Once the workflow has completed, you can now use the gene count table as an input intoDESeq2for statistical analysis using the R-programming language. It is highly reccomended to useRStudiowhen writing R code and generating R-related analyses. You can downloadRStudiofor your system here:...
. Effective detection of variation in single-cell transcriptomes using MATQ-seq. Nat Methods, 2017, 14:267-270. [3] Imdahl F, Vafadarnejad E, Homberger C, Saliba AE, Vogel J. Single-cell RNA-sequencing reports growth-conditionspecific global transcriptomes of individual bacteria. Nat ...
Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J, Levin JZ, Livny J, Earl AM, Gevers D, Ward DV, et al .: Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biol 2012, 13: r23....
Seq or miRNA data set — from bacteria to human— against a reference genome, and then offers extensive RNA-Seq data analysis tools to explore your results in-depth. Perform statistical analyses of differential gene expression using EdgeR or DESeq2, view Gene Set Enrichment Analysis (GSEA) ...
However, RNA-Seq is increasingly being used to study the transcriptomes of bacteria growing in animal hosts and/or as part of complex bacterial communities. Samples isolated from animal models are often contaminated with a large amount of host RNA. In RNA derived from microbial communities, ...
FASTA) │ │ └── raw_data/ <- Location of input RNAseq data │ │ └── output/ <- Data generated during processing steps │ ├── 01.fastqc/ <- Main alignment files for each sample │ ├── 02.trim/ <- Log from running STAR alignment step │ ├── 03.sortrRNA/ <- ...
RNA degradation is an essential process that allows bacteria to control gene expression and adapt to various environmental conditions. It is usually initiated by endoribonucleases (endoRNases), which produce intermediate fragments that are subsequently d
Fig. 2: Validation of smRandom-seq using reference bacteria samples. aScatter plot of UMI counts per cell barcode in the mixture.E. colinumber: 202.B. subtilisnumber: 45. Mixed cell number: 4.bSpecies specificity of UMI in the mixture.E. colinumber: 202.B. subtilisnumber: 45. Data in...
Cell最新发表了来自美国Broad研究所的一项研究,报道了一种高度可扩展的细菌单细胞RNA-seq技术——BacDrop,可对数百万个细菌细胞或数百个样本进行大规模分析,捕获bulk RNA-seq无法检测到的细菌细胞状态。作者用该技术在转录层面揭示了单菌株细菌的群落内异质性,并鉴定出群落中具有抗生素抗性和持留性表型的细菌亚群。该技...
Cell最新发表了来自美国Broad研究所的一项研究,报道了一种高度可扩展的细菌单细胞RNA-seq技术——BacDrop,可对数百万个细菌细胞或数百个样本进行大规模分析,捕获bulk RNA-seq无法检测到的细菌细胞状态。作者用该技术在转录层面揭示了单菌株细菌的群落内异质性,并鉴定出群落中具有抗生素抗性和持留性表型的细菌亚群。该技...