cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28049462
title: 129924_GGCTAC_3_1x_NMM_R1_001_edited_Reads_per_uniqueLocation.wig

description: G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes, including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in <em>Escherichia coli</em>that are important for growth in G4-stabilizing conditions. Reducing levels of translation elongation factor Tu or slowing translation initiation or elongation with kasugamycin, chloramphenicol, or spectinomycin suppress the effects of G4-stabilizing compounds. In contrast, reducing the expression of specific translation termination or ribosome recycling proteins is detrimental to growth in G4- stabilizing conditions. Proteomic and transcriptomic analyses demonstrate that ribosome assembly factors and other proteins involved in translation are less abundant in G4-stabilizing conditions. Our results support a model in which reducing the rate of translation by altering translation initiation/elongation, or ribosome assembly can compensate for G4-related stress in E. coli.
DOI: 10.6084/m9.figshare.28049462.v1
title: 129924_GGCTAC_3_1x_NMM_R1_001_edited_Reads_per_uniqueLocation.wig

description: G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes, including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in <em>Escherichia coli</em>that are important for growth in G4-stabilizing conditions. Reducing levels of translation elongation factor Tu or slowing translation initiation or elongation with kasugamycin, chloramphenicol, or spectinomycin suppress the effects of G4-stabilizing compounds. In contrast, reducing the expression of specific translation termination or ribosome recycling proteins is detrimental to growth in G4- stabilizing conditions. Proteomic and transcriptomic analyses demonstrate that ribosome assembly factors and other proteins involved in translation are less abundant in G4-stabilizing conditions. Our results support a model in which reducing the rate of translation by altering translation initiation/elongation, or ribosome assembly can compensate for G4-related stress in E. coli.
DOI: 10.6084/m9.figshare.28049465
title: Ctrl_118566_GCCAAT_S1_L001_R1_001_Reads_per_uniqueLocation.wig

description: G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes, including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in <em>Escherichia coli</em>that are important for growth in G4-stabilizing conditions. Reducing levels of translation elongation factor Tu or slowing translation initiation or elongation with kasugamycin, chloramphenicol, or spectinomycin suppress the effects of G4-stabilizing compounds. In contrast, reducing the expression of specific translation termination or ribosome recycling proteins is detrimental to growth in G4- stabilizing conditions. Proteomic and transcriptomic analyses demonstrate that ribosome assembly factors and other proteins involved in translation are less abundant in G4-stabilizing conditions. Our results support a model in which reducing the rate of translation by altering translation initiation/elongation, or ribosome assembly can compensate for G4-related stress in E. coli.
DOI: 10.6084/m9.figshare.28049468
title: 129925_CTTGTA_3_2x_NMM_R1_001_edited_Reads_per_uniqueLocation.wig

description: G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes, including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in <em>Escherichia coli</em>that are important for growth in G4-stabilizing conditions. Reducing levels of translation elongation factor Tu or slowing translation initiation or elongation with kasugamycin, chloramphenicol, or spectinomycin suppress the effects of G4-stabilizing compounds. In contrast, reducing the expression of specific translation termination or ribosome recycling proteins is detrimental to growth in G4- stabilizing conditions. Proteomic and transcriptomic analyses demonstrate that ribosome assembly factors and other proteins involved in translation are less abundant in G4-stabilizing conditions. Our results support a model in which reducing the rate of translation by altering translation initiation/elongation, or ribosome assembly can compensate for G4-related stress in E. coli.
DOI: 10.6084/m9.figshare.28049459
title: 129923_TAGCTT_2_2x_NMM_R1_001_edited_Reads_per_uniqueLocation.wig

description: G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes, including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in <em>Escherichia coli</em>that are important for growth in G4-stabilizing conditions. Reducing levels of translation elongation factor Tu or slowing translation initiation or elongation with kasugamycin, chloramphenicol, or spectinomycin suppress the effects of G4-stabilizing compounds. In contrast, reducing the expression of specific translation termination or ribosome recycling proteins is detrimental to growth in G4- stabilizing conditions. Proteomic and transcriptomic analyses demonstrate that ribosome assembly factors and other proteins involved in translation are less abundant in G4-stabilizing conditions. Our results support a model in which reducing the rate of translation by altering translation initiation/elongation, or ribosome assembly can compensate for G4-related stress in E. coli.
DOI: 10.6084/m9.figshare.28049465.v1
title: Ctrl_118566_GCCAAT_S1_L001_R1_001_Reads_per_uniqueLocation.wig

description: G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes, including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in <em>Escherichia coli</em>that are important for growth in G4-stabilizing conditions. Reducing levels of translation elongation factor Tu or slowing translation initiation or elongation with kasugamycin, chloramphenicol, or spectinomycin suppress the effects of G4-stabilizing compounds. In contrast, reducing the expression of specific translation termination or ribosome recycling proteins is detrimental to growth in G4- stabilizing conditions. Proteomic and transcriptomic analyses demonstrate that ribosome assembly factors and other proteins involved in translation are less abundant in G4-stabilizing conditions. Our results support a model in which reducing the rate of translation by altering translation initiation/elongation, or ribosome assembly can compensate for G4-related stress in E. coli.
DOI: 10.6084/m9.figshare.28049468.v1
title: 129925_CTTGTA_3_2x_NMM_R1_001_edited_Reads_per_uniqueLocation.wig

description: G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes, including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in <em>Escherichia coli</em>that are important for growth in G4-stabilizing conditions. Reducing levels of translation elongation factor Tu or slowing translation initiation or elongation with kasugamycin, chloramphenicol, or spectinomycin suppress the effects of G4-stabilizing compounds. In contrast, reducing the expression of specific translation termination or ribosome recycling proteins is detrimental to growth in G4- stabilizing conditions. Proteomic and transcriptomic analyses demonstrate that ribosome assembly factors and other proteins involved in translation are less abundant in G4-stabilizing conditions. Our results support a model in which reducing the rate of translation by altering translation initiation/elongation, or ribosome assembly can compensate for G4-related stress in E. coli.
DOI: 10.6084/m9.figshare.28049471
title: NMM_118567_CTTGTA_S2_L001_R1_001_Reads_per_uniqueLocation.wig

description: G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes, including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in <em>Escherichia coli</em>that are important for growth in G4-stabilizing conditions. Reducing levels of translation elongation factor Tu or slowing translation initiation or elongation with kasugamycin, chloramphenicol, or spectinomycin suppress the effects of G4-stabilizing compounds. In contrast, reducing the expression of specific translation termination or ribosome recycling proteins is detrimental to growth in G4- stabilizing conditions. Proteomic and transcriptomic analyses demonstrate that ribosome assembly factors and other proteins involved in translation are less abundant in G4-stabilizing conditions. Our results support a model in which reducing the rate of translation by altering translation initiation/elongation, or ribosome assembly can compensate for G4-related stress in E. coli.
DOI: 10.6084/m9.figshare.28049471.v1
title: NMM_118567_CTTGTA_S2_L001_R1_001_Reads_per_uniqueLocation.wig

description: G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes, including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in <em>Escherichia coli</em>that are important for growth in G4-stabilizing conditions. Reducing levels of translation elongation factor Tu or slowing translation initiation or elongation with kasugamycin, chloramphenicol, or spectinomycin suppress the effects of G4-stabilizing compounds. In contrast, reducing the expression of specific translation termination or ribosome recycling proteins is detrimental to growth in G4- stabilizing conditions. Proteomic and transcriptomic analyses demonstrate that ribosome assembly factors and other proteins involved in translation are less abundant in G4-stabilizing conditions. Our results support a model in which reducing the rate of translation by altering translation initiation/elongation, or ribosome assembly can compensate for G4-related stress in E. coli.
DOI: 10.6084/m9.figshare.28049474
title: 129922_GATCAG_2_1x_NMM_R1_001_edited_Reads_per_uniqueLocation.wig

description: G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes, including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in <em>Escherichia coli</em>that are important for growth in G4-stabilizing conditions. Reducing levels of translation elongation factor Tu or slowing translation initiation or elongation with kasugamycin, chloramphenicol, or spectinomycin suppress the effects of G4-stabilizing compounds. In contrast, reducing the expression of specific translation termination or ribosome recycling proteins is detrimental to growth in G4- stabilizing conditions. Proteomic and transcriptomic analyses demonstrate that ribosome assembly factors and other proteins involved in translation are less abundant in G4-stabilizing conditions. Our results support a model in which reducing the rate of translation by altering translation initiation/elongation, or ribosome assembly can compensate for G4-related stress in E. coli.
DOI: 10.6084/m9.figshare.28049474.v1
title: 129922_GATCAG_2_1x_NMM_R1_001_edited_Reads_per_uniqueLocation.wig

description: G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes, including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in <em>Escherichia coli</em>that are important for growth in G4-stabilizing conditions. Reducing levels of translation elongation factor Tu or slowing translation initiation or elongation with kasugamycin, chloramphenicol, or spectinomycin suppress the effects of G4-stabilizing compounds. In contrast, reducing the expression of specific translation termination or ribosome recycling proteins is detrimental to growth in G4- stabilizing conditions. Proteomic and transcriptomic analyses demonstrate that ribosome assembly factors and other proteins involved in translation are less abundant in G4-stabilizing conditions. Our results support a model in which reducing the rate of translation by altering translation initiation/elongation, or ribosome assembly can compensate for G4-related stress in E. coli.
DOI: 10.6084/m9.figshare.c.3637148_d1.v1
title: Additional file 2: of Context-specific functional module based drug efficacy prediction

description: Comparison concordance index between our model and elastic net. It contains concordance index of our model and elastic net in each drug. It contains p-value of concordance index of our model and elastic net in each drug. It contains drug target information. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3637148_d4.v1
title: Additional file 3: of Context-specific functional module based drug efficacy prediction

description: Comparison Pearson correlation coefficient between our model and elastic net. It contains correlation coefficient of our model and elastic net in each drug. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3637238_d9.v1
title: Additional file 2: of Cross-tissue and cross-species analysis of gene expression in skeletal muscle and electric organ of African weakly-electric fish (Teleostei; Mormyridae)

description: Blast results of C. compressirostris transcriptome assembly. Tabular blast report showing the results of the blastx comparison between the transcriptome of C. compressirostris and the proteome of D. rerio. (TXT 14648Â kb)
DOI: 10.6084/m9.figshare.c.3637238_d7.v1
title: Additional file 4: of Cross-tissue and cross-species analysis of gene expression in skeletal muscle and electric organ of African weakly-electric fish (Teleostei; Mormyridae)

description: Changes in gene expression between EO and SM for C. compressirostris transcriptome. Results of the edgeR DE-analysis. The table reports the fold-change in the expression levels and relative uncorrected and corrected p-values between EO and SM for all genes in the C. compressirostris transcriptome. (TXT 5878Â kb)
DOI: 10.6084/m9.figshare.c.3637244_d4.v1
title: Additional file 2: Table S1. of Natural variation in expression of genes associated with carotenoid biosynthesis and accumulation in cassava (Manihot esculenta Crantz) storage root

description: Compiled information on germplasm documentation of the 23 collected and studied landraces. Compiled information for the 23 cassava landraces used in this document: origin, genetic background, geographical location of origin, color classes, and local utilization of cassava landraces in a center of origin and domestication of cassava in the Brazilian Amazon. W = White, IY = intense yellow, Y = yellow, PY = pale yellow, and P = Pink. (XLS 12090 kb)
DOI: 10.6084/m9.figshare.c.3637244_d8.v1
title: Additional file 9: Table S3. of Natural variation in expression of genes associated with carotenoid biosynthesis and accumulation in cassava (Manihot esculenta Crantz) storage root

description: Information on primers used for qRT-PCR. Abbreviations are phytoene synthase (CasPSY), carotene isomerase (CasCRTISO), phytoene desaturase (CasPDS), lycopene cyclase Î˛ (CasLCYb), carotene hydroxylase Î˛ CasBCHb) and neoxanthin synthase (CasNXS) for cassava cDNA from storage root. (XLS 12142 kb)
DOI: 10.6084/m9.figshare.c.3637244_d9.v1
title: Additional file 8: Table S2. of Natural variation in expression of genes associated with carotenoid biosynthesis and accumulation in cassava (Manihot esculenta Crantz) storage root

description: Cassava genome annotation. Compiled information on annotation of genes coding for enzymes related to carotenoids biosynthesis and plastid division and gene sequences used for gene expression analysis with three biological replications. Proteins sequences, related to carotenoid biosynthesis, generated in this study, were registered in NCBI data baseÂ  http://www.ncbi.nlm.nih.gov/protein/?term=carvalho+cassava . Protein sequences derived from cDNA sequence for microarray elements, related to plastid division, were obtained at NCBI http://www.ncbi.nlm.nih.gov/protein/?term=carvalho+cassava . Both protein sequences were annotated to cassava proteome data base Â  http://www.ncbi.nlm.nih.gov/protein/?term=carvalho+cassava
DOI: 10.6084/m9.figshare.c.3637256_d1.v1
title: Additional file 5: of The prognostic potential of alternative transcript isoforms across human tumors

description: Transcript signatures of tumor stage (XLS 189 kb)
DOI: 10.6084/m9.figshare.c.3637256_d2.v1
title: Additional file 4: of The prognostic potential of alternative transcript isoforms across human tumors

description: Enriched cancer hallmarks. (XLS 66 kb)
DOI: 10.6084/m9.figshare.c.3637256_d3.v1
title: Additional file 6: of The prognostic potential of alternative transcript isoforms across human tumors

description: Correlation of predictive isoforms with stromal and immune scores. (XLS 173 kb)
DOI: 10.6084/m9.figshare.c.3637256_d4.v1
title: Additional file 1: of The prognostic potential of alternative transcript isoforms across human tumors

description: Patient data, blind predictions, and gene-isoform annotations. (XLS 4554 kb)
DOI: 10.6084/m9.figshare.c.3637256_d5.v1
title: Additional file 9: of The prognostic potential of alternative transcript isoforms across human tumors

description: Models in ER+/ER– breast and MITF+/MITF– melanoma tumors. (XLS 177 kb)
DOI: 10.6084/m9.figshare.c.3637256_d7.v1
title: Additional file 8: of The prognostic potential of alternative transcript isoforms across human tumors

description: Predictive signatures based on gene expression and splicing events. (XLS 278 kb)
DOI: 10.6084/m9.figshare.c.3637256_d8.v1
title: Additional file 7: of The prognostic potential of alternative transcript isoforms across human tumors

description: Transcript signatures in pooled tumor types. (XLS 34 kb)
DOI: 10.6084/m9.figshare.c.3637325_d12.v1
title: Additional file 8: Table S7. of Effect of Wild and Cultivated Rice Genotypes on Rhizosphere Bacterial Community Composition

description: Differential representation of Taxa in AA genome cultivated vs wild rhizosphere. (XLSX 66.0 kb)
DOI: 10.6084/m9.figshare.c.3637328_d2.v1
title: Additional file 9: of Geminin prevents DNA damage in vagal neural crest cells to ensure normal enteric neurogenesis

description: Figure S8. ENS progenitors established in the gut are resistant to γ-irradiation in the first 2 hours following exposure. Cryosections at the level of the foregut of Wnt1Cre|EYFP control E10.5 embryos (A, B) or Wnt1Cre|EYFP embryos 2 hours (C, D) or 5 hours (E, F) following exposure to irradiation, immunostained for GFP (green) and processed for TUNEL (red). (G), Quantification of GFP+ ENCCs that are undergoing apoptosis (TUNEL+). One-way ANOVA followed by Fisher’s LSD multiple comparison test, ****P value
DOI: 10.6084/m9.figshare.c.3637346_d1.v1
title: Additional file 1: Table S1. of Mutational landscape of mucinous ovarian carcinoma and its neoplastic precursors

description: Clinicopathological data for MOTs. Table S2. Summary of whole exome sequencing statistics. Table S3. List of all somatic coding mutations identified by whole exome sequencing and targeted Sanger sequencing. Table S4. Primers used for the validation screens of ELF3, GNAS, KLF5 and ERBB3. Table S5. Mean mutation rates. Table S6. Somatic mutations identified in the validation cohort. (XLSX 208 kb)
DOI: 10.6084/m9.figshare.c.3637484_d4.v1
title: MOESM4 of Effect of helium pre- or postconditioning on signal transduction kinases in patients undergoing coronary artery bypass graft surgery

description: Additional file 4. Raw data of the western blots.
DOI: 10.6084/m9.figshare.c.3637490_d1.v1
title: Additional file 2 of Boosting the discriminatory power of sparse survival models via optimization of the concordance index and stability selection

description: R Code. This R-file provides the underlying functions to reproduce the results of the simulation and the breast cancer analysis. (R 21 kb)
DOI: 10.6084/m9.figshare.c.3637499_d2.v1
title: Additional file 2: Table S1. of Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development

description: Output of Binning in E16CE – P0CE and P0CE –P0NE comparisons. Custom bioinformatics pipeline and binning of E16CE - P0CE and P0CE-P0NE comparisons at the gene level (S1.1, S1.3) and isoform level (S1.2, S1.4) as discussed in the strategy in Fig. 1c. (XLSX 10709 kb)
DOI: 10.6084/m9.figshare.c.3637499_d1.v1
title: Additional file 4: Table S3. of Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development

description: Microarray analysis results. Clusters generated through K-means clustering in Genesis for the microarray. (XLSX 330 kb)
DOI: 10.6084/m9.figshare.c.3637499_d3.v1
title: Additional file 6: Table S5. of Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development

description: DE based analysis results for static and temporal comparisons. DE based analyses for static (P21WT vs. P21KO) (S5.1) and temporal (P0 vs. P21WT and P0 vs. P21KO) comparisons (S5.2, S5.3). (XLSX 4196 kb)
DOI: 10.6084/m9.figshare.c.3637499_d5.v1
title: Additional file 7: Table S6. of Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development

description: DAVID analysis output of DE based analyses for static and temporal comparisons. Results of DAVID analysis based on DE genes for P0 vs. P21WT (S6.1), P0 vs. P21KO (S6.2), and P21WT vs. P21KO (S6.3) comparisons. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.c.3637499_d6.v1
title: Additional file 3: Table S2. of Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development

description: DAVID analysis output for static and temporal comparisons. DAVID output for genes belonging to bins in E16CE-P0CE comparison (S2.1), P0CE-P0NE comparison (S2.2), P0 vs. P21-Nrl-WT comparison (S2.3),P0 vs. P21-Nrl-KO comparison (S2.4) and P21-Nrl-WT vs. P21-Nrl-KO comparison (S2.5). (XLSX 140 kb)