cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7006616
title: Additional file 4: of Long non-coding RNAs potentially function synergistically in the cellular reprogramming of SCNT embryos

description: DE lncRNAs with significant difference compared 4-cell with 2-cell of NTM group. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.7006676.v1
title: Additional file 1: of Genetic characterization of inbred lines from Shaan A and B groups for identifying loci associated with maize grain yield

description: Table S1. Numbers, groups and names of the AM126 lines. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7006607.v1
title: Additional file 1: of Long non-coding RNAs potentially function synergistically in the cellular reprogramming of SCNT embryos

description: DE lncRNAs with significant difference compared zygote with oocytes. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.7006625.v1
title: Additional file 7: of Long non-coding RNAs potentially function synergistically in the cellular reprogramming of SCNT embryos

description: DE lncRNAs with significant difference compared 4-cell of NTC with 4-cell of in vivo embryos. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7006694.v1
title: Additional file 4: of Genetic characterization of inbred lines from Shaan A and B groups for identifying loci associated with maize grain yield

description: Table S3. Pairwise kinship coefficients between AM126 lines calculated with 46,046 SNPs. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.19589399.v1
title: Additional file 5 of Evaluations of candidate markers of dihydroartemisinin-piperaquine resistance in Plasmodium falciparum isolates from the China–Myanmar, Thailand–Myanmar, and Thailand–Cambodia borders

description: Additional file 5: Table S4. SNPs of pfcrt and pfkelch13 were used for building a haplotype network of 173 P. falciparum collected from different border regions.
DOI: 10.6084/m9.figshare.7006688
title: Additional file 3: of Genetic characterization of inbred lines from Shaan A and B groups for identifying loci associated with maize grain yield

description: The hapmap file of SNP genotyping data of the AM126 lines. (TXT 13628 kb)
DOI: 10.6084/m9.figshare.7006688.v1
title: Additional file 3: of Genetic characterization of inbred lines from Shaan A and B groups for identifying loci associated with maize grain yield

description: The hapmap file of SNP genotyping data of the AM126 lines. (TXT 13628 kb)
DOI: 10.6084/m9.figshare.7006694
title: Additional file 4: of Genetic characterization of inbred lines from Shaan A and B groups for identifying loci associated with maize grain yield

description: Table S3. Pairwise kinship coefficients between AM126 lines calculated with 46,046 SNPs. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.18482470
title: Additional file 14 of A nuclear function for an oncogenic microRNA as a modulator of snRNA and splicing

description: Additional file 14 Supplementary Data 4. Changes in alternative splicing caused by U6 ASO 1. GBM4 cells were transfected with U6 ASO1 and the corresponding control oligonucleotide for 72 h, and alternatively spliced mRNA isoforms profiled by deep RNAseq. Splicing alterations are summarized for five major categories (SE, MXE, A5SS, A3SS, RI). More details are described in the Methods.
DOI: 10.6084/m9.figshare.7006676
title: Additional file 1: of Genetic characterization of inbred lines from Shaan A and B groups for identifying loci associated with maize grain yield

description: Table S1. Numbers, groups and names of the AM126 lines. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7006700
title: Additional file 6: of Genetic characterization of inbred lines from Shaan A and B groups for identifying loci associated with maize grain yield

description: Table S4. Co-ancestral membership of AM126 when Kâ =â 6. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.19589561
title: Expression status and prognostic value of autophagy-related lncRNAs in prostate cancer

description: LncRNAs involve in the autophagy to regulate prostate cancer (PCA) initiation and progression. Therefore, it urges to explore more significant AR-lncRNAs in PCa. mRNA data and clinical information of PCa were achieved from TCGA database, and ARGs were obtained from the HADb. AR-lncRNAs were identified by correlation analysis of DE ARGs and lncRNAs. Univariate Cox regression, LASSO regression, and multivariate Cox regression were used to identify the prognostic AR-lncRNA signature and constructed a risk model. GESA was used to biological function analysis between high- and low-risk score group. A nomogram was constructed and used to predicate the survival of PCa patients. A calibration curve was used to determine the accuracy of the predication model. AR-related ceRNA network was constructed by correlation analysis. Expression of six AR-related lncRNAs were detected by qRT-PCR. 222 ARGs and 385 AR-lncRNAs were screened from PCa and normal tissues, and 17 AR-lncRNAs were identified as prognostic signature for PCa. Based on the expression of prognostic signature, a risk score was calculated, and PCa samples were distributed into high- and low-risk score groups. The biological function and predicated value of the prognostic signature were also examined. Finally, based on the correlation between each ARG and its prognostic signature, three modules of AR-lncRNA-miRNA-mRNA regulatory networks were constructed based on 6 AR-lncRNAs, 17 miRNAs, and 12 ARGs. And we found that AC012085.2, UBXN10-AS1, LINC00261 downregulated, whereas AP004608.1, AC104667.2, AC008610.1 upregulated in PCa compared with BPH tissues. Our finding supplied the potential AR-lncRNAs prognostic signature for PCa.
DOI: 10.6084/m9.figshare.7006700.v1
title: Additional file 6: of Genetic characterization of inbred lines from Shaan A and B groups for identifying loci associated with maize grain yield

description: Table S4. Co-ancestral membership of AM126 when Kâ =â 6. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.19589561.v2
title: Expression status and prognostic value of autophagy-related lncRNAs in prostate cancer

description: LncRNAs involve in the autophagy to regulate prostate cancer (PCA) initiation and progression. Therefore, it urges to explore more significant AR-lncRNAs in PCa. mRNA data and clinical information of PCa were achieved from TCGA database, and ARGs were obtained from the HADb. AR-lncRNAs were identified by correlation analysis of DE ARGs and lncRNAs. Univariate Cox regression, LASSO regression, and multivariate Cox regression were used to identify the prognostic AR-lncRNA signature and constructed a risk model. GESA was used to biological function analysis between high- and low-risk score group. A nomogram was constructed and used to predicate the survival of PCa patients. A calibration curve was used to determine the accuracy of the predication model. AR-related ceRNA network was constructed by correlation analysis. Expression of six AR-related lncRNAs were detected by qRT-PCR. 222 ARGs and 385 AR-lncRNAs were screened from PCa and normal tissues, and 17 AR-lncRNAs were identified as prognostic signature for PCa. Based on the expression of prognostic signature, a risk score was calculated, and PCa samples were distributed into high- and low-risk score groups. The biological function and predicated value of the prognostic signature were also examined. Finally, based on the correlation between each ARG and its prognostic signature, three modules of AR-lncRNA-miRNA-mRNA regulatory networks were constructed based on 6 AR-lncRNAs, 17 miRNAs, and 12 ARGs. And we found that AC012085.2, UBXN10-AS1, LINC00261 downregulated, whereas AP004608.1, AC104667.2, AC008610.1 upregulated in PCa compared with BPH tissues. Our finding supplied the potential AR-lncRNAs prognostic signature for PCa.
DOI: 10.6084/m9.figshare.7006682
title: Additional file 2: of Genetic characterization of inbred lines from Shaan A and B groups for identifying loci associated with maize grain yield

description: Table S2. The grain yield data of the AM126 lines. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.7006739
title: Additional file 4: of Exosomal double-stranded DNA as a biomarker for the diagnosis and preoperative assessment of pheochromocytoma and paraganglioma

description: Table S3. Common SNP in exo-DNA I and genomic DNA of PC12 cells. (XLS 1157 kb)
DOI: 10.6084/m9.figshare.7006739.v1
title: Additional file 4: of Exosomal double-stranded DNA as a biomarker for the diagnosis and preoperative assessment of pheochromocytoma and paraganglioma

description: Table S3. Common SNP in exo-DNA I and genomic DNA of PC12 cells. (XLS 1157 kb)
DOI: 10.5281/zenodo.10653491
title: Signatures of FuLeeca scheme

description: Generated signatures from the FuLeeca reference implementation for all three security categories.

The format starts with the secret key a,b on the first two rows.Then followed by signatures v = (x|y) with x,y on two separate rows.
DOI: 10.5281/zenodo.10653492
title: Signatures of FuLeeca scheme

description: Generated signatures from the FuLeeca reference implementation for all three security categories.

The format starts with the secret key a,b on the first two rows.Then followed by signatures v = (x|y) with x,y on two separate rows.
DOI: 10.6084/m9.figshare.19589614
title: Down-regulated Circ_0000190 promotes cervical cancer by facilitating the activity of proto-oncogene protein EIF4E

description: Circular RNAs (circRNAs), a new class of non-coding RNAs, have been recently confirmed to regulate cell development, functions and certain types of pathological responses. In addition, it has been proved that circ_0000190 can serve as a tumor suppressor in several cancers. However, the underlying mechanism and biological functions of it in cervical cancer (CC) remain to be revealed. In our study, relative expression of indicated molecules was detected by RT-qPCR analysis. Loss-of-function and gain-of-function experiments were conducted to detect cell functions. Mechanism experiments including RIP assay, luciferase reporter assay and pull down assay were applied to verify the interaction among the indicated molecules. Overexpressed circ_0000190 attenuated CC progression <i>in vitro</i> and <i>in vivo</i>. Circ_0000190 functioned through the modulation of miR-1252-5p/EIF4EBP2 axis. Rescue experiments found that miR-1252-5p overexpression or EIF4EBP2 knockdown could reverse the influence on CC cells caused by circ_0000190 overexpression. Interestingly, it was found that EIF4EBP2 could bind to proto-oncogene eIF4E and prevent eIF4E from forming into complex and functioning. Circ_0000190 served as a tumor suppressor in CC and down-regulated circ_0000190 expression could weaken the binding ability of EIF4EBP2 to eIF4E thus leading to CC tumorigenesis. In our investigation, a novel tumor suppressive gene circ_0000190 was recognized, which could be treated as a promising biomarker for the diagnosis of CC.
DOI: 10.6084/m9.figshare.19589561.v1
title: Expression status and prognostic value of autophagy-related lncRNAs in prostate cancer

description: LncRNAs involve in the autophagy to regulate Prostate cancer (PCa) initiation and progression. Therefore, it urges to explore more significant AR-lncRNAs in PCa. mRNA data and clinical information of PCa were achieved from TCGA database, and ARGs were obtained from the HADb. AR-lncRNAs were identified by correlation analysis of DE ARGs and lncRNAs. Univariate Cox regression, LASSO regression, and multivariate Cox regression were used to identify the prognostic AR-lncRNA signature and constructed a risk model. GESA was used to biological function analysis between high- and low-risk score group. A nomogram was constructed and used to predicate the survival of PCa patients. A calibration curve was used to determines accuracy of the predication model. AR-related ceRNA network was constructed by correlation analysis. Expression of six AR-related lncRNAs were detected by qRT-PCR. 222 ARGs and 385 AR-lncRNAs were screened from PCa and normal tissues, and 17 AR-lncRNAs were identified as prognostic signature for PCa. Based on the expression of prognostic signature, a risk score was calculated, and PCa samples were distributed into high- and low-risk score groups. The biological function and predicated value of the prognostic signature were also examined. Finally, based on the correlation between each ARG and its prognostic signature, three modules of AR-lncRNA-miRNA-mRNA regulatory networks were constructed based on 6 AR-lncRNAs, 17 miRNAs, and 12 ARGs. And we found that AC012085.2, UBXN10-AS1, LINC00261 downregulated, whereas AP004608.1, AC104667.2, AC008610.1 upregulated in PCa compared with BPH tissues. Our finding supplied the potential AR-lncRNAs prognostic signature for PCa.
DOI: 10.6084/m9.figshare.18482470.v1
title: Additional file 14 of A nuclear function for an oncogenic microRNA as a modulator of snRNA and splicing

description: Additional file 14 Supplementary Data 4. Changes in alternative splicing caused by U6 ASO 1. GBM4 cells were transfected with U6 ASO1 and the corresponding control oligonucleotide for 72 h, and alternatively spliced mRNA isoforms profiled by deep RNAseq. Splicing alterations are summarized for five major categories (SE, MXE, A5SS, A3SS, RI). More details are described in the Methods.
DOI: 10.6084/m9.figshare.19589614.v1
title: Down-regulated Circ_0000190 promotes cervical cancer by facilitating the activity of proto-oncogene protein EIF4E

description: Circular RNAs (circRNAs), a new class of non-coding RNAs, have been recently confirmed to regulate cell development, functions and certain types of pathological responses. In addition, it has been proved that circ_0000190 can serve as a tumor suppressor in several cancers. However, the underlying mechanism and biological functions of it in cervical cancer (CC) remain to be revealed. In our study, relative expression of indicated molecules was detected by RT-qPCR analysis. Loss-of-function and gain-of-function experiments were conducted to detect cell functions. Mechanism experiments including RIP assay, luciferase reporter assay and pull down assay were applied to verify the interaction among the indicated molecules. Overexpressed circ_0000190 attenuated CC progression <i>in vitro</i> and <i>in vivo</i>. Circ_0000190 functioned through the modulation of miR-1252-5p/EIF4EBP2 axis. Rescue experiments found that miR-1252-5p overexpression or EIF4EBP2 knockdown could reverse the influence on CC cells caused by circ_0000190 overexpression. Interestingly, it was found that EIF4EBP2 could bind to proto-oncogene eIF4E and prevent eIF4E from forming into complex and functioning. Circ_0000190 served as a tumor suppressor in CC and down-regulated circ_0000190 expression could weaken the binding ability of EIF4EBP2 to eIF4E thus leading to CC tumorigenesis. In our investigation, a novel tumor suppressive gene circ_0000190 was recognized, which could be treated as a promising biomarker for the diagnosis of CC.
DOI: 10.6084/m9.figshare.19589651
title: Oncogenic magnesium transporter 1 upregulates programmed death-1-ligand 1 expression and contributes to growth and radioresistance of glioma cells through the ERK/MAPK signaling pathway

description: Radiotherapy has been established as a major therapeutic modality for glioma, whereas new therapeutic targets are needed to prevent tumor recurrence. This study intends to explore the regulatory role of magnesium transporter 1 (MAGT1) in radiotherapy resistance of glioma through modulating ERK and programmed death-1-ligand 1 (PD-L1). Our bioinformatics analysis identified differentially expressed MAGT1 in glioma, expression of which was subsequently determined in cohort data of TCGA database and microarray dataset as well as glioma cell lines. Artificial modulation of MAGT1, ERK, and PD-L1 expression was performed to examine their effects on glioma cell proliferation and radioresistance, as reflected by MTT and colony formation assays under irradiation. Mouse glioma cells with manipulated MAGT1 and ERK inhibitors were further injected into mice to assess the <i>in vivo</i> tumor formation ability of glioma cells. It was noted that MAGT1 expression was highly expressed in glioma tissues of TCGA data and microarray dataset, which was then validated in glioma cell lines. Ectopic expression of MAGT1 was revealed to promote the proliferation and radioresistance of glioma cells, which was attributed to the MAGT1-mediated activation of the ERK/MAPK signaling pathway. It was illuminated that MAGT1 stimulated PD-L1 expression through the ERK/MAPK pathway and thus facilitated glioma cell growth. Additionally, MAGT1 overexpression accelerated the <i>in vivo</i> tumor formation of glioma cells, while the ERK inhibitor negated its effect. In conclusion, MAGT1 enhances the growth and radioresistance of glioma cells through the ERK/MAPK signaling pathway-mediated upregulation of PD-L1 expression.
DOI: 10.6084/m9.figshare.19589651.v1
title: Oncogenic magnesium transporter 1 upregulates programmed death-1-ligand 1 expression and contributes to growth and radioresistance of glioma cells through the ERK/MAPK signaling pathway

description: Radiotherapy has been established as a major therapeutic modality for glioma, whereas new therapeutic targets are needed to prevent tumor recurrence. This study intends to explore the regulatory role of magnesium transporter 1 (MAGT1) in radiotherapy resistance of glioma through modulating ERK and programmed death-1-ligand 1 (PD-L1). Our bioinformatics analysis identified differentially expressed MAGT1 in glioma, expression of which was subsequently determined in cohort data of TCGA database and microarray dataset as well as glioma cell lines. Artificial modulation of MAGT1, ERK, and PD-L1 expression was performed to examine their effects on glioma cell proliferation and radioresistance, as reflected by MTT and colony formation assays under irradiation. Mouse glioma cells with manipulated MAGT1 and ERK inhibitors were further injected into mice to assess the <i>in vivo</i> tumor formation ability of glioma cells. It was noted that MAGT1 expression was highly expressed in glioma tissues of TCGA data and microarray dataset, which was then validated in glioma cell lines. Ectopic expression of MAGT1 was revealed to promote the proliferation and radioresistance of glioma cells, which was attributed to the MAGT1-mediated activation of the ERK/MAPK signaling pathway. It was illuminated that MAGT1 stimulated PD-L1 expression through the ERK/MAPK pathway and thus facilitated glioma cell growth. Additionally, MAGT1 overexpression accelerated the <i>in vivo</i> tumor formation of glioma cells, while the ERK inhibitor negated its effect. In conclusion, MAGT1 enhances the growth and radioresistance of glioma cells through the ERK/MAPK signaling pathway-mediated upregulation of PD-L1 expression.
DOI: 10.6084/m9.figshare.7006811.v1
title: Additional file 9: of Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation

description: Table S4. Transcriptional changes of active enhancers upon Hdac3 deletion. (XLSX 264Â kb)
DOI: 10.6084/m9.figshare.7531046
title: Additional file 2: of Homology-independent multiallelic disruption via CRISPR/Cas9-based knock-in yields distinct functional outcomes in human cells

description: Individual data values for Fig. 2j; Individual data values for Fig. 2k; Individual data values for Fig. 3c; Individual data values for Fig. 4c; Individual data values for Fig. 5c. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7006751
title: Additional file 11: of Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation

description: Table S5. Rank of upregulated enhancers upon Hdac3 deletion by NRSA. (XLSX 123Â kb)
DOI: 10.6084/m9.figshare.7006784
title: Additional file 1: of Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation

description: Table S1. Identified enhancers using K562 GRO-seq (S1a), GM12878 GRO-seq (S1b), two replicates of U2OS GRO-seq (GSM1634453 (S1c) & GSM1634455 (S1d)), and K562 PRO-seq (S1e). (XLSX 1158Â kb)
DOI: 10.6084/m9.figshare.7531046.v1
title: Additional file 2: of Homology-independent multiallelic disruption via CRISPR/Cas9-based knock-in yields distinct functional outcomes in human cells

description: Individual data values for Fig. 2j; Individual data values for Fig. 2k; Individual data values for Fig. 3c; Individual data values for Fig. 4c; Individual data values for Fig. 5c. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7006745
title: Additional file 5: of Exosomal double-stranded DNA as a biomarker for the diagnosis and preoperative assessment of pheochromocytoma and paraganglioma

description: Table S4. Common SNP of susceptibility genes in exo-DNA III and the parental tumor cells from patient 13. Table S5. Common SNP of susceptibility genes in exo-DNA III and the parental tumor celsl from patient 14. Table S6. Common SNP of susceptibility genes in exo-DNA III and the parental tumor cells from patient 15. Table S7. Common SNP counts in three of the patients. (ZIP 184 kb)
DOI: 10.6084/m9.figshare.7006745.v1
title: Additional file 5: of Exosomal double-stranded DNA as a biomarker for the diagnosis and preoperative assessment of pheochromocytoma and paraganglioma

description: Table S4. Common SNP of susceptibility genes in exo-DNA III and the parental tumor cells from patient 13. Table S5. Common SNP of susceptibility genes in exo-DNA III and the parental tumor celsl from patient 14. Table S6. Common SNP of susceptibility genes in exo-DNA III and the parental tumor cells from patient 15. Table S7. Common SNP counts in three of the patients. (ZIP 184 kb)
DOI: 10.6084/m9.figshare.7006799
title: Additional file 5: of Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation

description: Table S2. Transcriptional changes in gene body regions (S2a) and promoter-proximal regions (S2b) for active genes in Hdac3 KO vs. WT mouse livers. (XLSX 2301Â kb)
DOI: 10.6084/m9.figshare.7006805.v1
title: Additional file 7: of Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation

description: Table S3. Identified enhancers using Hdac3 WT and KO PRO-seq data derived from the mouse liver. (XLSX 381Â kb)
DOI: 10.11583/dtu.19692238
title: Impurities in 2D Materials Database

description: This dataset contains DFT relaxed atomic structures and total energies of 2D materials doped with single intrinisic and extrinsic point defects in interstitial and adsorption site positions. The database is stored in the ASE Database format and features additional information <em>via</em> KVPs such as formation energies ('eform'), dopant atom ('dopant'), host formula ('host'), <em>etc.</em>
<br>
A detailed description of the data and how it was generated can be found in the related article: https://doi.org/10.1038/s41699-023-00380-6
<br>
Version log:
An updated version of the database with improved convergence was uploaded (24.06.2022)Updated funding information (08.07.2022)Database hosted on CMR server (12.07.2022)Related materials: article DOI added (13.02.2024)
<br>
DOI: 10.6084/m9.figshare.7531106.v1
title: Additional file 2: of Characterization of miRNA profiles in the mammary tissue of dairy cattle in response to heat stress

description: Novel miRNAs identified in this study. (XLS 45 kb)
DOI: 10.6084/m9.figshare.7006805
title: Additional file 7: of Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation

description: Table S3. Identified enhancers using Hdac3 WT and KO PRO-seq data derived from the mouse liver. (XLSX 381Â kb)
DOI: 10.6084/m9.figshare.7531100
title: Additional file 1: of Characterization of miRNA profiles in the mammary tissue of dairy cattle in response to heat stress

description: The primers of real-time quantitative RT-PCR used in this study. (XLS 31 kb)
DOI: 10.6084/m9.figshare.7531100.v1
title: Additional file 1: of Characterization of miRNA profiles in the mammary tissue of dairy cattle in response to heat stress

description: The primers of real-time quantitative RT-PCR used in this study. (XLS 31 kb)