cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8305397
title: Additional file 9: of Transcriptome profiling reveals significant changes in the gastric muscularis externa with obesity that partially overlap those that occur with idiopathic gastroparesis

description: Table S6. Reanalysis of RNA sequencing data following combining low and high BMI gastroparesis subjects into one group. (XLSX 13418 kb)
DOI: 10.6084/m9.figshare.8305397.v1
title: Additional file 9: of Transcriptome profiling reveals significant changes in the gastric muscularis externa with obesity that partially overlap those that occur with idiopathic gastroparesis

description: Table S6. Reanalysis of RNA sequencing data following combining low and high BMI gastroparesis subjects into one group. (XLSX 13418 kb)
DOI: 10.6084/m9.figshare.8305445
title: Additional file 2: of Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress

description: Table S1. Statistical analyses and mapping results of RNA sequencing reads. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.13024007
title: Additional file 7 of A WRKY transcription factor, TaWRKY42-B, facilitates initiation of leaf senescence by promoting jasmonic acid biosynthesis

description: Additional file 7: Table S1. Primers and probes used in this study.
DOI: 10.6084/m9.figshare.8305445.v1
title: Additional file 2: of Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress

description: Table S1. Statistical analyses and mapping results of RNA sequencing reads. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.13024007.v1
title: Additional file 7 of A WRKY transcription factor, TaWRKY42-B, facilitates initiation of leaf senescence by promoting jasmonic acid biosynthesis

description: Additional file 7: Table S1. Primers and probes used in this study.
DOI: 10.6084/m9.figshare.8305454
title: Additional file 3: of Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress

description: Table S2. List of the core gene set of sesame involved in response to drought stress. (XLSX 278 kb)
DOI: 10.6084/m9.figshare.8305454.v1
title: Additional file 3: of Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress

description: Table S2. List of the core gene set of sesame involved in response to drought stress. (XLSX 278 kb)
DOI: 10.6084/m9.figshare.8305460
title: Additional file 4: of Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress

description: Table S3. Robust differentially expressed genes between DT and DS during the drought stress. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.8305460.v1
title: Additional file 4: of Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress

description: Table S3. Robust differentially expressed genes between DT and DS during the drought stress. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.8305463
title: Additional file 5: of Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress

description: Table S4. Important drought-responsive metabolites identified by PLS-DA in DT. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.8305463.v1
title: Additional file 5: of Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress

description: Table S4. Important drought-responsive metabolites identified by PLS-DA in DT. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.8305466
title: Additional file 6: of Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress

description: Table S5. Important drought-responsive metabolites identified by PLS-DA in DS. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.8305466.v1
title: Additional file 6: of Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress

description: Table S5. Important drought-responsive metabolites identified by PLS-DA in DS. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.8305481
title: Additional file 8: of Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress

description: Table S7. Detailed results from the metabolomic pathway analysis. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8305481.v1
title: Additional file 8: of Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress

description: Table S7. Detailed results from the metabolomic pathway analysis. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8305487
title: Additional file 9: of Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress

description: Table S8. List of primers used for quantitative real-time RT-PCR analysis. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8305487.v1
title: Additional file 9: of Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress

description: Table S8. List of primers used for quantitative real-time RT-PCR analysis. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9878378
title: Essential roles of HDAC1 and 2 in lineage development and genome-wide DNA methylation during mouse preimplantation development

description: Epigenetic modifications, including DNA methylation and histone modifications, are reprogrammed considerably following fertilization during mammalian early embryonic development. Incomplete epigenetic reprogramming is a major factor leading to poor developmental outcome in embryos generated by assisted reproductive technologies, such as somatic cell nuclear transfer. However, the role of histone modifications in preimplantation development is poorly understood. Here, we show that co-knockdown (cKD) of <i>Hdac1</i> and <i>2</i> (but not individually) resulted in developmental failure during the morula to blastocyst transition. This outcome was also confirmed with the use of small-molecule HDAC1/2-specific inhibitor FK228. We observed reduced cell proliferation and increased incidence of apoptosis in cKD embryos, which were likely caused by increased acetylation of TRP53. Importantly, both RNA-seq and immunostaining analysis revealed a failure of lineage specification to generate trophectoderm and pluripotent cells. Among many gene expression changes, a substantial decrease of <i>Cdx2</i> may be partly accounted for by the aberrant Hippo pathway occurring in cKD embryos. In addition, we observed an increase in global DNA methylation, consistent with increased DNA methyltransferases and UHRF1. Interestingly, deficiency of RBBP4 and 7 (both are core components of several HDAC1/2-containing epigenetic complexes) results in similar phenotypes as those of cKD embryos. Overall, HDAC1 and 2 play redundant functions required for lineage specification, cell viability and accurate global DNA methylation, each contributing to critical developmental programmes safeguarding a successful preimplantation development.
DOI: 10.6084/m9.figshare.9878378.v1
title: Essential roles of HDAC1 and 2 in lineage development and genome-wide DNA methylation during mouse preimplantation development

description: Epigenetic modifications, including DNA methylation and histone modifications, are reprogrammed considerably following fertilization during mammalian early embryonic development. Incomplete epigenetic reprogramming is a major factor leading to poor developmental outcome in embryos generated by assisted reproductive technologies, such as somatic cell nuclear transfer. However, the role of histone modifications in preimplantation development is poorly understood. Here, we show that co-knockdown (cKD) of <i>Hdac1</i> and <i>2</i> (but not individually) resulted in developmental failure during the morula to blastocyst transition. This outcome was also confirmed with the use of small-molecule HDAC1/2-specific inhibitor FK228. We observed reduced cell proliferation and increased incidence of apoptosis in cKD embryos, which were likely caused by increased acetylation of TRP53. Importantly, both RNA-seq and immunostaining analysis revealed a failure of lineage specification to generate trophectoderm and pluripotent cells. Among many gene expression changes, a substantial decrease of <i>Cdx2</i> may be partly accounted for by the aberrant Hippo pathway occurring in cKD embryos. In addition, we observed an increase in global DNA methylation, consistent with increased DNA methyltransferases and UHRF1. Interestingly, deficiency of RBBP4 and 7 (both are core components of several HDAC1/2-containing epigenetic complexes) results in similar phenotypes as those of cKD embryos. Overall, HDAC1 and 2 play redundant functions required for lineage specification, cell viability and accurate global DNA methylation, each contributing to critical developmental programmes safeguarding a successful preimplantation development.
DOI: 10.6084/m9.figshare.20364142
title: Additional file 11 of Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane

description: Additional file 11.
DOI: 10.6084/m9.figshare.20364151
title: Additional file 2 of Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane

description: Additional file 2.
DOI: 10.6084/m9.figshare.25303594
title: Supplementary Material for: Comprehensive sex-stratified genetic analysis of 28 blood biomarkers and depression reveals a significant association between depression and low levels of total protein in females

description: Introduction
Major depression (MD) is more common amongst women than men, and MD episodes have been associated with fluctuations in reproductive hormones amongst women. To investigate biological underpinnings of heterogeneity in MD, the associations between depression, stratified by sex and including perinatal depression (PND), and blood biomarkers, using UK Biobank (UKB) data, were evaluated, and extended to include the association of depression with biomarker polygenic scores (PGS), generated as proxy for each biomarker. 
Method
Using female (N=39,761) and male (N=38,821) UKB participants, lifetime major depression (MD) and PND, were tested for association with 28 blood biomarkers. A GWAS was conducted for each biomarker and genetic correlations with depression subgroups were estimated. Using independent data from the Australian Genetics of Depression Study, PGS were constructed for each biomarker, and tested for association with depression status (n [female cases/controls]=9,006/6,442; n [male cases/controls]=3,106/6,222). Regions of significant local genetic correlation between depression subgroups and biomarkers highlighted by the PGS analysis were identified.
Results
Depression in females was significantly associated with levels of twelve biomarkers, including total protein (OR=0.90, CI=[0.86,0.94], P=3.9x10-6) and vitamin D (OR=0.94, CI=[0.90, 0.97], P=2.6x10-4), and PND with five biomarker levels, also including total protein (OR=0.88, CI=[0.81, 0.96], P=4.7x10-3). Depression in males was significantly associated with levels of eleven biomarkers. In the independent Australian Genetics of Depression Study, PGS analysis found significant associations for female depression and PND with total protein (female depression: OR=0.93, CI=[0.88, 0.98], P=3.6x10-3; PND: OR=0.91, CI=[0.86, 0.96], P=1.1x10-3), as well as with vitamin D (female depression: OR=0.93, CI=[0.89, 0.97], P=2.0x10-3; PND: OR=0.92, CI=[0.87, 0.97], P=1.4x10-3). The male depression sample did not report any significant results, and the point estimate of total protein (OR=0.98, CI=[0.92-1.04], P=4.7x10-1) did not indicate any association. Local genetic correlation analysis highlighted significant genetic correlation between PND and total protein, located in 5q13.3 (rG=0.68, CI=[0.33, 1.0], P=3.6x10-4). 
Discussion and Conclusion
Multiple lines of evidence from genetic analysis highlight an association between total serum protein levels and depression in females. Further research involving prospective measurement of total protein and depressive symptoms is warranted.
DOI: 10.6084/m9.figshare.25303594.v1
title: Supplementary Material for: Comprehensive sex-stratified genetic analysis of 28 blood biomarkers and depression reveals a significant association between depression and low levels of total protein in females

description: Introduction
Major depression (MD) is more common amongst women than men, and MD episodes have been associated with fluctuations in reproductive hormones amongst women. To investigate biological underpinnings of heterogeneity in MD, the associations between depression, stratified by sex and including perinatal depression (PND), and blood biomarkers, using UK Biobank (UKB) data, were evaluated, and extended to include the association of depression with biomarker polygenic scores (PGS), generated as proxy for each biomarker. 
Method
Using female (N=39,761) and male (N=38,821) UKB participants, lifetime major depression (MD) and PND, were tested for association with 28 blood biomarkers. A GWAS was conducted for each biomarker and genetic correlations with depression subgroups were estimated. Using independent data from the Australian Genetics of Depression Study, PGS were constructed for each biomarker, and tested for association with depression status (n [female cases/controls]=9,006/6,442; n [male cases/controls]=3,106/6,222). Regions of significant local genetic correlation between depression subgroups and biomarkers highlighted by the PGS analysis were identified.
Results
Depression in females was significantly associated with levels of twelve biomarkers, including total protein (OR=0.90, CI=[0.86,0.94], P=3.9x10-6) and vitamin D (OR=0.94, CI=[0.90, 0.97], P=2.6x10-4), and PND with five biomarker levels, also including total protein (OR=0.88, CI=[0.81, 0.96], P=4.7x10-3). Depression in males was significantly associated with levels of eleven biomarkers. In the independent Australian Genetics of Depression Study, PGS analysis found significant associations for female depression and PND with total protein (female depression: OR=0.93, CI=[0.88, 0.98], P=3.6x10-3; PND: OR=0.91, CI=[0.86, 0.96], P=1.1x10-3), as well as with vitamin D (female depression: OR=0.93, CI=[0.89, 0.97], P=2.0x10-3; PND: OR=0.92, CI=[0.87, 0.97], P=1.4x10-3). The male depression sample did not report any significant results, and the point estimate of total protein (OR=0.98, CI=[0.92-1.04], P=4.7x10-1) did not indicate any association. Local genetic correlation analysis highlighted significant genetic correlation between PND and total protein, located in 5q13.3 (rG=0.68, CI=[0.33, 1.0], P=3.6x10-4). 
Discussion and Conclusion
Multiple lines of evidence from genetic analysis highlight an association between total serum protein levels and depression in females. Further research involving prospective measurement of total protein and depressive symptoms is warranted.
DOI: 10.6084/m9.figshare.20364151.v1
title: Additional file 2 of Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane

description: Additional file 2.
DOI: 10.6084/m9.figshare.20364154
title: Additional file 3 of Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane

description: Additional file 3.
DOI: 10.6084/m9.figshare.20364154.v1
title: Additional file 3 of Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane

description: Additional file 3.
DOI: 10.6084/m9.figshare.20364142.v1
title: Additional file 11 of Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane

description: Additional file 11.
DOI: 10.6084/m9.figshare.20364145
title: Additional file 12 of Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane

description: Additional file 12.
DOI: 10.6084/m9.figshare.20364157
title: Additional file 4 of Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane

description: Additional file 4.
DOI: 10.6084/m9.figshare.20364145.v1
title: Additional file 12 of Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane

description: Additional file 12.
DOI: 10.6084/m9.figshare.20364157.v1
title: Additional file 4 of Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane

description: Additional file 4.
DOI: 10.6084/m9.figshare.20364166
title: Additional file 7 of Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane

description: Additional file 7.
DOI: 10.6084/m9.figshare.20364166.v1
title: Additional file 7 of Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane

description: Additional file 7.
DOI: 10.6084/m9.figshare.20364169
title: Additional file 8 of Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane

description: Additional file 8.
DOI: 10.6084/m9.figshare.20364169.v1
title: Additional file 8 of Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane

description: Additional file 8.
DOI: 10.6084/m9.figshare.20364172
title: Additional file 9 of Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane

description: Additional file 9.
DOI: 10.6084/m9.figshare.20364172.v1
title: Additional file 9 of Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane

description: Additional file 9.
DOI: 10.6084/m9.figshare.13024157.v1
title: Additional file 6 of Selection signatures of Fuzhong Buffalo based on whole-genome sequences

description: Additional file 6: Table S6. A summary of genes from XP-EHH.
DOI: 10.15468/dl.thb8v5
title: Occurrence Download

description: A dataset containing 774291 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2020-07-08",
 "EventDate is less than or equal to 2020-08-07",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 }
 ]
}

 The dataset includes 774291 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0397518-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-58936
title: Redemption tidings, vol. 40, nos. 1-50, 3 Jan. - 25 Dec. 1964

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.
DOI: 10.15468/dl.cq8wf9
title: Occurrence Download

description: A dataset containing 94 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Arracacia longipedunculata J.M.Coult. & Rose"
 ]
}

 The dataset includes 94 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052442-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vhb7xv
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Uncia uncia (Schreber, 1775)",
 "HasCoordinate is true",
 "HasGeospatialIssue is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000111-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zd2kty
title: Occurrence Download

description: A dataset containing 2424 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Micronycteris megalotis (Gray, 1842)"
 ]
}

 The dataset includes 2424 records from 119 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0353806-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-58914
title: Redemption tidings, vol. 40, nos. 1-50, 3 Jan. - 25 Dec. 1964

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.
DOI: 10.15468/dl.8vbs32
title: Occurrence Download

description: A dataset containing 293 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bronchocela marmorata Gray, 1845)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 293 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052441-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-57925
title: Redemption tidings, vol. 40, nos. 1-50, 3 Jan. - 25 Dec. 1964

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.
DOI: 10.15468/dl.obzqiv
title: Occurrence Download

description: A dataset containing 855 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sarracenia rubra Walter"
 ]
}

 The dataset includes 855 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002222-180925134338326/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8yf832
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bryaninops annella Suzuki & Randall, 2014"
 ]
}

 The dataset includes 7 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069787-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-57955
title: Redemption tidings, vol. 40, nos. 1-50, 3 Jan. - 25 Dec. 1964

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.