cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12293108
title: Metadata record for the manuscript: Polygenic risk score for the prediction of breast cancer is related to lesser terminal duct lobular unit involution of the breast

description: <b>Summary</b>The data described in this metadata record underlie the findings of the related manuscript, which evaluated whether a recently developed polygenic risk score (PRS) based on 313-common variants for breast cancer prediction is related to terminal duct lobular unit (TDLU) involution in the background, normal breast tissue, as this could provide mechanistic clues on the genetic predisposition to breast cancer. <br><b>Data access</b>The PRS data are in the R file ‘BC.impute.313.Rdata’. The BREAST Stamp Project data are not publicly available because the informed consent signed by the patients did not include public data sharing. However, these data are available through the Susan G. Komen Tissue Bank (KTB)’s virtual repository (http://virtualtissuebank.iu.edu). To request these data, contact Dr. Gretchen Gierach (gierachg@mail.nih.gov). The phenotype and polygenic risk scores are available from the dbGaP repository under the following accession ID: https://identifiers.org/dbgap:phs002062.v1.p1<br><b>Data contact details</b>Dr. Gretchen Gierach<br>National Cancer Institute<br>Division of Cancer Epidemiology and Genetics<br>Bethesda, MD 20892<br>United States<br>gierachg@mail.nih.gov<br><br><b>Name of Institutional Review Board or ethics committee that approved the study</b>Approval for this study was obtained from the Indiana University Institutional Review Board (IRB) and the National Institutes of Health Office of Human Subjects Research (NIH OHSR #4508).<br>
DOI: 10.6084/m9.figshare.12293108.v1
title: Metadata record for the manuscript: Polygenic risk score for the prediction of breast cancer is related to lesser terminal duct lobular unit involution of the breast

description: <b>Summary</b>The data described in this metadata record underlie the findings of the related manuscript, which evaluated whether a recently developed polygenic risk score (PRS) based on 313-common variants for breast cancer prediction is related to terminal duct lobular unit (TDLU) involution in the background, normal breast tissue, as this could provide mechanistic clues on the genetic predisposition to breast cancer. <br><b>Data access</b>The PRS data are in the R file ‘BC.impute.313.Rdata’. The BREAST Stamp Project data are not publicly available because the informed consent signed by the patients did not include public data sharing. However, these data are available through the Susan G. Komen Tissue Bank (KTB)’s virtual repository (http://virtualtissuebank.iu.edu). To request these data, contact Dr. Gretchen Gierach (gierachg@mail.nih.gov). The phenotype and polygenic risk scores are available from the dbGaP repository under the following accession ID: https://identifiers.org/dbgap:phs002062.v1.p1<br><b>Data contact details</b>Dr. Gretchen Gierach<br>National Cancer Institute<br>Division of Cancer Epidemiology and Genetics<br>Bethesda, MD 20892<br>United States<br>gierachg@mail.nih.gov<br><br><b>Name of Institutional Review Board or ethics committee that approved the study</b>Approval for this study was obtained from the Indiana University Institutional Review Board (IRB) and the National Institutes of Health Office of Human Subjects Research (NIH OHSR #4508).<br>
DOI: 10.6084/m9.figshare.12544781
title: Additional file 1 of Iodine adequacy in reproductive age and pregnant women living in the Western region of Saudi Arabia

description: Additional file 1.
DOI: 10.6084/m9.figshare.12544781.v1
title: Additional file 1 of Iodine adequacy in reproductive age and pregnant women living in the Western region of Saudi Arabia

description: Additional file 1.
DOI: 10.6084/m9.figshare.12544754
title: Additional file 5 of Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

description: Additional file 5: Table S12. Trypanosome, Onchocerca filarial and gastro-intestinal parasites detected from five animals of each cattle breed detected by microscopy and molecular diagnostics using ribosomal nuclear makers.
DOI: 10.6084/m9.figshare.12544754.v1
title: Additional file 5 of Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

description: Additional file 5: Table S12. Trypanosome, Onchocerca filarial and gastro-intestinal parasites detected from five animals of each cattle breed detected by microscopy and molecular diagnostics using ribosomal nuclear makers.
DOI: 10.6084/m9.figshare.12544733
title: Additional file 3 of Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

description: Additional file 3: Table S3. High impact Namchi breed specific SNP. Table S4. High impact Kapsiki breed specific SNP. Table S5. High impact Red Fulani breed specific SNP. Table S6. High impact White Fulani breed specific SNP. Table S7. High impact Gudali breed specific SNP. Table S8. High impact Brahman breed specific SNP. Table S9. High impact Holstein breed specific SNP. Table S10. High impact N’Dama breed specific SNP.
DOI: 10.6084/m9.figshare.12544721
title: Additional file 1 of Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

description: Additional file 1: Table S1. Pairwise alignment of contigs assembled from unmapped reads to the non-redundant nucleotide database.
DOI: 10.6084/m9.figshare.12544733.v1
title: Additional file 3 of Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

description: Additional file 3: Table S3. High impact Namchi breed specific SNP. Table S4. High impact Kapsiki breed specific SNP. Table S5. High impact Red Fulani breed specific SNP. Table S6. High impact White Fulani breed specific SNP. Table S7. High impact Gudali breed specific SNP. Table S8. High impact Brahman breed specific SNP. Table S9. High impact Holstein breed specific SNP. Table S10. High impact N’Dama breed specific SNP.
DOI: 10.6084/m9.figshare.12544721.v1
title: Additional file 1 of Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

description: Additional file 1: Table S1. Pairwise alignment of contigs assembled from unmapped reads to the non-redundant nucleotide database.
DOI: 10.6084/m9.figshare.12544649
title: Additional file 4 of Histone deacetylase 3 is required for development and metamorphosis in the red flour beetle, Tribolium castaneum

description: Additional file 4.
DOI: 10.6084/m9.figshare.12544643
title: Additional file 3 of Histone deacetylase 3 is required for development and metamorphosis in the red flour beetle, Tribolium castaneum

description: Additional file 3.
DOI: 10.6084/m9.figshare.12544649.v1
title: Additional file 4 of Histone deacetylase 3 is required for development and metamorphosis in the red flour beetle, Tribolium castaneum

description: Additional file 4.
DOI: 10.6084/m9.figshare.12544637
title: Additional file 2 of Histone deacetylase 3 is required for development and metamorphosis in the red flour beetle, Tribolium castaneum

description: Additional file 2.
DOI: 10.6084/m9.figshare.12544637.v1
title: Additional file 2 of Histone deacetylase 3 is required for development and metamorphosis in the red flour beetle, Tribolium castaneum

description: Additional file 2.
DOI: 10.6084/m9.figshare.12544643.v1
title: Additional file 3 of Histone deacetylase 3 is required for development and metamorphosis in the red flour beetle, Tribolium castaneum

description: Additional file 3.
DOI: 10.6084/m9.figshare.12544565
title: Additional file 2 of Gene expression predictions and networks in natural populations supports the omnigenic theory

description: Additional file 2 Suppl. Table 2. Distribution of core, peripheral and peripheral no grey genes across modules.
DOI: 10.6084/m9.figshare.12544559
title: Additional file 1 of Gene expression predictions and networks in natural populations supports the omnigenic theory

description: Additional file 1 Suppl. Table 1. Module membership of each gene.
DOI: 10.6084/m9.figshare.12544559.v1
title: Additional file 1 of Gene expression predictions and networks in natural populations supports the omnigenic theory

description: Additional file 1 Suppl. Table 1. Module membership of each gene.
DOI: 10.6084/m9.figshare.12544565.v1
title: Additional file 2 of Gene expression predictions and networks in natural populations supports the omnigenic theory

description: Additional file 2 Suppl. Table 2. Distribution of core, peripheral and peripheral no grey genes across modules.
DOI: 10.6084/m9.figshare.12544508
title: Additional file 1 of MicroRNA-181a as novel liquid biopsy marker of central nervous system involvement in pediatric acute lymphoblastic leukemia

description: Additional file 1: Table S1. Detailed description of patient cohorts. Table S2. List of 47 microRNAs screened in discovery study. Table S3. Contribution of miR-181-family members to principal components. Table S4. Rate of expression decrease of microRNAs in discovery cerebrospinal fluid samples at day 15th.
DOI: 10.6084/m9.figshare.12544508.v1
title: Additional file 1 of MicroRNA-181a as novel liquid biopsy marker of central nervous system involvement in pediatric acute lymphoblastic leukemia

description: Additional file 1: Table S1. Detailed description of patient cohorts. Table S2. List of 47 microRNAs screened in discovery study. Table S3. Contribution of miR-181-family members to principal components. Table S4. Rate of expression decrease of microRNAs in discovery cerebrospinal fluid samples at day 15th.
DOI: 10.6084/m9.figshare.12544472
title: Additional file 9 of Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense)

description: Additional file 9 Table S4. Information on the associated times and corresponding traits for stable QTLs.
DOI: 10.6084/m9.figshare.12544472.v1
title: Additional file 9 of Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense)

description: Additional file 9 Table S4. Information on the associated times and corresponding traits for stable QTLs.
DOI: 10.6084/m9.figshare.12544457
title: Additional file 7 of Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense)

description: Additional file 7 Table S3. Stable QTLs of five fiber quality traits identified by multi-loci mixed linear model.
DOI: 10.6084/m9.figshare.12544457.v1
title: Additional file 7 of Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense)

description: Additional file 7 Table S3. Stable QTLs of five fiber quality traits identified by multi-loci mixed linear model.
DOI: 10.6084/m9.figshare.12544436
title: Additional file 4 of Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense)

description: Additional file 4 Table S2. Information on high quality SNPs genotyped by CottonSNP80K array.
DOI: 10.6084/m9.figshare.12544424
title: Additional file 1 of Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense)

description: Additional file 1 Table S1. Information on 279 sea island cotton accessions used in this study.
DOI: 10.6084/m9.figshare.12544436.v1
title: Additional file 4 of Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense)

description: Additional file 4 Table S2. Information on high quality SNPs genotyped by CottonSNP80K array.
DOI: 10.6084/m9.figshare.12544424.v1
title: Additional file 1 of Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense)

description: Additional file 1 Table S1. Information on 279 sea island cotton accessions used in this study.
DOI: 10.6084/m9.figshare.12544412
title: Additional file 12 of Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense)

description: Additional file 12 Table S7. Expression profile of genes located in QTL regions related to fiber qualities.
DOI: 10.6084/m9.figshare.12544409
title: Additional file 11 of Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense)

description: Additional file 11 Table S6. GO analysis of genes specifically and simultaneously associated under normal and salt environments, respectively.
DOI: 10.6084/m9.figshare.12544412.v1
title: Additional file 12 of Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense)

description: Additional file 12 Table S7. Expression profile of genes located in QTL regions related to fiber qualities.
DOI: 10.6084/m9.figshare.12544409.v1
title: Additional file 11 of Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense)

description: Additional file 11 Table S6. GO analysis of genes specifically and simultaneously associated under normal and salt environments, respectively.
DOI: 10.6084/m9.figshare.12544400
title: Additional file 10 of Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense)

description: Additional file 10 Table S5. Candidate genes associated with fiber quality traits within QTL regions.
DOI: 10.6084/m9.figshare.12544400.v1
title: Additional file 10 of Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense)

description: Additional file 10 Table S5. Candidate genes associated with fiber quality traits within QTL regions.
DOI: 10.6084/m9.figshare.12544361
title: Additional file 1 of Prevalence of renal dysfunction among HIV infected patients receiving Tenofovir at Mulago: a cross-sectional study

description: Additional file 1. The datasets generated and/or analyzed during the study are available in excel format and uploaded as supplemental information.
DOI: 10.6084/m9.figshare.12544361.v1
title: Additional file 1 of Prevalence of renal dysfunction among HIV infected patients receiving Tenofovir at Mulago: a cross-sectional study

description: Additional file 1. The datasets generated and/or analyzed during the study are available in excel format and uploaded as supplemental information.
DOI: 10.6084/m9.figshare.12544319
title: Additional file 1 of Evaluation of serum-based real-time PCR to detect Schistosoma mansoni infection before and after treatment

description: Additional file 1. Dataset
DOI: 10.6084/m9.figshare.12544319.v1
title: Additional file 1 of Evaluation of serum-based real-time PCR to detect Schistosoma mansoni infection before and after treatment

description: Additional file 1. Dataset
DOI: 10.6084/m9.figshare.12544283
title: Additional file 2 of The effect of variant interference on de novo assembly for viral deep sequencing

description: Additional file 2. Number of contigs generated by SPades using the simulated data of two variants differed from 75% PID to 99.6% PID, across 20%-80% GC content.
DOI: 10.6084/m9.figshare.12544268
title: Additional file 3 of Spatio-temporal analysis of socio-economic characteristics for pulmonary tuberculosis in Sichuan province of China, 2006–2015

description: Additional file 3. The posteriori distributions of parameters in the parametric spatio-temporal interactions model without socio-economic covariates with the prior information with the Gamma distribution (0.1,0.1) and the default prior information with uniform distribution (0,1000) in 181 counties of Sichuan province, 2006 to 2015.
DOI: 10.6084/m9.figshare.12544283.v1
title: Additional file 2 of The effect of variant interference on de novo assembly for viral deep sequencing

description: Additional file 2. Number of contigs generated by SPades using the simulated data of two variants differed from 75% PID to 99.6% PID, across 20%-80% GC content.
DOI: 10.6084/m9.figshare.12544265
title: Additional file 2 of Spatio-temporal analysis of socio-economic characteristics for pulmonary tuberculosis in Sichuan province of China, 2006–2015

description: Additional file 2. The DICs of the five models under different priors’ distribution without social-economic variables. The minimum DIC was 19,379.01 and the model V was the best model with the prior information with the Gamma distribution (0.1,0.1) and the default prior information with uniform distribution (0,1000).
DOI: 10.6084/m9.figshare.12544268.v1
title: Additional file 3 of Spatio-temporal analysis of socio-economic characteristics for pulmonary tuberculosis in Sichuan province of China, 2006–2015

description: Additional file 3. The posteriori distributions of parameters in the parametric spatio-temporal interactions model without socio-economic covariates with the prior information with the Gamma distribution (0.1,0.1) and the default prior information with uniform distribution (0,1000) in 181 counties of Sichuan province, 2006 to 2015.
DOI: 10.6084/m9.figshare.12544265.v1
title: Additional file 2 of Spatio-temporal analysis of socio-economic characteristics for pulmonary tuberculosis in Sichuan province of China, 2006–2015

description: Additional file 2. The DICs of the five models under different priors’ distribution without social-economic variables. The minimum DIC was 19,379.01 and the model V was the best model with the prior information with the Gamma distribution (0.1,0.1) and the default prior information with uniform distribution (0,1000).
DOI: 10.6084/m9.figshare.12544184
title: Additional file 8 of Replication origin location might contribute to genetic variability in Trypanosoma cruzi

description: Additional file 8: Table S1. Total number of raw paired-end reads for each sample and respective replicate, followed by the high quality paired-end reads after the pre-processing quality approach and the percentage of mapped paired-end reads in the CL Brenner EL and NEL genome haplotypes. Table S2. The average of %Genome coverage based on paired-end reads for each sample mapped to the genome haplotypes, based on the paired-end reads with highest mapping quality. Table S3. Filtered fold change analysis and MACS2 of MFA-seq in non-Esmeraldo-like haplotype Table S4. Filtered fold change analysis and MACS2 of MFA-seq in non-Esmeraldo-like haplotype (replicate 2) Table S5. Filtered fold change analysis and MACS2 of MFA-seq in Esmeraldo-like haplotype Table S6. Filtered fold change analysis and MACS2 of MFA-seq in Esmeraldo-like haplotype (replicate 2) Table S7. Comparison between MFA-seq peaks detected at replicates 1 and 2 Table S8. Position of MFA-seq peaks (Consensus) in non-Esmeraldo-like haplotype Table S9. Position of MFA-seq peaks (Consensus) in Esmeraldo-like haplotype Table S10. Genes where ORIs where found in chromosomes that do not harbor DGF-1 Table S11. Position of MFA-seq peaks (Consensus) in non Esmeraldo-like haplotype (replicate 2) Table S12. Position of MFA-seq peaks (Consensus) in Esmeraldo-like haplotype (replicate 2) Table S13. MFA-seq peaks (Consensus) that overlap between replicates Table S14. Percentage of DGF-1(bp) in the entire genome Table S15. Genomic location and IDs of subtelomeric genes described at Moraes-Barros 2012
DOI: 10.6084/m9.figshare.12544184.v1
title: Additional file 8 of Replication origin location might contribute to genetic variability in Trypanosoma cruzi

description: Additional file 8: Table S1. Total number of raw paired-end reads for each sample and respective replicate, followed by the high quality paired-end reads after the pre-processing quality approach and the percentage of mapped paired-end reads in the CL Brenner EL and NEL genome haplotypes. Table S2. The average of %Genome coverage based on paired-end reads for each sample mapped to the genome haplotypes, based on the paired-end reads with highest mapping quality. Table S3. Filtered fold change analysis and MACS2 of MFA-seq in non-Esmeraldo-like haplotype Table S4. Filtered fold change analysis and MACS2 of MFA-seq in non-Esmeraldo-like haplotype (replicate 2) Table S5. Filtered fold change analysis and MACS2 of MFA-seq in Esmeraldo-like haplotype Table S6. Filtered fold change analysis and MACS2 of MFA-seq in Esmeraldo-like haplotype (replicate 2) Table S7. Comparison between MFA-seq peaks detected at replicates 1 and 2 Table S8. Position of MFA-seq peaks (Consensus) in non-Esmeraldo-like haplotype Table S9. Position of MFA-seq peaks (Consensus) in Esmeraldo-like haplotype Table S10. Genes where ORIs where found in chromosomes that do not harbor DGF-1 Table S11. Position of MFA-seq peaks (Consensus) in non Esmeraldo-like haplotype (replicate 2) Table S12. Position of MFA-seq peaks (Consensus) in Esmeraldo-like haplotype (replicate 2) Table S13. MFA-seq peaks (Consensus) that overlap between replicates Table S14. Percentage of DGF-1(bp) in the entire genome Table S15. Genomic location and IDs of subtelomeric genes described at Moraes-Barros 2012
DOI: 10.6084/m9.figshare.12544079
title: Additional file 2 of Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation

description: Additional file 2: Table S4. Genome assembly overview. Table S7. GeneConv results. Table S8. Gene clusters in which positive selection was found. Table S10. Orthologue cluster genes containig SNPs associated to the strain isolation environment.
DOI: 10.6084/m9.figshare.12544079.v1
title: Additional file 2 of Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation

description: Additional file 2: Table S4. Genome assembly overview. Table S7. GeneConv results. Table S8. Gene clusters in which positive selection was found. Table S10. Orthologue cluster genes containig SNPs associated to the strain isolation environment.
DOI: 10.6084/m9.figshare.12544049
title: Additional file 1 of Genome-wide identification and characterization of SnRK family genes in Brassica napus

description: Additional file 1: Table S1. The information of A. thaliana SnRKs in queries. Table S2. Characteristics of SnRK family in B.napus. Table S3. List of the 114 BnSnRK genes identified in this study. Table S4. Conserved amino acid motifs and annotation of BnSnRKs. Table S5. Syntenic blocks and Ka/Ks values of BnSnRK genes. Table S6. One-to-one orthologous relationships between B.napus and A.thaliana. Table S7. The expression profiles (log2-based values) of the BnSnRKs under different tissues. Table S8. The expression profiles (ratio to control values) of the BnSnRKs under different abiotic stresses. Table S9. List of the BnSnRK SNPs identified in this study.