Journal: Frontiers in Plant Science

Article Title: Construction of High-Quality Rice Ribosome Footprint Library

doi: 10.3389/fpls.2020.572237

Figure Lengend Snippet: Reaction mixture for end repair.

Article Snippet: For isolation of ribosome footprints, the RNA concentration of rice polysome extract is first adjusted to 400 ng μL −1 , and then 200 μL aliquot is digested with the Illumina TruSeq Ribo Profile Nuclease (0.5 U μg −1 RNA) for approximately 1.4 h in a dry bath (Thermo) that is set at 25°C with shaking speed of 600 rpm.

Techniques:

Journal: Frontiers in Plant Science

Article Title: Construction of High-Quality Rice Ribosome Footprint Library

doi: 10.3389/fpls.2020.572237

Figure Lengend Snippet: Reaction mixture for circularization.

Article Snippet: For isolation of ribosome footprints, the RNA concentration of rice polysome extract is first adjusted to 400 ng μL −1 , and then 200 μL aliquot is digested with the Illumina TruSeq Ribo Profile Nuclease (0.5 U μg −1 RNA) for approximately 1.4 h in a dry bath (Thermo) that is set at 25°C with shaking speed of 600 rpm.

Techniques:

Journal: Frontiers in Plant Science

Article Title: Construction of High-Quality Rice Ribosome Footprint Library

doi: 10.3389/fpls.2020.572237

Figure Lengend Snippet: PCR reaction mixture for library enrichment.

Article Snippet: For isolation of ribosome footprints, the RNA concentration of rice polysome extract is first adjusted to 400 ng μL −1 , and then 200 μL aliquot is digested with the Illumina TruSeq Ribo Profile Nuclease (0.5 U μg −1 RNA) for approximately 1.4 h in a dry bath (Thermo) that is set at 25°C with shaking speed of 600 rpm.

Techniques:

Journal: Frontiers in Plant Science

Article Title: Construction of High-Quality Rice Ribosome Footprint Library

doi: 10.3389/fpls.2020.572237

Figure Lengend Snippet: Percentage distribution of ribosome footprints on gene body in various rice ribosome footprint libraries. (A) Percentage distribution of ribosome footprints on exon, intron, 5’ UTR and 3’ UTR in the rice ribosome footprint libraries constructed with seedling shoots of “Nipponbare” (NB) under normal growth condition (0 h) and after 24-h salt stress treatment (24 h), respectively. (B) Percentage distribution of ribosome footprints on exon, intron, 5’ UTR and 3’ UTR in the rice ribosome footprint libraries constructed with seedling shoots of “Sea Rice 86” (SR86) under normal growth condition (0 h) and after 24-h salt stress treatment (24 h), respectively. “UTR” is short for “untranslated region”. “rep1”, “rep2” and “rep3” represent the three biological repeats. (C) Ribosome footprint coverage for LOC_Os03g36540 in the rice ribosome footprint libraries constructed with seedling shoots of NB and SR86 under normal growth condition (0 h) and after 24-h salt stress treatment (24 h), respectively. The gene model for LOC_Os03g36540 is provide at the bottom of ribo-seq panels, and the filled thinner rectangles, thicker rectangles and lines in blue represent UTR, exon and intron regions, respectively.

Article Snippet: For isolation of ribosome footprints, the RNA concentration of rice polysome extract is first adjusted to 400 ng μL −1 , and then 200 μL aliquot is digested with the Illumina TruSeq Ribo Profile Nuclease (0.5 U μg −1 RNA) for approximately 1.4 h in a dry bath (Thermo) that is set at 25°C with shaking speed of 600 rpm.

Techniques: Construct

Journal: Frontiers in Plant Science

Article Title: Construction of High-Quality Rice Ribosome Footprint Library

doi: 10.3389/fpls.2020.572237

Figure Lengend Snippet: Discordance of differentially expressed genes (DEGs) at transcription and translation levels in seedling shoots of “Nipponbare” (NB) under salt stress. (A) RNA-seq and ribo-seq coverage for a representative ( LOC_Os05g41800 ) of Group I DEGs (genes transcriptionally down-regulated but translationally up-regulated) in seedling shoots of NB under normal growth condition (0 h) and after 24-h salt stress treatment (24 h). (B) RNA-seq and ribo-seq coverage for a representative ( LOC_Os01g05470 ) of Group II DEGs (genes only translationally up-regulated) in seedling shoots of NB under normal growth condition (0 h) and after 24-h salt stress treatment (24 h). (C) RNA-seq and ribo-seq coverage for a representative ( LOC_Os01g01170 ) of Group III DEGs (genes only transcriptionally down-regulated) in seedling shoots of NB under normal growth condition (0 h) and after 24-h salt stress treatment (24 h). (D) RNA-seq and ribo-seq coverage for a representative ( LOC_Os01g01620 ) of Group IV DEGs (genes only transcriptionally up-regulated) in seedling shoots of NB under normal growth condition (0 h) and after 24-h salt stress treatment (24 h). (E) RNA-seq and ribo-seq coverage for a representative ( LOC_Os01g03730 ) of Group V DEGs (genes only translationally down-regulated) in seedling shoots of NB under normal growth condition (0 h) and after 24-h salt stress treatment (24 h). (F) RNA-seq and ribo-seq coverage for a representative ( LOC_Os10g35050 ) of Group VI DEGs (genes transcriptionally up-regulated but translationally down-regulated) in seedling shoots of NB under normal growth condition (0 h) and after 24-h salt stress treatment (24 h). The cutoff values for DEGs are fold change >= 1.5 and P -value <= 0.01. “RPM” is short for “reads per million”. The filled rectangles in gray and red, and the black lines in gene models that are provided at the bottom of ribo-seq panels represent untranslated regions (UTRs), exons and introns, respectively.

Article Snippet: For isolation of ribosome footprints, the RNA concentration of rice polysome extract is first adjusted to 400 ng μL −1 , and then 200 μL aliquot is digested with the Illumina TruSeq Ribo Profile Nuclease (0.5 U μg −1 RNA) for approximately 1.4 h in a dry bath (Thermo) that is set at 25°C with shaking speed of 600 rpm.

Techniques: RNA Sequencing

Journal: Frontiers in Plant Science

Article Title: Construction of High-Quality Rice Ribosome Footprint Library

doi: 10.3389/fpls.2020.572237

Figure Lengend Snippet: Novel open reading frames (ORFs) identified in rice genome. (A) A representative upstream ORF (uORF) that was located at the upstream region of annotated gene LOC_Os03g15040 . (B) A representative downstream ORF (dORF) that was located at the downstream region of annotated gene LOC_Os02g48130 . (C) A representative overlapped ORF (oORF) that was overlapped with the upstream region of annotated gene LOC_Os03g59740 . (D) A representative oORF that was overlapped with the downstream region of annotated gene LOC_Os04g01520 . (E) A representative small ORF (sORF) from 21PHAS_NO1572 , a previously reported long non-coding RNA that is located from 11,413,259 to 11,413,848 in rice chromosome 12 and can yield 21-nt phasiRNAs . The filled rectangles in gray, red, blue and purple, and the black lines in gene models that are provided at the bottom of ribo-seq panels represent untranslated regions (UTRs), exons, novel ORFs, overlapping regions between novel ORFs and annotated genes, and introns, respectively.

Article Snippet: For isolation of ribosome footprints, the RNA concentration of rice polysome extract is first adjusted to 400 ng μL −1 , and then 200 μL aliquot is digested with the Illumina TruSeq Ribo Profile Nuclease (0.5 U μg −1 RNA) for approximately 1.4 h in a dry bath (Thermo) that is set at 25°C with shaking speed of 600 rpm.

Techniques:

Journal: Frontiers in Plant Science

Article Title: Construction of High-Quality Rice Ribosome Footprint Library

doi: 10.3389/fpls.2020.572237

Figure Lengend Snippet: Hybridization mixture.

Article Snippet: For isolation of ribosome footprints, the RNA concentration of rice polysome extract is first adjusted to 400 ng μL −1 , and then 200 μL aliquot is digested with the Illumina TruSeq Ribo Profile Nuclease (0.5 U μg −1 RNA) for approximately 1.4 h in a dry bath (Thermo) that is set at 25°C with shaking speed of 600 rpm.

Techniques: Hybridization

Journal: Cell Reports

Article Title: Raptor-Mediated Proteasomal Degradation of Deamidated 4E-BP2 Regulates Postnatal Neuronal Translation and NF-κB Activity

doi: 10.1016/j.celrep.2019.11.023

Figure Lengend Snippet:

Article Snippet: Components of the Epicenter TruSeq Ribo Profile (Mammalian) Kit (Illumina, RPHRM12126), with some modifications, were used to generate sequencing libraries.

Techniques: Produced, Ubiquitin Proteomics, Reporter Assay, Western Blot, RNA Sequencing, Recombinant, Plasmid Preparation, Software, Imaging