules undergoing megasporogenesis with those from the lacking megasporogenesis spl mutant ovules. A total of 862 genes were identified as FMs with levels that are consistently reduced in spl ovules in two biological replicates. Genes involved in biogenesis, metabolism, transporter activity and DNA binding were over-represented in female meiocytes, suggesting that female meiocytes are synthetically and metabolically more active. Total mRNA profiles of stage 10-11 old M-oM-,M-^Boral buds wild type (WT) and SPL-/- ovules with placenta were generated by deep sequencing, Repeat twice, using Illumina adaptor 2 (GEX adapter 2).
Project description:To elucidate the molecular basis underlying early female reproductive development, Here, we used high-throughput tag-sequencing analysis to identify genes preferentially expressed in female meiocytes (FMs) by comparing gene expression profiles from wild type ovules undergoing megasporogenesis with those from the lacking megasporogenesis spl mutant ovules. A total of 862 genes were identified as FMs with levels that are consistently reduced in spl ovules in two biological replicates. Genes involved in biogenesis, metabolism, transporter activity and DNA binding were over-represented in female meiocytes, suggesting that female meiocytes are synthetically and metabolically more active.
Project description:To understand regulation mechanism of miR163, transcriptomes of WT and mir163 mutant plants were dissected. Total RNAs from 7-day-old seedlings were isolated for library construction and analyzed by RNA-seq via Illumina HiSeq platform. Raw sequences were obtained from the Illumina Pipeline software Illumina bcl2fastq v2.17.1.14 and expected to generate 6 G per sample.
Project description:ATAC-seq of Col and hcr2 mutant from seedling and bud sample. Tagmentation was performed using the Tag DNA enzyme & buffer kit (Illumina, 20034210). Nextera DNA CD Index primers were used for library construction. The indexed libraries were subjected to paired-end 50-bp sequencing using an Illumina HiSeqX instrument (Microgen, Korea).
Project description:Total RNAs were extracted from the Testis and Epididymal Caput, Corpus and Cauda tissues of 2-month and 13-month-old WT and Gpx5 KO mice (C57BL/6). The 18 - 40 nt fraction small RNAs and transcriptomes were subjected to library construction and deep sequencing, using Illumina GAIIx or Hiseq 2000.
Project description:To understand the human placenta development, we investigated the features of two trophoblast models, trophoblast organoids and trophoblast stem cells, with the aim of identifying which type of trophoblast in vivo they most closely resemble. To this end, we profiled the transcriptomes from the two models by using the Truseq stranded mRNA library kit (Illumina).
Project description:Single-cell DNA methylation sequencing is a powerful method for elucidating important physiological and pathological processes, identifying cell subpopulations, and constructing epigenetic regulatory networks. Existing methylome analyses typically require substantial starting materials, complex operations, and high cost and are susceptible to contamination. These problems have impeded the development of single-cell methylome technology for rare cell profiling. In this work, we report Digital Microfluidics-based single-cell Reduced Representation Bisulfite Sequencing (Digital-scRRBS), the first microfluidics-based single-cell methylome library construction platform, which is an automatic, efficient, reproducible, and reagent-economy approach to dissect the single-cell methylome. Taking advantage of our uniquely designed digital microfluidic chip, we realized efficient single-cell isolation in less than 15 seconds. Furthermore, with the advantages of a confined environment, superhydrophobic surface, and nano-scale reaction volume of our digital microfluidic chip, more amplifiable DNA is retained for library construction compared to other approaches. We have successfully constructed single-cell methylation sequencing libraries with a unique genome mapping rate of up to 53.6%, covering up to 2.26 million CpG sites. The application of Digital-scRRBS allows us to discriminate cell identity and dynamically monitor DNA methylation levels during drug administration. Digital-scRRBS provides the technology for widespread application of single-cell methylation methods as a versatile tool for epigenetic analysis in rare cells and highly heterogeneous populations.
Project description:To understand regulation mechanism of IbTLD, transcriptomes of W38 and trangenic tobacco overexpressing IbTLD with/withouthydrogen peroxide were dissected. 12-day-old seedlings were treated with10 mM H2O2 for 6 hrs. Total RNAs were isolated for library construction and analyzed by RNA-seq via Solexa platform. Raw sequences were obtained from the Illumina Pipeline software bcl2fastq v2.0 and expected to generate 20M (million reads or Gb) per sample.
Project description:Genotype: FRT82B Method: Staged wild type wing imaginal discs were dissected and transferred to DPBS. The wing imaginal discs were dissociated in 0.25% Trypsin-EDTA solution at 37 ℃ for 10 min. Cells were then washed in DPBS and passed through 35μm filter before library preparation. Construction of 10x single cell libraries and sequencing on Illumina Hiseq platform were performed by Novogene.
Project description:Sequencing of 5' and 3'ends and RNA-seq of PROMPT and mRNA molecules from control and exosome-depleted cells. CAGE, 3'TAG and RNAseq library construction from RNA extracted from control and exosome-depleted cells.
