cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5797665.v1
title: MOESM9 of Working towards recalcitrance mechanisms: increased xylan and homogalacturonan production by overexpression of GAlactUronosylTransferase12 (GAUT12) causes increased recalcitrance and decreased growth in Populus

description: Additional file 9. Glycosyl residue composition and total carbohydrate of cell wall extracts from stem tissues of 9-month-old, greenhouse-grown P. deltoides WT and PdGAUT12.1-KD lines (AB30.1, AB30.3, AB30.8 and AB30.11). Data are average μg amount of each designated monosaccharide per mg alcohol insoluble residue (AIR), measured by GC–MS of tetramethylsilane (TMS) derivatives. Wall extracts are from sequential extractions of AIR using 50 mM ammonium oxalate, 50 mM sodium carbonate, 1 M KOH, 4 M KOH, 100 mM sodium chlorite (chlorite), 4 M KOH post-chlorite (PC), and the final residual insoluble pellet. The data, except for those of the insoluble wall fractions, were previously reported in mol% and mass (μg sugar/mg extract) [5]. Values in bold are those of the transgenic lines that are significantly different from WT values at *P &lt; 0.05 and **P &lt; 0.001 significant levels (one-way ANOVA followed by Tukey’s multiple comparison test).
DOI: 10.6084/m9.figshare.5797668
title: Additional file 5: of FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations

description: Top SSI protein-coding genes. (XLSX 60 kb)
DOI: 10.6084/m9.figshare.5797668.v1
title: Additional file 5: of FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations

description: Top SSI protein-coding genes. (XLSX 60 kb)
DOI: 10.6084/m9.figshare.5797671
title: Additional file 6: of Calcium-dependent protein kinases in cotton: insights into early plant responses to salt stress

description: Reads per kilobase of transcript per million mapped reads (RPKM) values of CPK genes in different cotton tissues. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.5797671.v1
title: Additional file 6: of Calcium-dependent protein kinases in cotton: insights into early plant responses to salt stress

description: Reads per kilobase of transcript per million mapped reads (RPKM) values of CPK genes in different cotton tissues. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.5797680
title: Additional file 6: of FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations

description: Top 100 FineMAV SNPs in each continental population (xâ =â 1). (XLSX 77 kb)
DOI: 10.6084/m9.figshare.5797680.v1
title: Additional file 6: of FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations

description: Top 100 FineMAV SNPs in each continental population (xâ =â 1). (XLSX 77 kb)
DOI: 10.6084/m9.figshare.5797686
title: Additional file 7: of Calcium-dependent protein kinases in cotton: insights into early plant responses to salt stress

description: Reads per kilobase of transcript per million mapped reads (RPKM) values of CPK genes in cotton leaves under salt stress. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.5797686.v1
title: Additional file 7: of Calcium-dependent protein kinases in cotton: insights into early plant responses to salt stress

description: Reads per kilobase of transcript per million mapped reads (RPKM) values of CPK genes in cotton leaves under salt stress. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.5797695
title: Additional file 8: of Calcium-dependent protein kinases in cotton: insights into early plant responses to salt stress

description: The cis-elements prediction of CPKs promoter. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.5797695.v1
title: Additional file 8: of Calcium-dependent protein kinases in cotton: insights into early plant responses to salt stress

description: The cis-elements prediction of CPKs promoter. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.5798295
title: Additional file 3 of Super-delta: a new differential gene expression analysis procedure with robust data normalization

description: Top 30 significant genesâ annotation. This file includes biological annotation of the 30 most significant genes, detected by each method, sorted by the magnitude of t-statistics. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.5798295.v1
title: Additional file 3 of Super-delta: a new differential gene expression analysis procedure with robust data normalization

description: Top 30 significant genesâ annotation. This file includes biological annotation of the 30 most significant genes, detected by each method, sorted by the magnitude of t-statistics. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.5798298
title: Additional file 4 of Super-delta: a new differential gene expression analysis procedure with robust data normalization

description: Gene set enrichment analysis. This file lists all the significant KEGG pathways obtained by the significant gene lists in Additional fileÂ 1. This gene set enrichment analysis was implemented in DAVID. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.5798298.v1
title: Additional file 4 of Super-delta: a new differential gene expression analysis procedure with robust data normalization

description: Gene set enrichment analysis. This file lists all the significant KEGG pathways obtained by the significant gene lists in Additional fileÂ 1. This gene set enrichment analysis was implemented in DAVID. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.5798301
title: Additional file 5 of Super-delta: a new differential gene expression analysis procedure with robust data normalization

description: A Comprehensive investigation of pairing genes. This file contains full information of the pairing genes of super-delta, including the gene set enrichment results of the pairing gene list of the significant genes in Additional fileÂ 1. (XLSX 152 kb)
DOI: 10.6084/m9.figshare.5798301.v1
title: Additional file 5 of Super-delta: a new differential gene expression analysis procedure with robust data normalization

description: A Comprehensive investigation of pairing genes. This file contains full information of the pairing genes of super-delta, including the gene set enrichment results of the pairing gene list of the significant genes in Additional fileÂ 1. (XLSX 152 kb)
DOI: 10.6084/m9.figshare.5798304
title: Additional file 6 of Super-delta: a new differential gene expression analysis procedure with robust data normalization

description: Rank difference analysis. This file contains information of most differently ranked significant genes between super-delta and quantile normalization. (XLSX 852 kb)
DOI: 10.6084/m9.figshare.5798304.v1
title: Additional file 6 of Super-delta: a new differential gene expression analysis procedure with robust data normalization

description: Rank difference analysis. This file contains information of most differently ranked significant genes between super-delta and quantile normalization. (XLSX 852 kb)
DOI: 10.6084/m9.figshare.5798307
title: Additional file 7 of Super-delta: a new differential gene expression analysis procedure with robust data normalization

description: Simulation study. This file contains the simulation result tables similar to TableÂ 2 of the main text, for all the sample size combinations used. (XLSX 3229 kb)
DOI: 10.6084/m9.figshare.5798307.v1
title: Additional file 7 of Super-delta: a new differential gene expression analysis procedure with robust data normalization

description: Simulation study. This file contains the simulation result tables similar to TableÂ 2 of the main text, for all the sample size combinations used. (XLSX 3229 kb)
DOI: 10.6084/m9.figshare.5798565
title: Additional file 8: Data S1. of Functional characterization of soybean strigolactone biosynthesis and signaling genes in Arabidopsis MAX mutants and GmMAX3 in soybean nodulation

description: Transcriptomic expression of different genes in GmMAX3b-OE and GmMAX3b-KD hairy roots. (XLS 89Â kb)
DOI: 10.6084/m9.figshare.5798565.v1
title: Additional file 8: Data S1. of Functional characterization of soybean strigolactone biosynthesis and signaling genes in Arabidopsis MAX mutants and GmMAX3 in soybean nodulation

description: Transcriptomic expression of different genes in GmMAX3b-OE and GmMAX3b-KD hairy roots. (XLS 89Â kb)
DOI: 10.6084/m9.figshare.5798595
title: Additional file 2: of Comparative transcriptome and proteome profiling of two Citrus sinensis cultivars during fruit development and ripening

description: Sequencing data and mapped reads by RNA-seq. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.5798595.v1
title: Additional file 2: of Comparative transcriptome and proteome profiling of two Citrus sinensis cultivars during fruit development and ripening

description: Sequencing data and mapped reads by RNA-seq. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.5798607
title: Additional file 6: of Comparative transcriptome and proteome profiling of two Citrus sinensis cultivars during fruit development and ripening

description: Analysis of co-expression of proteins and cognate mRNA identified at fruit delayed-harvest stage between two cultivars. (XLSX 478 kb)
DOI: 10.6084/m9.figshare.5798607.v1
title: Additional file 6: of Comparative transcriptome and proteome profiling of two Citrus sinensis cultivars during fruit development and ripening

description: Analysis of co-expression of proteins and cognate mRNA identified at fruit delayed-harvest stage between two cultivars. (XLSX 478 kb)
DOI: 10.6084/m9.figshare.5798616
title: Additional file 9: of Comparative transcriptome and proteome profiling of two Citrus sinensis cultivars during fruit development and ripening

description: The pairs of primers used to amplify the targeting genes by qPCR (XLSX 11 kb)
DOI: 10.6084/m9.figshare.5798616.v1
title: Additional file 9: of Comparative transcriptome and proteome profiling of two Citrus sinensis cultivars during fruit development and ripening

description: The pairs of primers used to amplify the targeting genes by qPCR (XLSX 11 kb)
DOI: 10.6084/m9.figshare.5798715
title: Additional file 1: of Differential responses of innate immunity triggered by different subtypes of influenza a viruses in human and avian hosts

description: Table S1. The sources of deep-sequencing transcriptome data of hosts infected with different subtypes of influenza viruses (XLSX 14 kb)
DOI: 10.6084/m9.figshare.5798715.v1
title: Additional file 1: of Differential responses of innate immunity triggered by different subtypes of influenza a viruses in human and avian hosts

description: Table S1. The sources of deep-sequencing transcriptome data of hosts infected with different subtypes of influenza viruses (XLSX 14 kb)
DOI: 10.6084/m9.figshare.5801808
title: Additional file 1: Table S1. of Influence of Schistosoma japonicum programmed cell death protein 10 on the growth and development of schistosomula

description: Primer sequences for real-time qPCR. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.5801808.v1
title: Additional file 1: Table S1. of Influence of Schistosoma japonicum programmed cell death protein 10 on the growth and development of schistosomula

description: Primer sequences for real-time qPCR. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.5801829
title: Additional file 2: Table S2. of Influence of Schistosoma japonicum programmed cell death protein 10 on the growth and development of schistosomula

description: Primer sequences for preparing dsRNA templates. Underlined sequences indicate the T7 promoter recognition site. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.5801829.v1
title: Additional file 2: Table S2. of Influence of Schistosoma japonicum programmed cell death protein 10 on the growth and development of schistosomula

description: Primer sequences for preparing dsRNA templates. Underlined sequences indicate the T7 promoter recognition site. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.5801847
title: Additional file 3: Table S3. of Influence of Schistosoma japonicum programmed cell death protein 10 on the growth and development of schistosomula

description: Semi-quantitative analysis of SjPCDP10 through the results of immunofluorescence. Stages included skin-stage schistosomula (30Â min), 3-day-old lung-stage schistosomula (3 d), 10-day-old liver-stage schistosomula (10 d), 14-day-old liver-stage schistosomula (14 d), 18-day-old liver-stage schistosomula (18 d), and 21-day-old liver-stage schistosomula (21 d). (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.5801847.v1
title: Additional file 3: Table S3. of Influence of Schistosoma japonicum programmed cell death protein 10 on the growth and development of schistosomula

description: Semi-quantitative analysis of SjPCDP10 through the results of immunofluorescence. Stages included skin-stage schistosomula (30Â min), 3-day-old lung-stage schistosomula (3 d), 10-day-old liver-stage schistosomula (10 d), 14-day-old liver-stage schistosomula (14 d), 18-day-old liver-stage schistosomula (18 d), and 21-day-old liver-stage schistosomula (21 d). (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.5801961
title: Additional file 1: of ReprDB and panDB: minimalist databases with maximal microbial representation

description: Title of data: Assembly accession numbers of genomes used to generate the in silico synthetic community. Description of data: a list of assembly accession numbers of genomes used to generate the in silico synthetic community. (TXT 1Â kb)
DOI: 10.6084/m9.figshare.5801961.v1
title: Additional file 1: of ReprDB and panDB: minimalist databases with maximal microbial representation

description: Title of data: Assembly accession numbers of genomes used to generate the in silico synthetic community. Description of data: a list of assembly accession numbers of genomes used to generate the in silico synthetic community. (TXT 1Â kb)
DOI: 10.6084/m9.figshare.5801976
title: Additional file 2: of ReprDB and panDB: minimalist databases with maximal microbial representation

description: Title of data: 16S RNA data downloaded from HMP and the variable regions sequenced. Description of data: a list of the 57 samples (SRS) downloaded from HMP, and the variable regions sequenced for each sample. (TXT 1Â kb)
DOI: 10.6084/m9.figshare.5801976.v1
title: Additional file 2: of ReprDB and panDB: minimalist databases with maximal microbial representation

description: Title of data: 16S RNA data downloaded from HMP and the variable regions sequenced. Description of data: a list of the 57 samples (SRS) downloaded from HMP, and the variable regions sequenced for each sample. (TXT 1Â kb)
DOI: 10.6084/m9.figshare.5801988
title: Additional file 10: Table S9. of The signature of liver cancer in immune cells DNA methylation

description: Multifactorial ANOVA analysis of 350 CGs. No interaction detected between group (HCC) and sex and age as independent variables with CG methylation as a dependent variable. (CSV 31 kb)
DOI: 10.6084/m9.figshare.5801988.v1
title: Additional file 10: Table S9. of The signature of liver cancer in immune cells DNA methylation

description: Multifactorial ANOVA analysis of 350 CGs. No interaction detected between group (HCC) and sex and age as independent variables with CG methylation as a dependent variable. (CSV 31 kb)
DOI: 10.6084/m9.figshare.5802009
title: Additional file 11: Table S10. of The signature of liver cancer in immune cells DNA methylation

description: Differentially methylated CG sites in T cell DNA between healthy controls and HCC. (CSV 1586 kb)
DOI: 10.6084/m9.figshare.5802009.v1
title: Additional file 11: Table S10. of The signature of liver cancer in immune cells DNA methylation

description: Differentially methylated CG sites in T cell DNA between healthy controls and HCC. (CSV 1586 kb)
DOI: 10.6084/m9.figshare.5802033
title: Additional file 12: Table S11. of The signature of liver cancer in immune cells DNA methylation

description: Correlation of methylation of CG sites associated with the PD-1 gene and progression of HCC. (CSV 2 kb)
DOI: 10.6084/m9.figshare.5802033.v1
title: Additional file 12: Table S11. of The signature of liver cancer in immune cells DNA methylation

description: Correlation of methylation of CG sites associated with the PD-1 gene and progression of HCC. (CSV 2 kb)
DOI: 10.6084/m9.figshare.5802045
title: Additional file 13: Table S12. of The signature of liver cancer in immune cells DNA methylation

description: Differentially methylated that correlate with HCC progression in PBMC. (CSV 57 kb)
DOI: 10.6084/m9.figshare.5802045.v1
title: Additional file 13: Table S12. of The signature of liver cancer in immune cells DNA methylation

description: Differentially methylated that correlate with HCC progression in PBMC. (CSV 57 kb)
DOI: 10.6084/m9.figshare.5802063
title: Additional file 14: Table S13. of The signature of liver cancer in immune cells DNA methylation

description: Clinical data of second cohort. (CSV 11 kb)
DOI: 10.6084/m9.figshare.5802063.v1
title: Additional file 14: Table S13. of The signature of liver cancer in immune cells DNA methylation

description: Clinical data of second cohort. (CSV 11 kb)
DOI: 10.6084/m9.figshare.5802066
title: Additional file 2: Table S2. of Genome-wide analysis of the potato Hsp20 gene family: identification, genomic organization and expression profiles in response to heat stress

description: FPKM values of 48 StHsp20 genes in various potato tissues. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.5802066.v1
title: Additional file 2: Table S2. of Genome-wide analysis of the potato Hsp20 gene family: identification, genomic organization and expression profiles in response to heat stress

description: FPKM values of 48 StHsp20 genes in various potato tissues. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.5802078
title: Additional file 15: Table S14. of The signature of liver cancer in immune cells DNA methylation

description: Clinical data of third cohort. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.5802078.v1
title: Additional file 15: Table S14. of The signature of liver cancer in immune cells DNA methylation

description: Clinical data of third cohort. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.5802096
title: Additional file 16: Table S15. of The signature of liver cancer in immune cells DNA methylation

description: Descriptive statistics for (Fig. 6a). (XLS 87 kb)
DOI: 10.6084/m9.figshare.5802096.v1
title: Additional file 16: Table S15. of The signature of liver cancer in immune cells DNA methylation

description: Descriptive statistics for (Fig. 6a). (XLS 87 kb)
DOI: 10.6084/m9.figshare.5802114
title: Additional file 17: Table S16. of The signature of liver cancer in immune cells DNA methylation

description: Clinical data of first cohort. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.5802114.v1
title: Additional file 17: Table S16. of The signature of liver cancer in immune cells DNA methylation

description: Clinical data of first cohort. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.5802132
title: Additional file 18: Table S17. of The signature of liver cancer in immune cells DNA methylation

description: Pyrosequencing primers. (CSV 867 bytes)
DOI: 10.6084/m9.figshare.5802132.v1
title: Additional file 18: Table S17. of The signature of liver cancer in immune cells DNA methylation

description: Pyrosequencing primers. (CSV 867 bytes)
DOI: 10.6084/m9.figshare.5802147
title: Additional file 1: Table S1. of The signature of liver cancer in immune cells DNA methylation

description: CG sites whose quantitative level of DNA methylation correlates with the stage of HCC as determined by a Pearson correlation analysis (P&lt;1x10-7). (CSV 675 kb)
DOI: 10.6084/m9.figshare.5802147.v1
title: Additional file 1: Table S1. of The signature of liver cancer in immune cells DNA methylation

description: CG sites whose quantitative level of DNA methylation correlates with the stage of HCC as determined by a Pearson correlation analysis (P&lt;1x10-7). (CSV 675 kb)
DOI: 10.6084/m9.figshare.5802150
title: Additionnal file 2: Table S4.

description: Regions with 3 fold higher recombinant ratio than genome average. D_Downstream, D_Exon, D_Intron, D_Upstream, D_Intergenic: SNP density in 2 kâ downstream, exon, intron, 2 kâ upstream of genic regions and SNP density in intergenic regions. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.5802150.v1
title: Additionnal file 2: Table S4.

description: Regions with 3 fold higher recombinant ratio than genome average. D_Downstream, D_Exon, D_Intron, D_Upstream, D_Intergenic: SNP density in 2 kâ downstream, exon, intron, 2 kâ upstream of genic regions and SNP density in intergenic regions. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.5802168
title: Additional file 2: Table S2. of The signature of liver cancer in immune cells DNA methylation

description: Differentially methylated sites between Stage 1 HCC and healthy controls. (CSV 929 kb)
DOI: 10.6084/m9.figshare.5802168.v1
title: Additional file 2: Table S2. of The signature of liver cancer in immune cells DNA methylation

description: Differentially methylated sites between Stage 1 HCC and healthy controls. (CSV 929 kb)
DOI: 10.6084/m9.figshare.5802186
title: Additional file 3: Table S3. of The signature of liver cancer in immune cells DNA methylation

description: Differentially methylated sites between Stage 2 HCC and healthy controls. (CSV 1433 kb)
DOI: 10.6084/m9.figshare.5802186.v1
title: Additional file 3: Table S3. of The signature of liver cancer in immune cells DNA methylation

description: Differentially methylated sites between Stage 2 HCC and healthy controls. (CSV 1433 kb)
DOI: 10.6084/m9.figshare.5802195
title: Additional file 4: Table S4. of The signature of liver cancer in immune cells DNA methylation

description: Differentially methylated sites between Stage 3 HCC and healthy controls. (CSV 2002 kb)
DOI: 10.6084/m9.figshare.5802195.v1
title: Additional file 4: Table S4. of The signature of liver cancer in immune cells DNA methylation

description: Differentially methylated sites between Stage 3 HCC and healthy controls. (CSV 2002 kb)
DOI: 10.6084/m9.figshare.5802207
title: Additional file 5: Table S5. of The signature of liver cancer in immune cells DNA methylation

description: Differentially methylated sites between Stage 4 HCC and healthy controls. (CSV 3562 kb)
DOI: 10.6084/m9.figshare.5802207.v1
title: Additional file 5: Table S5. of The signature of liver cancer in immune cells DNA methylation

description: Differentially methylated sites between Stage 4 HCC and healthy controls. (CSV 3562 kb)
DOI: 10.6084/m9.figshare.5802219
title: Additional file 6: Table S6. of The signature of liver cancer in immune cells DNA methylation

description: Annotated non-redundant list of 350CGs and 369 CGs that are differentially methylated between stages of HCC and healthy controls. (CSV 41 kb)
DOI: 10.6084/m9.figshare.5802219.v1
title: Additional file 6: Table S6. of The signature of liver cancer in immune cells DNA methylation

description: Annotated non-redundant list of 350CGs and 369 CGs that are differentially methylated between stages of HCC and healthy controls. (CSV 41 kb)
DOI: 10.6084/m9.figshare.5802234
title: Additional file 8: Table S7. of The signature of liver cancer in immune cells DNA methylation

description: List of CG DNA methylation markers derived from penalized regression model on 350 CG and 369CG sites distinguishing early stages HCC from late stages. (CSV 395 bytes)
DOI: 10.6084/m9.figshare.5802234.v1
title: Additional file 8: Table S7. of The signature of liver cancer in immune cells DNA methylation

description: List of CG DNA methylation markers derived from penalized regression model on 350 CG and 369CG sites distinguishing early stages HCC from late stages. (CSV 395 bytes)
DOI: 10.6084/m9.figshare.5802240
title: Additional file 9: Table S8. of The signature of liver cancer in immune cells DNA methylation

description: Multivariate analysis of 350 CGs. Table provides p values on the right and adjusted values (350 measurements, Bonferroni) on the left. (CSV 95 kb)
DOI: 10.6084/m9.figshare.5802240.v1
title: Additional file 9: Table S8. of The signature of liver cancer in immune cells DNA methylation

description: Multivariate analysis of 350 CGs. Table provides p values on the right and adjusted values (350 measurements, Bonferroni) on the left. (CSV 95 kb)