cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23665416
title: Additional file 5 of PHF5A regulates the expression of the DOCK5 variant to promote HNSCC progression through p38 MAPK activation

description: Additional File 5: Supplemental Table S3. Correlations between PHF5A expression and clinicopathological parameters in the HNSCC validation cohort.
DOI: 10.25582/data.2023-01.2721011/2289908
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723917/2289909
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2721008/2289910
title: Data for EMSL Project 60528 from January 2023
DOI: 10.6084/m9.figshare.12655429
title: Additional file 9 of FAM20B-catalyzed glycosaminoglycans control murine tooth number by restricting FGFR2b signaling

description: Additional file 9: Figures S9A-S9B. Fig. S9A-[GAGs did not show synergistic effects on FGF10-FGFR2b signaling]. Fig. S9B-[GAGs did not show inhibitory effects on FGF10-FGFR2b signaling]. HS and CS did not show significant synergistic or inhibitory effects on FGF10-FGFR2b signaling in BaF3 cells. A BaF3 cells expressing FGFR2b were cultured in RPMI 1640 media supplemented with 1000 pM FGF10 and 0–5 ng/ml GAGs (HS/HS2S/HS6S/CSA/heparin) for 45 h. Heparin (positive control) showed significant synergistic effects on FGFR2b signaling (P &lt; 0.001), while HS/HS2S/HS6S/CSA groups did not show any significant synergistic effects (P &gt; 0.05). B BaF3-FGFR2b cells were cultured in RPMI 1640 media supplemented with 1000 pM FGF10 and 1.5 μg/ml heparin to boost the baseline of FGFR2b signaling activity (indicated by cell viability OD value). HS/CSA/CSC/CSE/LMW heparin (0–5 ng/ml) supplemented to the culture media did not show any inhibitory effects on FGFR2b signaling (P &gt; 0.05). Two-way ANOVA was used to evaluate the differences among groups.
DOI: 10.25582/data.2023-01.2723339/2289911
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723400/2289912
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723284/2289913
title: Data for EMSL Project 60528 from January 2023
DOI: 10.6084/m9.figshare.10034219
title: Additional file 1 of Analysis of microRNAs, phased small interfering RNAs and their potential targets in Rosarugosa Thunb.

description: This is an MS Excel file. This file includes 28 supplementary tables. (XLSX 43750 kb)
DOI: 10.6084/m9.figshare.10034219.v1
title: Additional file 1 of Analysis of microRNAs, phased small interfering RNAs and their potential targets in Rosarugosa Thunb.

description: This is an MS Excel file. This file includes 28 supplementary tables. (XLSX 43750 kb)
DOI: 10.25582/data.2023-01.2724040/2289914
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723240/2289915
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723949/2289916
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723303/2289917
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723320/2289918
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723402/2289919
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2724033/2289920
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2022-12.2676266/2289921
title: Data for EMSL Project 60528 from December 2022
DOI: 10.25582/data.2023-01.2723919/2289922
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2724032/2289923
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723337/2289924
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723361/2289925
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2720992/2289926
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2724000/2289927
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2724046/2289928
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2022-12.2679701/2289929
title: Data for EMSL Project 60528 from December 2022
DOI: 10.25582/data.2023-01.2723365/2289930
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2720993/2289931
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723220/2289932
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2721009/2289933
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2022-11.2643854/2289934
title: Data for EMSL Project 60528 from November 2022
DOI: 10.25582/data.2023-01.2723304/2289935
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723279/2289936
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723239/2289937
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723978/2289938
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723232/2289939
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2724011/2289940
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723914/2289941
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723307/2289942
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2022-12.2679466/2289943
title: Data for EMSL Project 60528 from December 2022
DOI: 10.25582/data.2023-01.2723253/2289944
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2721015/2289945
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2022-12.2678427/2289946
title: Data for EMSL Project 60528 from December 2022
DOI: 10.25582/data.2023-01.2724007/2289947
title: Data for EMSL Project 60528 from January 2023
DOI: 10.6084/m9.figshare.10034363
title: Additional file 1: of Ai-lncRNA EGOT enhancing autophagy sensitizes paclitaxel cytotoxicity via upregulation of ITPR1 expression by RNA-RNA and RNA-protein interactions in human cancer

description: Table S1. Lists of primers. Lists including PCR primers used in this study, primers used for shRNAs and siRNA sequences. Table S2. Details of the gene sequence probe sets. Table S3. Guilt-by-association analysis in breast cancer data from TCGA. Table S4. Pan-cancer data of 33 cancer contexts in TCGA. All cancer IDs and patient numbers are listed. Table S5. Protein mass spectrometry analysis in MDA-MB-231. RNA pull-down assays using the Flag-MS2bp-MS2bs-based system (Additional file 2: Figure S4F), followed by mass spectrometry in MDA-MB-231 cells. Raw data listing all identified proteins and all peptides from each sample. (ZIP 9889 kb)
DOI: 10.6084/m9.figshare.10034363.v1
title: Additional file 1: of Ai-lncRNA EGOT enhancing autophagy sensitizes paclitaxel cytotoxicity via upregulation of ITPR1 expression by RNA-RNA and RNA-protein interactions in human cancer

description: Table S1. Lists of primers. Lists including PCR primers used in this study, primers used for shRNAs and siRNA sequences. Table S2. Details of the gene sequence probe sets. Table S3. Guilt-by-association analysis in breast cancer data from TCGA. Table S4. Pan-cancer data of 33 cancer contexts in TCGA. All cancer IDs and patient numbers are listed. Table S5. Protein mass spectrometry analysis in MDA-MB-231. RNA pull-down assays using the Flag-MS2bp-MS2bs-based system (Additional file 2: Figure S4F), followed by mass spectrometry in MDA-MB-231 cells. Raw data listing all identified proteins and all peptides from each sample. (ZIP 9889 kb)
DOI: 10.25582/data.2023-01.2723359/2289948
title: Data for EMSL Project 60528 from January 2023
DOI: 10.6084/m9.figshare.10034366
title: Additional file 2: of Ai-lncRNA EGOT enhancing autophagy sensitizes paclitaxel cytotoxicity via upregulation of ITPR1 expression by RNA-RNA and RNA-protein interactions in human cancer

description: Figure S1. EGOT enhances paclitaxel sensitivity in human cancer. Figure S2. EGOT is positively related to ITPR1 and induces ITPR1 expression. Figure S3. EGOT induces autophagy to enhance paclitaxel sensitivity through ITPR1. Figure S4. EGOT regulates ITPR1 expression in cis and in trans in human cancer. Figure S5. EGOT is transcriptionally regulated by stress stimuli in human cancer. Figure S6. EGOT is directly repressed by the NRIP1/AP-1 complex. Figure S7. EGOT/ITPR1 is associated with a favorable prognosis and enhances paclitaxel sensitivity in human cancer. Figure S8. Schematic illustration of the possible mechanisms involved in this study. (ZIP 9814 kb)
DOI: 10.6084/m9.figshare.10034366.v1
title: Additional file 2: of Ai-lncRNA EGOT enhancing autophagy sensitizes paclitaxel cytotoxicity via upregulation of ITPR1 expression by RNA-RNA and RNA-protein interactions in human cancer

description: Figure S1. EGOT enhances paclitaxel sensitivity in human cancer. Figure S2. EGOT is positively related to ITPR1 and induces ITPR1 expression. Figure S3. EGOT induces autophagy to enhance paclitaxel sensitivity through ITPR1. Figure S4. EGOT regulates ITPR1 expression in cis and in trans in human cancer. Figure S5. EGOT is transcriptionally regulated by stress stimuli in human cancer. Figure S6. EGOT is directly repressed by the NRIP1/AP-1 complex. Figure S7. EGOT/ITPR1 is associated with a favorable prognosis and enhances paclitaxel sensitivity in human cancer. Figure S8. Schematic illustration of the possible mechanisms involved in this study. (ZIP 9814 kb)
DOI: 10.25582/data.2023-01.2723291/2289949
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723264/2289950
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723943/2289951
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723306/2289952
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723354/2289953
title: Data for EMSL Project 60528 from January 2023
DOI: 10.6084/m9.figshare.23665422.v1
title: Additional file 1 of Transcriptomic analysis reveals the mechanism underlying the anthocyanin changes in Fragaria nilgerrensis Schlecht. and its interspecific hybrids

description: Additional file 1. Table S1. All108 metabolites identified from the FN vs BF1 and FN vs BF2 comparisons. Table S2. A total of 6967 co-significant DEGs were mapped into 109 KEGG database pathways. Table S3. Sixteen structural genes were predicted to be associated with anthocyanin biosynthesis. Table S4. 39 transcription factor DEGs were predicted to be associated with anthocyanin biosynthesis. Table S5. Analysis of the correlation between 39 transcription factor DEGs and 16 structural DEGs. Table S6. Analysis of the correlation between 39 transcription factor DEGs and 16 jointly up-regulated anthocyanins. Table S7. Primers used for qRT-PCR analysis.
DOI: 10.25582/data.2023-01.2723226/2289954
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723394/2289955
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723991/2289956
title: Data for EMSL Project 60528 from January 2023
DOI: 10.6084/m9.figshare.12655429.v1
title: Additional file 9 of FAM20B-catalyzed glycosaminoglycans control murine tooth number by restricting FGFR2b signaling

description: Additional file 9: Figures S9A-S9B. Fig. S9A-[GAGs did not show synergistic effects on FGF10-FGFR2b signaling]. Fig. S9B-[GAGs did not show inhibitory effects on FGF10-FGFR2b signaling]. HS and CS did not show significant synergistic or inhibitory effects on FGF10-FGFR2b signaling in BaF3 cells. A BaF3 cells expressing FGFR2b were cultured in RPMI 1640 media supplemented with 1000 pM FGF10 and 0–5 ng/ml GAGs (HS/HS2S/HS6S/CSA/heparin) for 45 h. Heparin (positive control) showed significant synergistic effects on FGFR2b signaling (P &lt; 0.001), while HS/HS2S/HS6S/CSA groups did not show any significant synergistic effects (P &gt; 0.05). B BaF3-FGFR2b cells were cultured in RPMI 1640 media supplemented with 1000 pM FGF10 and 1.5 μg/ml heparin to boost the baseline of FGFR2b signaling activity (indicated by cell viability OD value). HS/CSA/CSC/CSE/LMW heparin (0–5 ng/ml) supplemented to the culture media did not show any inhibitory effects on FGFR2b signaling (P &gt; 0.05). Two-way ANOVA was used to evaluate the differences among groups.
DOI: 10.25582/data.2023-01.2724014/2289957
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723350/2289958
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2720998/2289959
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723994/2289960
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723403/2289961
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723309/2289962
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2724008/2289963
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2724036/2289964
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723999/2289965
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723940/2289966
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723932/2289967
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2023-01.2723310/2289968
title: Data for EMSL Project 60528 from January 2023
DOI: 10.25582/data.2022-12.2677893/2289969
title: Data for EMSL Project 60528 from December 2022
DOI: 10.6084/m9.figshare.13180178
title: LowCon: A Design-based Subsampling Approach in a Misspecified Linear Model

description: We consider a measurement constrained supervised learning problem, that is, (i) full sample of the predictors are given; (ii) the response observations are unavailable and expensive to measure. Thus, it is ideal to select a subsample of predictor observations, measure the corresponding responses, and then fit the supervised learning model on the subsample of the predictors and responses. However, model fitting is a trial and error process, and a postulated model for the data could be misspecified. Our empirical studies demonstrate that most of the existing subsampling methods have unsatisfactory performances when the models are misspecified. In this paper, we develop a novel subsampling method, called “LowCon,” which outperforms the competing methods when the working linear model is misspecified. Our method uses orthogonal Latin hypercube designs to achieve a robust estimation. We show that the proposed design-based estimator approximately minimizes the so-called worst-case bias with respect to many possible misspecification terms. Both the simulated and real-data analyses demonstrate the proposed estimator is more robust than several subsample least-squares estimators obtained by state-of-the-art subsampling methods. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.23665380
title: Additional file 2 of Mapping genetic variants for nonsense-mediated mRNA decay regulation across human tissues

description: Additional file 2: Table S1. The 43 diseases with significant NMD-QTLs enrichment.
DOI: 10.6084/m9.figshare.10034462
title: Additional file 1: of BRCA1 mutations attenuate super-enhancer function and chromatin looping in haploinsufficient human breast epithelial cells

description: Table S2. List of primer sequences used in this study. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.10034462.v1
title: Additional file 1: of BRCA1 mutations attenuate super-enhancer function and chromatin looping in haploinsufficient human breast epithelial cells

description: Table S2. List of primer sequences used in this study. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.10034465
title: Additional file 2: of BRCA1 mutations attenuate super-enhancer function and chromatin looping in haploinsufficient human breast epithelial cells

description: Table S1. List of super-enhancers identified in this study. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.10034465.v1
title: Additional file 2: of BRCA1 mutations attenuate super-enhancer function and chromatin looping in haploinsufficient human breast epithelial cells

description: Table S1. List of super-enhancers identified in this study. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.6364451
title: miR-194 Original DATA.xls

description: Hypothermia has been
reported to be effective in protecting the brain in various clinical
conditions, including resuscitation after cardiac arrest and complex
cardiovascular surgery, and is considered to be a promising therapy for stroke. The present study aimed to confirm a
pivotal role for miRNA-194-5p in
deep hypothermia circulation arrest. We
observed a decline in expression of miR-194-5p in the circulation of 21 aortic
dissection patients who underwent deep hypothermia circulatory arrest.
Subsequently, the specific expression, target, and function of miR-194-5p was
investigated using primary neuron culture, polymerase chain reaction, in situ
hybridization, and flow cytometry methods. Our results showed that miR-194-5p
expression was significantly downregulated in neurons subjected to hypothermia and
oxygen-glucose deprivation in
vitro. Cortical neurons transfected with
miR-194-5p mimic exhibited increased death due to oxygen-glucose deprivation.
MiR-194-5p mediated the regulation of neuronal death, which involves the
downregulation of the specific target protein SUMO2, which is a crucial protein
in ischemia tolerance. Collectively, these data highlight the unique role of
miR-194-5p in mediating the deep hypothermia circulation arrest response via the regulation of SUMO2. These
findings suggest that miR-194-5p could be a potential therapeutic target for
intervention in ischemic disease.
DOI: 10.6084/m9.figshare.10034501
title: Additional file 2 of Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

description: The MS Excel file that contains Tables S3-S8.Â (XLSX 507â kb)
DOI: 10.6084/m9.figshare.10034501.v1
title: Additional file 2 of Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

description: The MS Excel file that contains Tables S3-S8.Â (XLSX 507â kb)
DOI: 10.6084/m9.figshare.10034507
title: Additional file 4: of Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

description: Table S9. List of 71 genes encoding TFs linked to PWMs that were found overrepresented in the genomic regions around CpGs whose methylation was negatively of positively correlated with gene expression. These TF genes were identified independently by three independent algorithms: by classical CMA analysis (of NEG and POS sets versus control), by CMAcorrel as well as by F-Match of enriched single PWMs. (XLSX 76â kb)
DOI: 10.6084/m9.figshare.10034507.v1
title: Additional file 4: of Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

description: Table S9. List of 71 genes encoding TFs linked to PWMs that were found overrepresented in the genomic regions around CpGs whose methylation was negatively of positively correlated with gene expression. These TF genes were identified independently by three independent algorithms: by classical CMA analysis (of NEG and POS sets versus control), by CMAcorrel as well as by F-Match of enriched single PWMs. (XLSX 76â kb)
DOI: 10.6084/m9.figshare.10034510
title: Additional file 5: of Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

description: Table S10. The list of 273 potential master-regulators (representing 97 genes - several isoforms of the same protein were considered as independent potential master-regulators by the algorithm) that may control activity of 19 TFs. (XLSX 101â kb)
DOI: 10.6084/m9.figshare.10034510.v1
title: Additional file 5: of Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

description: Table S10. The list of 273 potential master-regulators (representing 97 genes - several isoforms of the same protein were considered as independent potential master-regulators by the algorithm) that may control activity of 19 TFs. (XLSX 101â kb)
DOI: 10.6084/m9.figshare.10034513
title: Additional file 6: of Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

description: Table S11. Table of pairwise Pearson correlations between CpG methylation values of pre-selected markers. (XLSX 63â kb)
DOI: 10.6084/m9.figshare.10034513.v1
title: Additional file 6: of Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

description: Table S11. Table of pairwise Pearson correlations between CpG methylation values of pre-selected markers. (XLSX 63â kb)
DOI: 10.6084/m9.figshare.10034516
title: Additional file 7: of Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

description: Table S13. Detailed information about genes that contain chosen DNA methylation markers. We present information about their known role in molecular pathways and diseases (retrieved from HumanPSD database). These genes play various roles in different but functionally connected processes, pathways and diseases related to cancer. (XLSX 32â kb)
DOI: 10.6084/m9.figshare.10034516.v1
title: Additional file 7: of Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

description: Table S13. Detailed information about genes that contain chosen DNA methylation markers. We present information about their known role in molecular pathways and diseases (retrieved from HumanPSD database). These genes play various roles in different but functionally connected processes, pathways and diseases related to cancer. (XLSX 32â kb)
DOI: 10.6084/m9.figshare.22616843.v1
title: Additional file 1 of Integrated metabolomic and transcriptomic study unveils the gene regulatory mechanisms of sugarcane growth promotion during interaction with an endophytic nitrogen-fixing bacteria

description: Additional file 1: Table S1. Information of all metabolites identified in this study. Table S2. Information of differentially abundant metabolites in IN-vs-CN. Table S3. Information of differentially abundant metabolites in KN-vs-IN. Table S5. Statistics of RNA-seq data. Table S6. Statistics of transcriptome assembly and unigene annotation. Table S7. Information of differentially expression genes in IN-vs-CN. Table S8. Information of differentially expression genes in KN-vs-IN. Table S9. Information of differentially expression genes in LN-vs-KN. Table S10. The primers used for qRT-PCR.
DOI: 10.6084/m9.figshare.22616933.v1
title: Additional file 11 of Untargeted metabolomics reveals alternations in metabolism of bovine mammary epithelial cells upon IFN-γ treatment

description: Additional file 11: Table S1. Summary of the number of differentially expressed metabolites (DEMs) in each comparison group in both negative and positive ion modes
DOI: 10.6084/m9.figshare.22616936
title: Additional file 12 of Untargeted metabolomics reveals alternations in metabolism of bovine mammary epithelial cells upon IFN-γ treatment

description: Additional file 12: Table S2. List of differentially expressed metabolites (DEMs) upon 6 h IFN-γ treatment compared to control in both negative and positive ion modes.
DOI: 10.6084/m9.figshare.22616939.v1
title: Additional file 13 of Untargeted metabolomics reveals alternations in metabolism of bovine mammary epithelial cells upon IFN-γ treatment

description: Additional file 13: Table S3. List of differentially expressed metabolites (DEMs) upon 12 h IFN-γ treatment compared to control in both negative and positive ion modes.