Journal: PLOS ONE

Article Title: Ryegrass mottle virus complete genome determination and development of infectious cDNA by combining two methods– 3′ RACE and RNA-Seq

doi: 10.1371/journal.pone.0287278

Figure Lengend Snippet: T7 – T7 polymerase promoter; blue marking represents the 3’ UTR novel sequence identified by 3’ RACE; orange marking represents the 5’ UTRs novel sequence identified by HTS RNA-Seq.

Article Snippet: Hybridization of the fragmented RNA (100 ng) was performed using a barcode from the Xpress RNA-Seq Barcode 1–16 Kit (Thermo Fisher Scientific, Waltham, MA, USA), Ion Adaptor Mix, and Hybridization Solution from the Ion Total RNA-Seq Kit (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s protocol.

Techniques: Sequencing, RNA Sequencing Assay

Journal: bioRxiv

Article Title: Rice embryogenic trigger BABY BOOM1 promotes somatic embryogenesis by upregulation of auxin biosynthesis genes

doi: 10.1101/2020.08.24.265025

Figure Lengend Snippet: Changes in global gene expression in rice plants on Os BBM1-GR induction. A, RNA-sequencing analysis showing number of genes up regulated on induction of Os BBM1-GR with DEX alone or in the presence of CYC. B, A Venn diagram showing the down regulated transcripts by Os BBM1-GR in rice leaves. The numbers are genes deregulated by Os BBM1-GR under each treatment (Log 2 fold >1 and FDR < 0.05). C and D, RT-qPCR validation of some of the genes regulated by Os BBM1. C, Genes from up regulated category are Os04g45810 , a homeobox leucine zipper transcription factor, Os05g32350 , a zinc finger containing protein, Os04g55620 , a receptor kinase, Os08g37390 , a cyclin and Os02g53430 , a DNA-3-methyladenine glycosylase. D, From the down regulated category, the genes are Os05g10690 is a MYB domain transcription factor, Os02g07820 a DUF581 domain containing protein and Os05g03610 is phospholipase C protein. The log 2 fold change is calculated after normalization with mock and respective wild-type treatments. Error bars represent SEM, calculated from two independent biological replicates, each done in triplicates. DEX and CYC treatments were done for 6 h (see Materials and Methods). DEX, dexamethasone and CYC, cycloheximide.

Article Snippet: Libraries were prepared from two biological replicates for each sample with 80 ng of input RNA, using NuGEN Ovation RNA-seq Systems 1-16 following manufacturer instructions.

Techniques: Expressing, RNA Sequencing Assay, Quantitative RT-PCR