cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10730555.v1
title: MOESM10 of Transcriptome-wide analysis of changes in the fetal placenta associated with prenatal arsenic exposure in the New Hampshire Birth Cohort Study

description: Additional file 10. Gene sets enriched in both birth weight and U-As analyses in A) female and B) male fetal placenta at FDR &lt; 0.05. Gene sets showing opposite directions of association in 9A) are asterisked.
DOI: 10.6084/m9.figshare.17010175
title: Additional file 10 of Uncovering the Novel QTLs and Candidate Genes of Salt Tolerance in Rice with Linkage Mapping, RTM-GWAS, and RNA-seq

description: Additional file 10. Table S9. Haplotype analysis result of LOC_Os05g14880.
DOI: 10.6084/m9.figshare.10730570
title: MOESM2 of Transcriptome-wide analysis of changes in the fetal placenta associated with prenatal arsenic exposure in the New Hampshire Birth Cohort Study

description: Additional file 2. RNA-seq quality control data for A) female, and B) male placenta samples.
DOI: 10.6084/m9.figshare.10730570.v1
title: MOESM2 of Transcriptome-wide analysis of changes in the fetal placenta associated with prenatal arsenic exposure in the New Hampshire Birth Cohort Study

description: Additional file 2. RNA-seq quality control data for A) female, and B) male placenta samples.
DOI: 10.6084/m9.figshare.10730585
title: MOESM4 of Transcriptome-wide analysis of changes in the fetal placenta associated with prenatal arsenic exposure in the New Hampshire Birth Cohort Study

description: Additional file 4. Differentially expressed genes at high versus low U-As adjusted for maternal age at enrollment and batch. A) female placenta, B) male placenta.
DOI: 10.6084/m9.figshare.14905927.v1
title: Additional file 4 of Genome-wide identification of PTI1 family in Setaria italica and salinity-responsive functional analysis of SiPTI1–5

description: Additional file 4. The specific location of each SiPTI1 gene on the chromosomes.
DOI: 10.6084/m9.figshare.10730585.v1
title: MOESM4 of Transcriptome-wide analysis of changes in the fetal placenta associated with prenatal arsenic exposure in the New Hampshire Birth Cohort Study

description: Additional file 4. Differentially expressed genes at high versus low U-As adjusted for maternal age at enrollment and batch. A) female placenta, B) male placenta.
DOI: 10.6084/m9.figshare.10730597
title: MOESM6 of Transcriptome-wide analysis of changes in the fetal placenta associated with prenatal arsenic exposure in the New Hampshire Birth Cohort Study

description: Additional file 6. Gene sets enriched with differentially expressed genes at high versus low U-As at FDR &lt; 0.05, in A-B) female and C-D) male fetal placenta, and E) comparison.
DOI: 10.6084/m9.figshare.17010187.v1
title: Additional file 2 of Uncovering the Novel QTLs and Candidate Genes of Salt Tolerance in Rice with Linkage Mapping, RTM-GWAS, and RNA-seq

description: Additional file 2. Table S1. Meta-QTLs used in this study.
DOI: 10.6084/m9.figshare.10730597.v1
title: MOESM6 of Transcriptome-wide analysis of changes in the fetal placenta associated with prenatal arsenic exposure in the New Hampshire Birth Cohort Study

description: Additional file 6. Gene sets enriched with differentially expressed genes at high versus low U-As at FDR &lt; 0.05, in A-B) female and C-D) male fetal placenta, and E) comparison.
DOI: 10.6084/m9.figshare.17010199
title: Additional file 6 of Uncovering the Novel QTLs and Candidate Genes of Salt Tolerance in Rice with Linkage Mapping, RTM-GWAS, and RNA-seq

description: Additional file 6. Table S5. Known genes in Meta-QTLs.
DOI: 10.6084/m9.figshare.10730612
title: MOESM9 of Transcriptome-wide analysis of changes in the fetal placenta associated with prenatal arsenic exposure in the New Hampshire Birth Cohort Study

description: Additional file 9. Gene sets enriched with differentially expressed genes at high versus low birth weight at FDR &lt; 0.05, in A) female and B) male fetal placenta, and C) comparison.
DOI: 10.6084/m9.figshare.10730612.v1
title: MOESM9 of Transcriptome-wide analysis of changes in the fetal placenta associated with prenatal arsenic exposure in the New Hampshire Birth Cohort Study

description: Additional file 9. Gene sets enriched with differentially expressed genes at high versus low birth weight at FDR &lt; 0.05, in A) female and B) male fetal placenta, and C) comparison.
DOI: 10.6084/m9.figshare.12291638
title: Additional file 1 of Adaptive strategy of allohexaploid wheat to long-term salinity stress

description: Additional file 1: Figure S1. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment of differentially expressed genes in allohexaploid wheat leaf. Top 20 KEGG pathways with adjusted P value&lt;0.05 are displayed. Figure S2. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment of differentially expressed genes in allohexaploid wheat root. KEGG pathways with adjusted P value&lt;0.05 are displayed. Figure S3. Effects of long-term salinity stress on gene expression involved in wax biosynthesis. (a) Gene expression change was marked on the pathway of wax biosynthesis, and the red box indicates up-regulated expression under long-term salinity stress. The wax biosynthesis pathway diagram was adapted from the diagram of KEGG website. (b) Gene expression data involved in wax metabolism in wheat leaf under long-term salinity stress. FAR, alcohol-forming fatty acyl-CoA reductase. MAH1, midchain alkane hydroxylase; CYP96A15; WSD1, wax-ester synthase/diacylglycerol O-acyltransferase. Fold change = stress/control, Q value is the adjusted P value using the Benjamini-Hochberg method. Figure S4. Effects of long-term salinity stress on expression of two ferredoxin-NADP+ reductase (petH) genes in wheat leaves. Figure S5. Relationships among A, B and D homeologs in terms of expression fold change (stress/control) for all salinity-tolerant triads. Figure S6. Expression fold change (stress/control) of A, B and D homeologs of 15 typical salinity-tolerant triads. * indicates significant difference (adjusted P value &lt; 0.05 and |log2fold change| ≥ 1).
DOI: 10.6084/m9.figshare.14905954.v1
title: Additional file 2 of Stablization of ACOs by NatB mediated N-terminal acetylation is required for ethylene homeostasis

description: Additional file 2.
DOI: 10.6084/m9.figshare.25218842
title: Hemp Seed Oil Inhibits the Adipogenicity of the Differentiation-Induced Human Mesenchymal Stem Cells Through Suppressing the Cannabinoid Type 1 (CB1)

description: This research focuses on different aspects of hemp seed oil (HSO). Initially, the oil was extracted from shell (S) and no-shell (NS) seeds using different extraction methods and was compared to cold pressed oil in terms of composition. Furthermore, we determine its ability on adipogenic differentiation among hMSCs, and the involvement of the ECS system downstream gene and protein signaling cascade molecules expression levels have been analyzed during the differentiation process. Our results might lead to the involvement of hemp seed and its derivatives in the alteration of the ECS system and its association with lipid metabolism at the early stages of adipocyte differentiation.
DOI: 10.6084/m9.figshare.14906001.v1
title: Additional file 1 of Prognostic value of tumor immune cell infiltration patterns in colon adenocarcinoma based on systematic bioinformatics analysis

description: Additional file 1. Additional tables.
DOI: 10.6084/m9.figshare.12291623
title: Additional file 4 of APEC: an accesson-based method for single-cell chromatin accessibility analysis

description: Additional file 4. Table S3.
DOI: 10.6084/m9.figshare.12291701
title: Additional file 4 of Recruitability and effect of PEEP in SARS-Cov-2-associated acute respiratory distress syndrome

description: Additional file 4: Figure S4. Distribution of mean arterial pressure (MAP) (A) and heart rate (B) at positive end-expiratory pressure (PEEP) 5 cmH2O and 15 cmH2O in the highly recruitable and poorly recruitable patients groups. NS, not significant (p &gt; 0.05).
DOI: 10.6084/m9.figshare.5488045
title: Mortality Salience Effect in the Perspective of Uncertainty

description: Study1 directly explored how self-uncertainty affects conformity. Study2 tested the hypothesis that self-uncertainty mediates the effect of <i>MS </i>on conformity. Study 3 investigated the relationship of death-anxiety, self-uncertainty and conformity traits.
DOI: 10.6084/m9.figshare.17010297.v1
title: Additional file 3 of Myocardial protective effect and transcriptome profiling of Naoxintong on cardiomyopathy in zebrafish

description: Additional file 3: Table S2. DGEs of TFD+NXT vs. TFD.
DOI: 10.6084/m9.figshare.17010250.v1
title: Additional file 16 of A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit

description: Additional file 16. Primer list.
DOI: 10.6084/m9.figshare.10731083
title: MOESM3 of Characterization of a highly divergent Sugarcane mosaic virus from Canna indica L. by deep sequencing

description: Additional file 3: Table S1. Primers used for RT-PCR and Rapid Amplification of cDNA Ends (RACE) in this study.
DOI: 10.6084/m9.figshare.10731083.v1
title: MOESM3 of Characterization of a highly divergent Sugarcane mosaic virus from Canna indica L. by deep sequencing

description: Additional file 3: Table S1. Primers used for RT-PCR and Rapid Amplification of cDNA Ends (RACE) in this study.
DOI: 10.6084/m9.figshare.17010244
title: Additional file 14 of A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit

description: Additional file 14. List of selected stone cell-related genes in previously reported GWAS and QTL regions.
DOI: 10.6084/m9.figshare.17010300.v1
title: Additional file 4 of Myocardial protective effect and transcriptome profiling of Naoxintong on cardiomyopathy in zebrafish

description: Additional file 4: Table S3. GO and KEGG analysis of DGEs of TFD+NXT vs. TFD.
DOI: 10.6084/m9.figshare.12291701.v1
title: Additional file 4 of Recruitability and effect of PEEP in SARS-Cov-2-associated acute respiratory distress syndrome

description: Additional file 4: Figure S4. Distribution of mean arterial pressure (MAP) (A) and heart rate (B) at positive end-expiratory pressure (PEEP) 5 cmH2O and 15 cmH2O in the highly recruitable and poorly recruitable patients groups. NS, not significant (p &gt; 0.05).
DOI: 10.6084/m9.figshare.17010297
title: Additional file 3 of Myocardial protective effect and transcriptome profiling of Naoxintong on cardiomyopathy in zebrafish

description: Additional file 3: Table S2. DGEs of TFD+NXT vs. TFD.
DOI: 10.6084/m9.figshare.17010274
title: Additional file 7 of A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit

description: Additional file 7. The reported local eQTL for enzyme genes in sugar, organic acids, aroma metabolism pathway.
DOI: 10.6084/m9.figshare.17010256
title: Additional file 1 of A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit

description: Additional file 1. Summary of the 206 pear accessions.
DOI: 10.22002/fret7-3tg31
title: Helicobacter_pylori_dFliG

description: These are H. pylori cells that don't have a complete FliP. In addition, FliG was knocked out in  .  these cells. The aim is to study the assembly of the flagellar motor and the core complex.
description: <strong>Tilt Series Date:</strong> 2019-09-24</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> I received these cells from Carrie Schaffer from the university of Kentucky. These are wild . type cells but they don't express complete FliP protein. Therefore, they don't assemble full . flagella. We knocked out Flip protein of the flagellar motor to study the early assembly states . of flagellar motor.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. the cells were grown . for 48 hours and then spread on a new plate with a cotton swab and left to grow for 24 hours. . The grids were prepared from both batches (48 hours, and 24 hours, separately).</p>
<strong>Sample Preparation:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1. 100% humidity. Cu grids. 10 nm . gold.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-09-24-84/rawdata/</p>Hpylori_dFliG36_good.mrc,  Tilt Series (Pixel Size 0.4494 nm), 2.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-09-24-84/rawdata/Hpylori_dFliG36_good.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_dFliG36_good_part51_6.rec,  Reconstruction (Pixel Size 1.7976 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-09-24-84/3dimage_106460/Hpylori_dFliG36_good_part51_6.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/rg74g-hpe82
title: E_coli_EPEC_8612

description: The aim is to look for bacterial nanotubes (See Pal et al., 2019 Cell)
description: <strong>Tilt Series Date:</strong> 2020-02-13</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 8612, EPEC Δrof1-escLΔrof3-mpcΔescN-espFΔflhBAΔfliOPQRΔminCD</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 105.0 eV/Å²,  defocus: -6.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> These cells were obtained from Ritesh (Ilan Rosenshine lab) and Amit (Sigal ben Yehuda lab, . both from the Hebrew university). They were present during sample preparation.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> An overnight culture from -80C stock was made in 2ml LB and was grown at 37C in static . conditions. The next day, 1 ml of cells were spun down at 4000 rpm for six minutes and . concentrated 10 times. 3 ul of cells were spotted on glow-discharged grids located on a . DMEM high-glucose agar plates (1.5% agar) for 3 hours. Then, the grids were washed twice . in PBS and transferred to a starvation-medium agar plates (Starvation medium:DMEM without . phenol red, vitamins and amino acids). and incubated for 1 hour at 37C. Subsequently,the . samples were washed with PBS and plunge-frozen. </p>
<strong>Sample Preparation:</strong> The samples were hold with a tweezer from the starvation plates and washed with PBS. Blotted . with different conditions (B</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-13-6/rawdata/</p>EPEC_8612_003_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-13-6/rawdata/EPEC_8612_003_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        EPEC_8612_003_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-13-6/3dimage_110838/EPEC_8612_003_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/ja4yb-r7d31
title: H_pylori_dFliO_GC

description: These are fast tilt series taken by Georges Chreifi on the Krios for dFliO mutant of Helicobacter  .  pylori.
description: <strong>Tilt Series Date:</strong> 2019-10-25</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -6.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> I received these cells from Carrie Schaffer from the university of Kentucky. These are wild . . type cells but they don't express complete FliP protein. Therefore, they don't assemble full . . flagella. We knocked out FliO protein of the flagellar motor to study the early assembly states . of flagellar motor.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. the cells were grown . . for 48 hours and then spread on a new plate with a cotton swab and left to grow for 24 hours. . . The grids were prepared from both batches (48 hours, and 24 hours, separately).</p>
<strong>Sample Preparation:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100% humidity. Cu grids. 10 nm . . gold.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-10-25-133/rawdata/</p>Hpylori_FliO_135_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 3.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-10-25-133/rawdata/Hpylori_FliO_135_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_FliO_135_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-10-25-133/3dimage_107503/Hpylori_FliO_135_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/25xq0-5xt25
title: Hpylori_dFliM

description: These are fast tilt series that I collected on Hpylori_dFliM (dFliP also) on the Titan Krios.
description: <strong>Tilt Series Date:</strong> 2019-11-24</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> I received these cells from Carrie Schaffer from the university of Kentucky. These are wild type cells but they don't express complete FliP . protein. Therefore, they don't assemble full flagella. We knocked out FliM protein of the flagellar motor to study the early assembly states of . flagellar motor.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. the cells were grown for 48 hours and then spread on a new plate with a cotton swab and left to . grow for 24 hours. The grids were prepared from both batches (48 hours, and 24 hours, separately).</p>
<strong>Sample Preparation:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100% . humidity. Cu grids. 10 nm gold.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-11-24-100/rawdata/</p>Hpylori_dfliM_100_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-11-24-100/rawdata/Hpylori_dfliM_100_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_dfliM_100_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-11-24-100/3dimage_110054/Hpylori_dfliM_100_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.ye9re5
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pygidianops amphioxus)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012322-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.