RiceTFtarget是一个基于基因共表达、模式匹配和机器学习的预测转录因子和靶基因互作关系的在线工具。RiceTFtarget 收集了149个无冗余的水稻RNA-seq数据构建了水稻转录因子-靶基因共表达模型。除此之外,通过FIMO将TF识别基序扫描水稻基因启动子序列,获得假定的转录因子结合位点(TFBS)。借助水稻转录因子ChIP-seq数据,利用提...
RiceTFtarget是一个基于基因共表达、模式匹配和机器学习的预测转录因子和靶基因互作关系的在线工具。RiceTFtarget 收集了149个无冗余的水稻RNA-seq数据构建了水稻转录因子-靶基因共表达模型。除此之外,通过FIMO将TF识别基序扫描水稻基因启动子序列,获得假定的转录因子结合位点(TFBS)。借助水稻转录因子ChIP-seq数据,利用提...
图1. 水稻DNA调控元件数据库RiceENCODE的框架结构 该数据库收集了包括ChIP-seq, ATAC-seq, MNase-seq, FAIRE-seq, BS-seq, RNA-seq, ncRNA-seq, Hi-C和ChIA-PET 等共计972套水稻高通量组学数据,通过标准化的数据处理流程,得到了多维度的高质量表观和三维基因组数据(参见图1)。 研究者构建了综合的数据库...
图1 水稻DNA调控元件数据库RiceENCODE的框架结构 该数据库收集了包括ChIP-seq, ATAC-seq, MNase-seq, FAIRE-seq, BS-seq, RNA-seq, ncRNA-seq, Hi-C和ChIA-PET 等共计972套水稻高通量组学数据,通过标准化的数据处理流程,得到多维度高质量表观和三维基因组数据。展示了水稻不同类型的染色质调控元件,立体地呈...
The rice whole genome breeding chip of the present invention is Rice60K, an SNP chip manufactured based on Infinium technique. Each chip can detect 24 samples simultaneously and contains 58,290 SNP sites. The marker sites have DNA sequences represented by SEQ ID NO.1-58290. The chip can ...
(Vegetative tissues, Callus, Stem, Leaf, Sheath and Panicle). Furthermore, mRNA-Seq expression data of four-leaf stage seedling shoots provided by global epigenetic and transcriptional experiment analysis [12] have also been imported into Rice-Map. These mRNA-Seq data were mapped to the genome ...
Bin Han and colleagues present a genome-wide association analysis of grain size and shape in cultivated rice and identify a major locus for grain size encoding the transcription factor OsSPL13. They find that the large-grain allele in tropical japonica c
2.转录组学:microRNA芯片、LncRNA芯片、表达谱芯片、RNA-seq3.蛋白质组学:2D-DIGE、SILAC、iTRAQ、TMT、Label-free、MRM4.基因检测:DNA/RNA提取、RT-PCR、Real-timePCR5.蛋白质检测:Western blot、Co-ip EMSA、CHIP、免疫荧光、ELISA6.病理检测:HE染色、特殊染色、组织切片、免疫组化、流式细胞分选7.代谢组...
Model-based analysis of ChIP–Seq (MACS). Genome Biol. 9, R137 (2008). Article PubMed PubMed Central Google Scholar Zhao, Q., Huang, X. H., Lin, Z. X. & Han, B. SEG-Map: a novel software for genotype calling and genetic map construction from next-generation sequencing. Rice ...
Quality of total RNA of gall and control samples was verified with an RNA 6000 p chip (Agilent technologies) and concentrations were measured with a Quant-it Ribogreen RNA assay (Life technologies). Three hundred fifty ng of RNA was used with the Small RNA seq library prep for Illumina (...