之前已经学习完使用Seurat进行普通单细胞测序,现在希望将sgRNA信息匹配到细胞进行分析,目前正在寻找匹配办法。 现在记录下有关CROP-seq数据的降维和差异表达分析的大致流程。 1、利用已发表文章“《CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons》”的数据,在网站上下载...
data Contains the input matrices of the SSAE and the link to access the raw and preprocessed sequencing files of the CROP-seq library scripts Contains the scripts for the preprocessing of CROP-seq data, the preparation of SSAE input matrices, the execution of SSAE and the production of the ma...
AtGenExpress; Kilian et al., 2007) and next-generation sequencing-based profiling methods (e.g. RNA-Seq), which measure the abundance of thousands of transcripts in parallel. To date, over 100 publications have used microarrays to describe the transcriptomes of a total of 28 species exposed ...
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Using TruSeq stranded mRNA kit (Illumina), the 300 bp—400 bp heat fragmented RNA was reverse transcribed to create the first strand of cDNA with random hexamers and SuperScript™ II Reverse Transcriptase (Thermo Fisher Scientific) followed by second strand synthesis. The double-stranded cDNA ...
DNA yield and quality were checked by electrophoresis in 0.8% (w/v) agarose gels stained with GelRed and using a Qubit 3.0 fluorometer (Life Technologies, Grand Island, NY) prior to sequencing on an Illumina MiSeq platform at the genomics service of the Institute of Parasitology and ...
RNA-Seq data revealed alternative splicing; 9,875 genes (25.3%) encoded two or more isoforms, indicative of more functional variation than re- presented by the gene set alone. Overall, 87.9% of the gene models were supported by transcript and/or protein similarity with only 12.1% derived ...
RNAseq of wild-type and transgenic plants showed modulation in the expression of 71 genes associated with diverse aspects of growth, development, and mutually promoting increased biomass (Patel et al., 2019). 4.7. UV-B radiation Among all radiations faced by plants, UVB (280–320 nm) has ...
58. The PCR systems and conditions were consistent with Duan et al.58. Amplicon sequencing libraries were constructed using the MiSeq Reagent Kit v3 according to the manufacturer’s instructions. High-throughput paired-end sequencing was performed on the Illumina HiSeq 2500 platform (Illumina, San...
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