cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12855004.v1
title: Identification of a new strain of mouse kidney parvovirus associated with inclusion body nephropathy in immunocompromised laboratory mice

description: Inclusion body nephropathy (IBN) and kidney fibrosis in aged immunodeficient mice and, to lesser extent, in immunocompetent mice have been recently linked to infection of mouse kidney parvovirus (MKPV), also known as murine chapparvovirus (MuCPV). Knowledge about its prevalence and the complete genome sequence of more MKPV strains is essential for understanding phylogenetic relationships and pathogenicity among MKPV strains. In the present study using PCR and genome walking, we determined the complete 4440-nucleotide genome of a new MKPV strain, namely MIT-WI1, which was identified in IBN-affected <i>Il2rg<sup>−/–</sup>Rag2<sup>−/–</sup> c-Kit <sup>W–sh/W–sh</sup></i> mice housed in the vivarium at Whitehead Institute for Biomedical Research (WI). The overall nucleotide (&gt;94%) and deduced amino acid sequences (&gt;98%) of p10, p15, NS1 (replicase), NS2 and VP1 (capsid protein) within the MIT-WI1 genome, are closely related to MKPV/MuCPV strains described in laboratory and wild <i>Mus musculus</i> mice. In addition, PCR and qPCR assays using newly designed primers conserved among the known MKPV/MuCPV genomes were developed and utilized to assess MKPV status in selected laboratory mice. MKPV was also detected in immunodeficient (NSG) and immunocompetent (Crl:CD1(ICR), UTX<sup>flox</sup>) mouse strains/stocks. The abundance of the MKPV genome copies was significantly correlated with the severity of IBN. Our data indicate that MKPV is present in selected mouse strains/stocks, and provides new insights into the genome evolution of MKPV.
DOI: 10.6084/m9.figshare.7612178
title: MOESM1 of An integrative genomic analysis of transcriptional profiles identifies characteristic genes and patterns in HIV-infected long-term non-progressors and elite controllers

description: Additional file 1. Clinical parameters of patients involved.
DOI: 10.6084/m9.figshare.7612178.v1
title: MOESM1 of An integrative genomic analysis of transcriptional profiles identifies characteristic genes and patterns in HIV-infected long-term non-progressors and elite controllers

description: Additional file 1. Clinical parameters of patients involved.
DOI: 10.6084/m9.figshare.7612181
title: Additional file 1: of Transcriptome analyses provide insights into the expression pattern and sequence similarity of several taxol biosynthesis-related genes in three Taxus species

description: Table S1. The detail information of raw reads from different sample groups. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7612181.v1
title: Additional file 1: of Transcriptome analyses provide insights into the expression pattern and sequence similarity of several taxol biosynthesis-related genes in three Taxus species

description: Table S1. The detail information of raw reads from different sample groups. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7612187
title: MOESM2 of An integrative genomic analysis of transcriptional profiles identifies characteristic genes and patterns in HIV-infected long-term non-progressors and elite controllers

description: Additional file 2. DEGs in NPs compared with PPs in MADNT.
DOI: 10.6084/m9.figshare.7612187.v1
title: MOESM2 of An integrative genomic analysis of transcriptional profiles identifies characteristic genes and patterns in HIV-infected long-term non-progressors and elite controllers

description: Additional file 2. DEGs in NPs compared with PPs in MADNT.
DOI: 10.6084/m9.figshare.7612193
title: MOESM3 of An integrative genomic analysis of transcriptional profiles identifies characteristic genes and patterns in HIV-infected long-term non-progressors and elite controllers

description: Additional file 3. DEGs in NPs compared with PPs in CD8+ T cells.
DOI: 10.6084/m9.figshare.7612193.v1
title: MOESM3 of An integrative genomic analysis of transcriptional profiles identifies characteristic genes and patterns in HIV-infected long-term non-progressors and elite controllers

description: Additional file 3. DEGs in NPs compared with PPs in CD8+ T cells.
DOI: 10.6084/m9.figshare.7612196
title: Additional file 3: of Transcriptome analyses provide insights into the expression pattern and sequence similarity of several taxol biosynthesis-related genes in three Taxus species

description: Table S2. KEGG classification of the unigenes. (XLSX 580 kb)
DOI: 10.6084/m9.figshare.7612196.v1
title: Additional file 3: of Transcriptome analyses provide insights into the expression pattern and sequence similarity of several taxol biosynthesis-related genes in three Taxus species

description: Table S2. KEGG classification of the unigenes. (XLSX 580 kb)
DOI: 10.6084/m9.figshare.7612199
title: MOESM4 of An integrative genomic analysis of transcriptional profiles identifies characteristic genes and patterns in HIV-infected long-term non-progressors and elite controllers

description: Additional file 4. Pathways enriched in CD8+ T cells from ECs analyzed by GSEA.
DOI: 10.6084/m9.figshare.7612199.v1
title: MOESM4 of An integrative genomic analysis of transcriptional profiles identifies characteristic genes and patterns in HIV-infected long-term non-progressors and elite controllers

description: Additional file 4. Pathways enriched in CD8+ T cells from ECs analyzed by GSEA.
DOI: 10.6084/m9.figshare.7612205
title: Additional file 1: of CCNE1 amplification is associated with poor prognosis in patients with triple negative breast cancer

description: Table S3. Genomic alteration data for the â Pilot-TNBCâ cohort. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.7612205.v1
title: Additional file 1: of CCNE1 amplification is associated with poor prognosis in patients with triple negative breast cancer

description: Table S3. Genomic alteration data for the â Pilot-TNBCâ cohort. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.7612208
title: MOESM5 of An integrative genomic analysis of transcriptional profiles identifies characteristic genes and patterns in HIV-infected long-term non-progressors and elite controllers

description: Additional file 5. Genes in modules correlated with protection in CD8+ T cells (EC).
DOI: 10.6084/m9.figshare.7612208.v1
title: MOESM5 of An integrative genomic analysis of transcriptional profiles identifies characteristic genes and patterns in HIV-infected long-term non-progressors and elite controllers

description: Additional file 5. Genes in modules correlated with protection in CD8+ T cells (EC).
DOI: 10.6084/m9.figshare.7612211
title: Additional file 5: of Transcriptome analyses provide insights into the expression pattern and sequence similarity of several taxol biosynthesis-related genes in three Taxus species

description: Table S3. The significant values of each JA-related GO terms in various comparisons. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7612211.v1
title: Additional file 5: of Transcriptome analyses provide insights into the expression pattern and sequence similarity of several taxol biosynthesis-related genes in three Taxus species

description: Table S3. The significant values of each JA-related GO terms in various comparisons. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7612217
title: Additional file 6: of Transcriptome analyses provide insights into the expression pattern and sequence similarity of several taxol biosynthesis-related genes in three Taxus species

description: Table S4. The expression levels of the JA-related genes in different Taxus species. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.19146554
title: Composition, Age, and Origin of Ordovician-Devonian Tanjianshan granitoids in the North Qaidam Orogenic Belt of northern Tibet: Implications for Tectonic Evolution

description: The North Qaidam Orogenic Belt (NQOB) is characterized by widespread Palaeozoic magmatism and high to ultrahigh-pressure metamorphism that provides important information regarding the continental crust growth and tectonic evolution in the North Qaidam. Our work focuses on the geology, geochronology, whole-rock geochemistry, and Sr–Nd isotopy of granitoids in the Tanjianshan area in the northern NQOB. The results indicate that the 486–469 Ma adakitic and TTG-like granitoids originated from the partial melting of Middle–Late Mesoproterozoic lower crustal materials with the addition of juvenile mafic lower crust at high pressures under an active continental margin setting. The 396–392 Ma I-type granitoids originated from the partial melting of juvenile crustal materials with the addition of ancient crustal component in a post-collisional setting. Geochronological studies show that there are significant regional differences in magmatism between the northern and rest parts of the NQOB. In the northern part, extensive and prolonged magmatism was widespread during oceanic subduction (~526–460 Ma) and post-collisional extension (~420–350 Ma) but magmatism in the stage of orogenic collision was absent. The Early Palaeozoic adakitic magmatism suggest a significant continental crustal reworking in a subduction zone during 486–469 Ma along the NQOB. The initial oceanic subduction may have occurred prior to ca. 526 Ma. An intense and multiple-stage extension developed at ~420–350 Ma in the northern part of the NQOB following the orogenic collapse. Lithospheric delamination and subsequent mafic magma underplating may be the main geodynamic mechanism resulting in the uprooting of the continental crust and ore mineralization in response.
DOI: 10.6084/m9.figshare.7612217.v1
title: Additional file 6: of Transcriptome analyses provide insights into the expression pattern and sequence similarity of several taxol biosynthesis-related genes in three Taxus species

description: Table S4. The expression levels of the JA-related genes in different Taxus species. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.19146554.v1
title: Composition, Age, and Origin of Ordovician-Devonian Tanjianshan granitoids in the North Qaidam Orogenic Belt of northern Tibet: Implications for Tectonic Evolution

description: The North Qaidam Orogenic Belt (NQOB) is characterized by widespread Palaeozoic magmatism and high to ultrahigh-pressure metamorphism that provides important information regarding the continental crust growth and tectonic evolution in the North Qaidam. Our work focuses on the geology, geochronology, whole-rock geochemistry, and Sr–Nd isotopy of granitoids in the Tanjianshan area in the northern NQOB. The results indicate that the 486–469 Ma adakitic and TTG-like granitoids originated from the partial melting of Middle–Late Mesoproterozoic lower crustal materials with the addition of juvenile mafic lower crust at high pressures under an active continental margin setting. The 396–392 Ma I-type granitoids originated from the partial melting of juvenile crustal materials with the addition of ancient crustal component in a post-collisional setting. Geochronological studies show that there are significant regional differences in magmatism between the northern and rest parts of the NQOB. In the northern part, extensive and prolonged magmatism was widespread during oceanic subduction (~526–460 Ma) and post-collisional extension (~420–350 Ma) but magmatism in the stage of orogenic collision was absent. The Early Palaeozoic adakitic magmatism suggest a significant continental crustal reworking in a subduction zone during 486–469 Ma along the NQOB. The initial oceanic subduction may have occurred prior to ca. 526 Ma. An intense and multiple-stage extension developed at ~420–350 Ma in the northern part of the NQOB following the orogenic collapse. Lithospheric delamination and subsequent mafic magma underplating may be the main geodynamic mechanism resulting in the uprooting of the continental crust and ore mineralization in response.
DOI: 10.6084/m9.figshare.7612223
title: Additional file 7: of Transcriptome analyses provide insights into the expression pattern and sequence similarity of several taxol biosynthesis-related genes in three Taxus species

description: Table S5. Identifications of transcription factors of the three Taxus species. (XLSX 205 kb)
DOI: 10.6084/m9.figshare.7612223.v1
title: Additional file 7: of Transcriptome analyses provide insights into the expression pattern and sequence similarity of several taxol biosynthesis-related genes in three Taxus species

description: Table S5. Identifications of transcription factors of the three Taxus species. (XLSX 205 kb)
DOI: 10.6084/m9.figshare.7612226
title: Additional file 4: of CCNE1 amplification is associated with poor prognosis in patients with triple negative breast cancer

description: Table S1. Normalized mRNA expression data for the â Pilot-TNBCâ cohort. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7612226.v1
title: Additional file 4: of CCNE1 amplification is associated with poor prognosis in patients with triple negative breast cancer

description: Table S1. Normalized mRNA expression data for the â Pilot-TNBCâ cohort. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7612229
title: Additional file 8: of Transcriptome analyses provide insights into the expression pattern and sequence similarity of several taxol biosynthesis-related genes in three Taxus species

description: Table S6. The numbers of differential expressed TFs in the three comparisons. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7612229.v1
title: Additional file 8: of Transcriptome analyses provide insights into the expression pattern and sequence similarity of several taxol biosynthesis-related genes in three Taxus species

description: Table S6. The numbers of differential expressed TFs in the three comparisons. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7612235
title: Additional file 5: of CCNE1 amplification is associated with poor prognosis in patients with triple negative breast cancer

description: Table S2. Normalized mRNA expression data for the â Discovery-TNBCâ cohort. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.7612235.v1
title: Additional file 5: of CCNE1 amplification is associated with poor prognosis in patients with triple negative breast cancer

description: Table S2. Normalized mRNA expression data for the â Discovery-TNBCâ cohort. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.12855149
title: Metadata record for the manuscript: The genomic landscape of metastatic histologic special types of invasive breast cancer

description: <b>Summary</b><br>This metadata record provides details of the data supporting the claims of the related manuscript: “The genomic landscape of metastatic histologic special types of invasive breast cancer ”. The related study aimed to define the repertoire of somatic genetic alterations of metastatic histologic special types of breast cancer. The study re-analyzed targeted capture sequencing data of 309 special types of breast cancer, including metastatic and primary invasive lobular carcinomas (n=132 and n=127, respectively), mixed mucinous (n=5 metastatic and n=14 primary), micropapillary (n=12 metastatic and n=8 primary) and metaplastic breast cancers (n=6 metastatic and n=5 primary), and compared metastatic histologic special types of breast cancer to metastatic invasive ductal carcinomas of no special type (IDC-NSTs) matched according to clinicopathologic characteristics and to primary special type breast cancers.<br><b>Data access</b>The data supporting the related study are as follows:- Histologic images supporting Figures 1, 2, 3, 4, and Supplementary Figure 7: these are not publicly available, but can be requested from the corresponding author, Dr. Fresia Pareja.- MSK-IMPACT sequencing data supporting Figures 1, 2, 3, 4, 5, Supplementary Figures 1, 2, 3, 4, 5, 6, and Supplementary Table 3, 4, 5: these data are publicly available in cBioPortal at the following accession: https://identifiers.org/cbioportal:breast_msk_2018 - Clinical data supporting supplementary Tables 1, 2, 5 and 6: these data are available in the original publication by Razavi et al (https://doi.org/10.1016/j.ccell.2018.08.008).<br><b>Corresponding author</b>Dr. Fresia Pareja Memorial Sloan Kettering Cancer CenterDepartment of Pathology1275 York AvenueNew York, NY 10065United States212-639-3707parejaf@mskcc.org<br><b>Name of Institutional Review Board or ethics committee that approved the study</b><br>The study was approved by Memorial Sloan Kettering Cancer Center Institutional Review Board as part of the project whose findings were initially published by Razavi et al (2018). Informed consent was provided in the original study by Razavi et al “2018).<br>
DOI: 10.6084/m9.figshare.12855149.v1
title: Metadata record for the manuscript: The genomic landscape of metastatic histologic special types of invasive breast cancer

description: <b>Summary</b><br>This metadata record provides details of the data supporting the claims of the related manuscript: “The genomic landscape of metastatic histologic special types of invasive breast cancer ”. The related study aimed to define the repertoire of somatic genetic alterations of metastatic histologic special types of breast cancer. The study re-analyzed targeted capture sequencing data of 309 special types of breast cancer, including metastatic and primary invasive lobular carcinomas (n=132 and n=127, respectively), mixed mucinous (n=5 metastatic and n=14 primary), micropapillary (n=12 metastatic and n=8 primary) and metaplastic breast cancers (n=6 metastatic and n=5 primary), and compared metastatic histologic special types of breast cancer to metastatic invasive ductal carcinomas of no special type (IDC-NSTs) matched according to clinicopathologic characteristics and to primary special type breast cancers.<br><b>Data access</b>The data supporting the related study are as follows:- Histologic images supporting Figures 1, 2, 3, 4, and Supplementary Figure 7: these are not publicly available, but can be requested from the corresponding author, Dr. Fresia Pareja.- MSK-IMPACT sequencing data supporting Figures 1, 2, 3, 4, 5, Supplementary Figures 1, 2, 3, 4, 5, 6, and Supplementary Table 3, 4, 5: these data are publicly available in cBioPortal at the following accession: https://identifiers.org/cbioportal:breast_msk_2018 - Clinical data supporting supplementary Tables 1, 2, 5 and 6: these data are available in the original publication by Razavi et al (https://doi.org/10.1016/j.ccell.2018.08.008).<br><b>Corresponding author</b>Dr. Fresia Pareja Memorial Sloan Kettering Cancer CenterDepartment of Pathology1275 York AvenueNew York, NY 10065United States212-639-3707parejaf@mskcc.org<br><b>Name of Institutional Review Board or ethics committee that approved the study</b><br>The study was approved by Memorial Sloan Kettering Cancer Center Institutional Review Board as part of the project whose findings were initially published by Razavi et al (2018). Informed consent was provided in the original study by Razavi et al “2018).<br>
DOI: 10.6084/m9.figshare.7612406
title: Additional file 4: of Soybean (Glycine max L. Merr.) seedlings response to shading: leaf structure, photosynthesis and proteomic analysis

description: MS identified information. (XLSX 2750 kb)
DOI: 10.6084/m9.figshare.7612406.v1
title: Additional file 4: of Soybean (Glycine max L. Merr.) seedlings response to shading: leaf structure, photosynthesis and proteomic analysis

description: MS identified information. (XLSX 2750 kb)
DOI: 10.6084/m9.figshare.7612412
title: Additional file 5: of Soybean (Glycine max L. Merr.) seedlings response to shading: leaf structure, photosynthesis and proteomic analysis

description: Differentially expressed statistics. (XLSX 62 kb)
DOI: 10.6084/m9.figshare.7612412.v1
title: Additional file 5: of Soybean (Glycine max L. Merr.) seedlings response to shading: leaf structure, photosynthesis and proteomic analysis

description: Differentially expressed statistics. (XLSX 62 kb)
DOI: 10.6084/m9.figshare.7612433
title: MOESM10 of Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis

description: Additional file 10: Table S5. Overview of differentially expressed transcription factors during seed development of H. benghalensis.
DOI: 10.6084/m9.figshare.7612433.v1
title: MOESM10 of Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis

description: Additional file 10: Table S5. Overview of differentially expressed transcription factors during seed development of H. benghalensis.
DOI: 10.6084/m9.figshare.7612442
title: MOESM11 of Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis

description: Additional file 11: Table S6. Overview of the predicted lncRNAs in H. benghalensis seeds.
DOI: 10.6084/m9.figshare.7612442.v1
title: MOESM11 of Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis

description: Additional file 11: Table S6. Overview of the predicted lncRNAs in H. benghalensis seeds.
DOI: 10.6084/m9.figshare.7612448
title: MOESM12 of Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis

description: Additional file 12: Table S7. Overview of the differentially expressed lncRNAs co-expressed with the major lipid-related genes in H. benghalensis seeds.
DOI: 10.6084/m9.figshare.7612448.v1
title: MOESM12 of Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis

description: Additional file 12: Table S7. Overview of the differentially expressed lncRNAs co-expressed with the major lipid-related genes in H. benghalensis seeds.
DOI: 10.6084/m9.figshare.7612454
title: MOESM13 of Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis

description: Additional file 13: Table S8. Expression level correlations between FPKM and 2−ΔΔCt.
DOI: 10.6084/m9.figshare.7612454.v1
title: MOESM13 of Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis

description: Additional file 13: Table S8. Expression level correlations between FPKM and 2−ΔΔCt.
DOI: 10.6084/m9.figshare.7612460
title: MOESM14 of Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis

description: Additional file 14: Table S9. Primers used in qRT-PCR.
DOI: 10.6084/m9.figshare.7612460.v1
title: MOESM14 of Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis

description: Additional file 14: Table S9. Primers used in qRT-PCR.
DOI: 10.6084/m9.figshare.7612463
title: MOESM1 of Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis

description: Additional file 1: Table S1. Ricinoleic acid content of seeds from six Hiptage species.
DOI: 10.6084/m9.figshare.7612463.v1
title: MOESM1 of Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis

description: Additional file 1: Table S1. Ricinoleic acid content of seeds from six Hiptage species.
DOI: 10.6084/m9.figshare.7612475
title: MOESM3 of Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis

description: Additional file 3: Table S2. Summary of the Illumina sequencing data.
DOI: 10.6084/m9.figshare.7612475.v1
title: MOESM3 of Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis

description: Additional file 3: Table S2. Summary of the Illumina sequencing data.
DOI: 10.6084/m9.figshare.7612490
title: MOESM6 of Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis

description: Additional file 6: Table S3. Expression of lipid metabolism associated genes in H. benghalensis.
DOI: 10.6084/m9.figshare.7612490.v1
title: MOESM6 of Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis

description: Additional file 6: Table S3. Expression of lipid metabolism associated genes in H. benghalensis.