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Ribosome Tunnel Environment Drives the Formation of α-helix During Co-Translational Folding
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Figure 6 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes
Figure 6. Cladogram showing the evolution of Opalinata* based on the proposed evolution of morphological traits (white circles; Delvinquier and Patterson 1993) and the characteristics of the rRNA genes (green circles). The relationships within Proteromonadida are not clear and are represented as a polytomy. Evolutionary steps are as follows. (1) Uninucleated cells develop cytoplasmic membranes with ridges or folds supported by a cortical cytoskeleton; few flagella* with a transitional helix in its structure; rRNA with secondary structure and GC content similar to that of outgroup taxons (i.e. Blastocystis). (2) Multiple flagella covering the cell surface; marginal falx. (3) Insertions made of short tandem repeats (STRs) in the expansion regions of rRNA; low GC in rRNA insertions and ITS1–ITS2 regions. (4) Binucleated (occasionally four-nucleated) cells. (5) Increase in number and length of rRNA insertions; very low GC content in rRNA insertions and ITS1–ITS2 regions. (6) Axial falx. (7) Multinucleate cells. (8) Partial loss of kineties. The position of Hegneriella* if valid* cannot be determined with available data.
FIGURE 9 in Phylogenetic analysis of the Prionini (Coleoptera: Cerambycidae: Prioninae) from China based on mitochondrial ribosomal RNA genes and Cytochrome oxidase I gene
FIGURE 9. Phylogeny of the Chinese Prionini based on combined sequences of 12S rRNA, 16S rRNA and COI (excluding Priotyrannus closteroides). A: Bootstrap 50% majority-rule consensus tree of distance method by PAUP* with bootstrap values (%), Wtd. S.S. = 0.0245, APSD = 3.011, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; B: Bootstrap 50% majority-rule consensus tree of maximum likelihood method by PAUP* with bootstrap values (%), -Ln likelihood =8113.8589, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; C: Bootstrap 50% majority-rule consensus tree of parsimony method by PAUP* with bootstrap values (%), tree length = 1415, CI = 0.6919, RI =0.3344, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; D: Bayesian tree by MrBayes with Bayesian posterior probabilities (%), the scale bar in the bottom left corner of the tree meaning 0.1 nucleotide substitutions per site.
FIGURE 5 in Phylogenetic analysis of the Prionini (Coleoptera: Cerambycidae: Prioninae) from China based on mitochondrial ribosomal RNA genes and Cytochrome oxidase I gene
FIGURE 5. Phylogeny of the Chinese Prionini based on partial sequences of COI. A: Bootstrap 50% majority-rule consensus tree of distance method by PAUP* with bootstrap values (%), Wtd. S.S. = 0.0455, APSD = 4.103, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; B: Bootstrap 50% majority-rule consensus tree of maximum likelihood method by PAUP* with bootstrap values (%), -Ln likelihood = 3935.3320, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; C: Bootstrap 50% majority-rule consensus tree of parsimony method by PAUP* with bootstrap values (%), tree length =726, CI = 0.6364, RI = 0.2941, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; D: Bayesian tree by MrBayes with Bayesian posterior probabilities (%), the scale bar in the bottom left corner of the tree meaning 0.1 nucleotide substitutions per site.
FIGURE 8 in Phylogenetic analysis of the Prionini (Coleoptera: Cerambycidae: Prioninae) from China based on mitochondrial ribosomal RNA genes and Cytochrome oxidase I gene
FIGURE 8. Phylogeny of the Chinese Prionini based on combined sequences of 12S rRNA, 16S rRNA and COI. A: Bootstrap 50% majority-rule consensus tree of distance method by PAUP* with bootstrap values (%), Wtd. S.S. = 0.0496, APSD = 3.764, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; B: Bootstrap 50% majority-rule consensus tree of maximum likelihood method by PAUP* with bootstrap values (%), -Ln likelihood = 8567.6164, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; C: Bootstrap 50% majority-rule consensus tree of parsimony method by PAUP* with bootstrap values (%), tree length = 1518, CI = 0.6726, RI = 0.3329, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; D: Bayesian tree by MrBayes with Bayesian posterior probabilities (%), the scale bar in the bottom left corner of the tree meaning 0.1 nucleotide substitutions per site.
FIGURE 4 in Identification and molecular phylogeny of agriculturally important spider mites (Acari: Tetranychidae) based on mitochondrial and nuclear ribosomal DNA sequences, with an emphasis on Tetranychus
FIGURE 4. ML tree based on ITS1 sequences. Sequence data for the ITS1 was aligned from a total of 23 individuals from nine species. The outgroups Neoseiulus swirskii and Typhlodromus pyri (GenBank nos. EU310505 and FM179376, respectively) were used to root the ITS1 tree. Numbers on the branches indicate the percentage bootstrap values (>50) based on NJ bootstrapping with ML settings (1,000 replicates).
FIGURE 3 in Identification and molecular phylogeny of agriculturally important spider mites (Acari: Tetranychidae) based on mitochondrial and nuclear ribosomal DNA sequences, with an emphasis on Tetranychus
FIGURE 3. Neighbor-joining (NJ) tree (a) and maximum likelihood (ML) tree (b) based on COI sequences. Twentythree of the COI sequences were obtained from the nine Chinese tetranychid species analyzed in this study. In addition, thirteen acarine COI sequences were obtained from the GenBank: the COI sequence (GenBank nos. DQ789590 and AY320029) from Brevipalpus obovatus and Cenopalpus pulcher were used as outgroups; the other COI sequences Tetranychus truncatus, T. turkestani, T. piercei, T. neocaledonicus, Panonychus citri, Pa. ulmi, Pa. mori, Amphitetranychus viennensis, A. quercivorus, Petrobia harti and P. tunisiae (GenBank nos. AB257317, AJ316604, AB257314, X80859, AB041252, AB041253, AB041256, X99875, X99873, EU487121 and EU487119 respectively) from GenBank also included into our phylogenetic analysis. Numbers adjacent to branches show the bootstrap values (> 50%) of 1000 replicates.
RNA G-quadruplex(rG4) exacerbates cellular senescence by mediating ribosome pausing [Ribo-seq]
GEO Series GSE255110. Homo sapiens. 6 samples. Type: Other.
Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome - Phalo
GEO Series GSE284588. Planococcus halocryophilus. 128 samples. Type: Expression profiling by high throughput sequencing.
Effects of the RNA Exosome on damage induced small RNAs in the 28S ribosomal locus
GEO Series GSE113109. Homo sapiens. 18 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Mechanisms Coordinating Ribosomal Protein Gene Transcription in Response to Stress
GEO Series GSE155235. Saccharomyces cerevisiae. 22 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
Pol II Preferentially Regulates Ribosomal Protein Expression by Trapping Disassociated Subunits [TT-seq]
GEO Series GSE225451. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Ribosome profiling of harringtonine-treated SUM1315 cells
GEO Series GSE59815. Homo sapiens. 2 samples. Type: Other.
Activation of PARP-1 by snoRNAs Controls Ribosome Biogenesis and Cell Growth via the RNA Helicase DDX21 (RIP-Seq)
GEO Series GSE115759. Homo sapiens. 4 samples. Type: Other.
Advancing Trypanosoma brucei genome annotation through ribosome profiling and spliced leader mapping
GEO Series GSE72463. Trypanosoma brucei. 22 samples. Type: Expression profiling by high throughput sequencing.
Ribosomal protein S3: a functional component of NF-kB p65 binding complexes
GEO Series GSE7231. Homo sapiens. 6 samples. Type: Expression profiling by array.
Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome - extradata1
GEO Series GSE302005. Pyrococcus furiosus. 6 samples. Type: Expression profiling by high throughput sequencing.
Sciatic nerve crush regulation of ribosome-associated RNA in DRG neurons, alternative polyadenylation analytsis [DRGinjuryRiboTag2018-QuntSeq72h]
GEO Series GSE233823. Mus musculus. 12 samples. Type: Other.
RiboMeth-seq profiling of ribose methylations in ribosomal RNA of proliferating, quiescent and senescent primary human dermal fibroblasts.
GEO Series GSE171050. Homo sapiens. 18 samples. Type: Non-coding RNA profiling by high throughput sequencing.
CMTR1 is recruited to transcription start sites and has enhanced influence over ribosomal protein and histone genes [ChIP-seq]
GEO Series GSE175628. Mus musculus. 18 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.