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107 results for “RNA features”

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zenodo40/100

RNAProt: An efficient and feature-rich RNA binding protein binding site predictor

RNAProt Supplementary Data Archive, containing benchmark and training datasets (see content.txt for more details on included datasets)

opencc-by-4.0Mar 2021View details →

zenodo32/100

Atypical molecular features of RNA silencing against the phloem-restricted polerovirus TuYV

The dataset contains all the original raw files sorted by figure and figure panel. NGS data has been deposited on GEO (GSE176378). The content of each file is the following:   FIGURE 1: -1A: Northern blots raw TIFF image files for the detection of TuYVs81 RNA on membrane HMW7 and methylene blue staining of the same membrane. -1B: Pictures of Col-0, ago1-57, ago1-27 and ago1-38 infected with TuYVs81 WT and -P0. -1C: Axiozoom pictures of TuMV-GFP AS9 infected plants of Col-0, ago2-1, ago1-57 (sup149.1) and ago2-1/ago1-57. Both raw czi and jpg files are provided. Additional pictures for each genotype are also provided. -1D: Western blot (W579) and Coomassie staining raw image files for the detection of GFP from TuMV-AS9-GFP infected plants. -1E&G: Northern blots raw film scan for the detection of TuYVs81 RNA and TRV-PDS RNS on membrane HMW24 and HMW25 respectively. Methylene blue staining of the same membrane. Total RNA quantification and input volumes on gel (spreadsheet). -1F&H: -1I: Signal quantification of HMW24/25 using imageJ (spreadsheet). -1J: Northern blots raw film scan and TIFF images/raw phoshphoimager .gel files for the detection of TuYVs81 RNA 3’, 5’, TuYV siRNA, mir159 and U6 probe on membrane PPM70. For the detection of PDS, mir408 and U6 on membrane PPM71 Pictures of Col-0, ago2-1, ago1-57 (sup149.1) and ago2-1/ago1-57 infected with TuYVs81 WT and TRV-PDS at 20dpi. Total RNA quantification and input volumes on gel (spreadsheet). -1K: Shortstack quantification of normalized reads per category (see legend). Original bargraph and html document retracing the analysis steps. -1L: Distribution of TuYVs81-derived sRNA reads (20-nt to 25-nt) along the TuYVs81 genome in Col-0 total RNA (library JBT5) and AGO1 IP replicate 1 (library JBT13), with MISIS. Output files from MISIS and final .png image of the distribution.   FIGURE 2: -2A&C: Kinetic of systemic TuYVs81 and TuMV-GFP WT infection in Col-0, ago1-57, ago1-27 and ago1-38 represented as the cumulated percentage of infected plants in the inoculated population. Raw spreadsheet with day to day counting. Original graphs. -2B: Northern blots raw TIFF image files for the detection of TuYVs81 RNA on membrane HMW22 and methylene blue staining of the same membrane. -2D: Western blot (W555) and Coomassie staining raw image files for the detection of GFP from TuMV-GFP infected plants. -2E: qPCR data for the quantification of TuYV RNA in inoculated leaves of Col-0, ago1-27 and ago1-57. 2F: Western blot (W779) and Coomassie staining raw image files for the detection of RT viral proteins from TuYVs81 inoculated leaves. 2G: Western blot (W626-W629) and Coomassie staining raw image files for the detection of CFP-AGO1 and P0-myc in N. benthamiana leaves. Northern blot raw TIFF image files for the detection of P0 CABYV, P0 BMYV and P0 PLRV on membrane HMW28 and methylene blue staining of the same membrane. Protein sequence of the P0 constructs used. 2H&I: DAS-ELISA result and fresh weight of Col-0 and ago1-57 plants infected via aphids with WT TuYV.   FIGURE 3: -3A: Northern blots TIFF images/raw phoshphoimager .gel files for the detection of TuYVs81 RNA 3’, TuYV siRNA, siR255, IR71, siR1003 and U6 probe on membrane PPM102. Total RNA quantification and input volumes on gel (spreadsheet). -3B: Pictures of Col-0, dcl2-1, dcl4-2, ago1-57, dcl2-1/dcl4-2, dcl2-5/dcl3-1, dcl2-1/ago1-57, dcl4-2/ago1-57, dcl2-1/dcl4-2/ago1-57 infected with TuYVs81 WT at 16dpi. -3C: qPCR data for the quantification of TuYV RNA in TuYVs81 infected Col-0, dcl2-1, dcl4-2, ago1-57, dcl2-1/dcl4-2, dcl2-5/dcl3-1, dcl2-1/ago1-57, dcl4-2/ago1-57, dcl2-1/dcl4-2/ago1-57 leaves. -3D: All raw .lif files and Fiji processed TIFF microscopy images of B2-GFP expressing N. benthamiana plants infiltrated with tRFP, DCL2-tRFP and DCL4-tRFP are in the folder Figure S5 (related to this panel)   FIGURE 4: 4A: qPCR data for the quantification of TuYV RNA in TuYVs81 infected leaves and vasculature of Col-0 and dcl2-1 at 17dpi. 4B: Northern blots TIFF images/raw phoshphoimager .gel files for the detection of TuYVs81 RNA 3’, TuYV siRNA, siR255, IR71, miR822, miR168, miR162 and U6 probe on membrane PPM90. Total RNA quantification and input volumes on gel (spreadsheet). 4C: Western blot and Coomassie staining raw image files for the detection of DCL1 (W746) and the RT viral protein (W721) from TuYVs81 infected leaves and vasculatures. 4D: qPCR data for the quantification of DCL2 and DCL4 RNA in whole leaves and vasculatures of TuYVs81 infected Col-0 and dcl2-1 plants. 4E: Northern blots TIFF images/raw phoshphoimager .gel files for the detection of PDS, TRV 3’UTR and U6 (PPM96) and TRV 3’UTR (HMW38) in leaf and vasculature of plants infected with TRV-PDS. Total RNA quantification and input volumes on gel (spreadsheet). 4F: qPCR data for the quantification of TuYV RNA in TuYVs81 WT and P0- infected leaves and vasculature of Col-0 plants. Raw Ct and calculation spreadsheet are with Figure 4A. 4G: Northern blots TIFF images/raw phoshphoimager .gel files for the detection of TuYV RNA 3’, TuYV siRNA and U6 (PPM102) in leaf and vasculature of Col-0 and dcl2-1 plants infected withTuYVs81 WT or P0-. Total RNA quantification and input volumes on gel (spreadsheet).   FIGURE 5: -5A: qPCR data for the quantification of TuYV RNA in whole leaves and vasculatures of TuYVs81 infected Col-0 and ago1-57 plants. -5B: Western blot and Coomassie staining raw image files for the detection of AGO1 (W758) and AGO2(W759) from TuYVs81 infected leaves and vasculatures. -5C: AGO1 signal quantification across five biological replicates in Mock and TuYVs81 infected leaves and vasculatures. -5D&E: All raw .lif files and Fiji processed TIFF microscopy images of B2-GFP expressing N. benthamiana plants infiltrated with tRFP-AGO1 and P0-tRFP are in the folder Figure S8 (related to this panel). -5F: qPCR data for the quantification of AGO1 and AGO2 RNA in TuYVs81 infected leaves and vasculature of Col-0 and ago1-57 plants. Raw Ct and calculation spreadsheet are with Figure 5A. -5G: Western blot and Coomassie staining raw image files for the detection of AGO1 and RT viral protein (W809) and AGO2 (W810) from TuYVs81 WT and TuYVs81 P0- infected leaves and vasculatures. -5H: Pictures of SUC-SUL (SS, parental), SS/pCoYMV:P0-HA WT (CWSS6-3) and SS/pCoYMV-P0-HA LP1 (CLSS6-3) adult plants. -5I: Western blot and Coomassie staining raw image files for the detection of AGO1 and P0-HA (W723) from SUC-SUL (SS), SS/pCoYMV:P0-HA WT (CWSS6-3) and SS/pCoYMV-P0-HA LP1 (CLSS6-3) leaves and vasculatures. -5J: Northern blots TIFF images/raw phoshphoimager .gel files for the detection of SUL siRNA, miR160c, miR160*, miR168, miR159 and U6 (PPM89) in leaf and vasculature from SUC-SUL (SS), SS/pCoYMV:P0-HA WT (CWSS6-3) and SS/pCoYMV-P0-HA LP1 (CLSS6-3) plants. Total RNA quantification and input volumes on gel (spreadsheet). -5K: qPCR data for the quantification of CHLI1, CHLI2 and AGO1 RNA in leaves and vasculature of SUC-SUL (SS), SS/pCoYMV:P0-HA WT (CWSS6-3) and SS/pCoYMV-P0-HA LP1 (CLSS6-3) plants. -5L: Raw heatmap of all AGO1 IP libraries (DESeq2). Top 20 most deregulated loci.   FIGURE S1: S1A: qPCR data for the quantification of TuYV RNA in whole leaves of TuYVs81 infected Col-0 and different ago single and combination mutants. S1B: Western blot and Coomassie staining raw image files for the detection of AGO1 and AGO2 (W603) from Col-0, ago2-1, ago1-57 and ago2-1/ago1-57 infected with TuYVs81 WT and TRV-PDS S1C: Northern blots raw TIFF image files for the detection of TuYV RNA 3’, TuYV siRNA, s81 insert siRNA, miR403, miR408, miR159 and U6 on membrane PPM60 (AGO1 IP) and PPM62 (AGO2 IP). Total RNA quantification and input volumes on gel (spreadsheet). S1D: Western blot and Coomassie staining raw image files for the detection of AGO1 (W537) and AGO2 (W538) from Col-0, ago1-57, ago1-27 infected with TuYVs81 WT. S1E: Northern blots TIFF images/raw phoshphoimager .gel files for the detection of SUL siRNA, miR408, miR159 and U6 (PPM93) in AGO1 and AGO2 IPs from Col-0, SUC-SUL (SS), SS/ago1-57 rosette leaves. Total RNA quantification and input volumes on gel (spreadsheet). S1F: Western blot and Coomassie staining raw image files for the detection of AGO1 and AGO2 (W766) from Col-0, SUC-SUL (SS), SS/ago1-57 rosette leaves before and after AGO1 and AGO2 IP.   FIGURE S2: S2A: Total RNA quantification of TuYVs81 infected Col-0 and ago1-57 plant pools (#1 and #2) used for sRNA deepseq. Powerpoint presentation of all plant pool used, WB results and bioanalyzer profile of the total RNA. Spreadsheet with sequencing and mapping statistic for all 16 JBT libraries. S2B: Western blot and Coomassie staining raw image files for the detection of AGO1 (W398-W402) before and after AGO1 IP for sRNA deepseq samples. S2C: See figure 1K. Original bargraphs for 21-nt, 22-nt and 24-nt mapped reads in all JBT libraries. S2D: Distribution of TuYVs81-derived sRNA reads (20-nt to 25-nt) along the TuYVs81 genome in Col-0 total RNA (libraries JBT5 and JBT6), ago1-57 total RNA (libraries JBT7 and JBT8), Col-0 AGO1 IP (libraries JBT13 and JBT14) and ago1-57 AGO1 IP (libraries JBT15 and JBT16),  with MISIS. Output files from MISIS and final .png image of the distribution. S2E: TuYVs81 nucleotide composition % (spreadsheet) and 5’ nucleotide frequency of the vsiRNA reads mapped to the TuYVs81 genome in JBT5, JBT7, JBT13 and JBT15 (.png). 5’ graphs were generated using MISIS.   FIGURE S3: S3A: Kinetic of systemic TuYVs81, TuMV-GFP and TRV-PDS infection in Col-0 and ago1-57, represented as the cumulated percentage of infected plants in the inoculated population. Raw spreadsheet with day to day counting. Original graphs. S3B: qPCR data for the quantification of TuYV RNA in inoculated leaves of Col-0, ago1-27 and ago1-57. Biological replicate to the experiment in Figure 2E.   FIGURE S4: S4A: Leaf pictures of Col-0, dcl2-1, dcl4-2, dcl2-1/dcl4-2, rdr6-12, sgs3-14 infected with TuYVs81 WT at 17dpi. Leaves are from two different individuals. S4B: Northern blots raw TIFF images and scans files for the detection of TuYVs81 RNA 3’ siRNA and U6 in Col-0, ago1-57, dcl2-1, dcl4-2, dcl2-1/dcl4-2, rdr6-12, sgs3-14 infected with TuYVs81 WT on membrane PPM39. Total RNA quantification and input volumes on gel (spreadsheet). S4C: Northern blots raw TIFF images files for the detection of TuYVs81 RNA 3’ in Col-0, ago1-57, dcl2-1, rdr6-12, sgs3-14 infected with TuYVs81 WT on membrane HMW8. Methylene blue stain of the membrane. Total RNA quantification and input volumes on gel (spreadsheet) with figure S4B. S4D: Kinetic of systemic TuYVs81 infection in Col-0, ago1-57, dcl2-1, dcl4-2, dcl2-1/dcl4-2, rdr6-12, sgs3-14 represented as the cumulated percentage of infected plants in the inoculated population. Raw spreadsheet with day to day counting. Original graphs.   FIGURE S5: All raw .lif files and Fiji processed TIFF microscopy images of B2-GFP expressing N. benthamiana plants infiltrated with tRFP, DCL2-tRFP and DCL4-tRFP. Note that more images are available that those in the manuscript.   FIGURE S6: S6A: qPCR data for the quantification of TuYV RNA in whole leaves and vasculatures of TuYVs81 infected Col-0. S6B: See Figure 4B S6C: qPCR data for the quantification of DCL2 and DCL4 RNA in whole leaves and vasculatures of TuYVs81 infected Col-0 plants.   FIGURE S7: S7A: qPCR data for the quantification of TuYV RNA in vasculatures and protoplast cells of TuYVs81 infected Col-0. S7B: Western blot and Coomassie staining raw image files for the detection of AGO1 and RT viral protein (W283), AGO2 and AGO4 (W328) in vasculatures and protoplast cells of TuYVs81 infected Col-0 and ago1-57. S7C: Northern blots raw TIFF images for the detection of miR168 and U6 on membrane PPM47 in vasculatures and protoplast cells of TuYVs81 infected Col-0. Total RNA quantification and input volumes on gel (spreadsheet). S7D: qPCR data for the quantification of TuYV and AGO1 RNA in mock and TuYVs81 infected leaves of Col-0, ago1-57, pSUC:Flag-AGO1 #1 (ASWW1b3) and #2 (ASWW2b1). S7E: qPCR data for the quantification of AGO1 RNA in TuYVs81 WT and P0- infected leaves and vasculature of Col-0 and dcl2-1 plants. S7F: Western blot and Coomassie staining raw image files for the detection of AGO1 and RT viral protein (W708) in whole leaves of TuYVs81 infected Col-0, ago1-57, pSUC:Flag-AGO1 #1 (ASWW1b3) and #2 (ASWW2b1). S7G: qPCR data for the quantification of Flag-AGO1 RNA in mock and TuYVs81 infected leaves of Col-0, pSUC:Flag-AGO1 #1 (ASWW1b3) and #2 (ASWW2b1).   FIGURE S8: S8A: All raw .lif files and Fiji processed TIFF microscopy images of B2-GFP expressing N. benthamiana plants infiltrated with tRFP-AGO1. Note that more images are available that those in the manuscript. S8B: All raw .lif files and Fiji processed TIFF microscopy images of B2-GFP expressing N. benthamiana plants infiltrated with P0-tRFP. Note that more images are available that those in the manuscript.   FIGURE S9: S9A: Pictures of 11-day old seedlings grown on MS media: Col-0, SUC-SUL (SS), SS/pSuc:P15-FHA, SS/pCoYMV:P0-HA WT (CWSS6-3) and SS/pCoYMV:P0-HA LP1 (CLSS6-3). S9B: qPCR data for the quantification of P0-HA and AGO1 RNA in seedlings of Col-0, SUC-SUL (SS), SS/pSuc:P15-FHA, SS/pCoYMV:P0-HA WT (CWSS6-3) and SS/pCoYMV:P0-HA LP1 (CLSS6-3).   FIGURE S10: S10A: Raw heatmap of all AGO1 Total RNA libraries (DESeq2). Top 18 most deregulated loci. S10B: MA plot of AGO1 IP in Col-0 TuYV vs. AGO1 IP in Col-0 mock (DESeq2). MA plot of AGO1 IP in ago1-57 TuYV vs. AGO1 IP in ago1-57 mock (DESeq2). S10C: Northern blots raw TIFF images/raw phoshphoimager .gel files for the detection of SUL3’ siRNA, TuYV 3’ siRNA and U6 on membrane PPM64 (Col-0, ago1-57, dcl2-1, dcl4-2, dcl2/4 infected with TuYVs81 and Col-0 plus ago1-57 infected with aphid transmitted TuYV WT) and PPM68 (Col-0, ago1-57, rdr6-12, sgs3-14, dcl2/4 infected with TuYVs81 as well as Col-0 and ago1-57 infected with TuMV-GFP). Total RNA quantification and input volumes on gel (spreadsheet).

opencc-by-4.0Aug 2021View details →

dryad28/100

Data from: Global pairwise RNA interaction landscapes reveal core features of protein recognition

RNA–protein interactions permeate biology. Transcription, translation, and splicing all hinge on the recognition of structured RNA elements by RNA-binding proteins. Models of RNA–protein interactions are generally limited to short linear motifs and structures because of the vast sequence sampling required to access longer elements. Here, we develop an integrated approach that calculates global pairwise interaction scores from in vitro selection and high-throughput sequencing. We examine four RNA-binding proteins of phage, viral, and human origin. Our approach reveals regulatory motifs, discriminates between regulated and non-regulated RNAs within their native genomic context, and correctly predicts the consequence of mutational events on binding activity. We design binding elements that improve binding activity in cells and infer mutational pathways that reveal permissive versus disruptive evolutionary trajectories between regulated motifs. These coupling landscapes are broadly applicable for the discovery and characterization of protein–RNA recognition at single nucleotide resolution.

opencc-zeroDec 2017View details →

dryad28/100

Data from: Global pairwise RNA interaction landscapes reveal core features of protein recognition

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Dataset results

RNAProt: An efficient and feature-rich RNA binding protein binding site predictor

Atypical molecular features of RNA silencing against the phloem-restricted polerovirus TuYV

Data from: Global pairwise RNA interaction landscapes reveal core features of protein recognition

Data from: Global pairwise RNA interaction landscapes reveal core features of protein recognition

Single-cell RNA sequencing reveals molecular features of postnatal maturation in the murine retinal pigment epithelium

Single-cell RNA sequencing reveals distinct transcriptional features of the purinergic signaling in mouse trigeminal ganglion

Epigenomic and transcriptomic features induced by silencing of ZNF280C in colon cancer cells and knock-out of Zfp280c in mice [RNA-Seq]

Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome

Gene-environment interaction elicits dystonia-like features and impaired translational regulation in a DYT-TOR1A mouse model (RNA-Seq)

Single-cell RNA sequencing reveals T and B cell-related immune features in foot and mouth disease virus-infected mice

The role of Vitamin C and TET dioxygenases in genome-wide features of regulatory T cells [RNA-seq]

Single Cell Analysis Identifies Conserved Features of Immune Dysfunction in Simulated Microgravity and Spaceflight [RNA-Seq]

LARP6 promotes carcinogenic features of triple negative breast cancer cell line by directly modulating alternative splicing of associated genes [RNA-Seq]

Integrated multi-omics analysis identifies features that predict human pluripotent stem cell-derived progenitor differentiation to cardiomyocytes [RNA-Seq]

RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history

Investigation of the metabolic features of cancer therapy induced senescent cells with TPEF, mass spectrometry and RNA sequencing analysis

DNA methylation features of LUSC in promoter and enhancer region [RNA-seq]

Self-organized cerebral organoids with human specific features predict effective drugs to combat Zika virus infection [RNA-seq]

High-throughput mapping of single-neuron projection and molecular features by retrograde barcoded labelling [bulk RNA-seq]

A robust and practical myogenic cell system to explore cellular and genomic features of muscle differentiation [RNA-Seq]

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