Project description:We selected 11 tissues from sorghum reference genome line BTX623 for comparative study between Maize and sorghum. These 11 tissues were selected at different development stages at Cold Spring Harbor Laboratory upland farm, RNA were extracted, library was made and sequenced on HiSeq2500 PE125 platform at Woodbury Genome Center.
Project description:Maize and sorghum are both important crops with similar overall plant architectures, but they have key differences, especially in regard to their inflorescences. To better understand these two organisms at the molecular level, we compared the expression profiles of both protein-coding and non-coding transcripts in 11 matched tissues using single-molecule long-read and deep RNA sequencing. In this study, maize B73 line was planted at Cold Spring Harbor Laboratory upland farm, 11 tissues together with previously reported six tissues were collected, RNA was extracted, library was made and sequenced on the HiSeq 2500 PE125 platform at Woodbury Genome Center.
Project description:Pseudouridine is an isomer of uridine and is the most common RNA modification in both procaryotes and eucaryotes. It is found in ribosomal, transfer, and other structural RNA as well as in some mRNA and non-coding RNA. We have found abundant pseudouridine in small RNA and their precursors in Arabidopsis. This work was supported by the Howard Hughes Medical Institute and by grants from the National Institutes of Health (R35GM144206), the National Science Foundation Plant Genome Research Program and the Robertson Research Foundation (to R.A.M.). Work in the Kouzarides laboratory is supported by a grant from Cancer Research UK (grant no. RG96894), in addition to benefiting from core support from the Wellcome Trust (WT203144) and Cancer Research UK (grant no. C6946/A24843). V.M. was funded by a Kay Kendall Leukemia Fund project grant (grant no. RG88664) and Cancer Research UK (grant no. RG96894). J.D. was funded by a grant from the Polish National Science Center (2020/39/D/NZ1/01918). We acknowledge assistance from the Cold Spring Harbor Laboratory Shared Resources, which are funded in part by the Cancer Center support grant (5PP30CA045508)
Project description:To understand the role of GCN2 in stress response, the total transcript and translation state were compared between Arabidopsis thaliana wild type (ecotype Landsberg erecta) and gcn2 (Genetrap line GT8359, Cold Spring Harbor Laboratory) seedlings with or without herbicide chlorosufuron treatment RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels. We used Affymetrix ATH1 microarrays.
Project description:To understand the role of GCN2 in regulating translation, we compared the polysome loading state and overall transcript level between Arabidopsis thaliana wild type (ecotype Landsberg erecta) and gcn2 (Genetrap line GT8359, Cold Spring Harbor Laboratory) seedlings with or without herbicide chlorosufuron treatment RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels. We used Affymetrix ATH1 microarrays.
