cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25582/data.2023-01.2710437/2297603
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.14328654
title: A perfect functional marker for the gene of intermediate amylose content Wx-in in rice (Oryza sativa L.)

description: Abstract The amylose content (AC) of rice is a key determinant of the grain cooking and eating quality. The Waxy (Wx) gene, which encodes granule-bound starch synthase I (GBSSI), is the major gene controlling AC in rice. The A - C substitution in exon 6 (Ex6A/C) alters the amino acid codon from serine to tyrosine and is associated with intermediate-AC rice (Wx-in). In this paper, we reported a perfect functional marker for the SNP Ex6A/C of Wx-in based on polymerase chain reaction with confronting two-pair primers (PCR-CTPP) in a single-tube PCR assay. Specificity and applicability of the PCR assay were verified in a Chinese mini core collection (MCC) of Oryza sativa L. and a breeding population. Were commend the use of the simple, inexpensive assay for routine genotyping for intermediate AC in the breeding population or discrimination of Wx-in genotypes in rice germplasm.
DOI: 10.6084/m9.figshare.14328654.v1
title: A perfect functional marker for the gene of intermediate amylose content Wx-in in rice (Oryza sativa L.)

description: Abstract The amylose content (AC) of rice is a key determinant of the grain cooking and eating quality. The Waxy (Wx) gene, which encodes granule-bound starch synthase I (GBSSI), is the major gene controlling AC in rice. The A - C substitution in exon 6 (Ex6A/C) alters the amino acid codon from serine to tyrosine and is associated with intermediate-AC rice (Wx-in). In this paper, we reported a perfect functional marker for the SNP Ex6A/C of Wx-in based on polymerase chain reaction with confronting two-pair primers (PCR-CTPP) in a single-tube PCR assay. Specificity and applicability of the PCR assay were verified in a Chinese mini core collection (MCC) of Oryza sativa L. and a breeding population. Were commend the use of the simple, inexpensive assay for routine genotyping for intermediate AC in the breeding population or discrimination of Wx-in genotypes in rice germplasm.
DOI: 10.25582/data.2023-02.2732511/2297604
title: Data for EMSL Project 51287 from February 2023
DOI: 10.6084/m9.figshare.14328660
title: HRM-facilitated rapid identification and genotyping of mutations induced by CRISPR/Cas9 mutagenesis in rice

description: Abstract The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) technology has recently emerged as a powerful genomic editing tool with great potential for crop breeding. However, commonly used protocols for screening of CRISPR/Cas9-induced mutations are laborious, time-consuming, and costly. In the present study we examined the applicability of high resolution melting (HRM) analysis fast screening CRISPR/Cas9-induced mutations in T0 plants and subsequent genotyping of T1 populations. Comparative analysis demonstrated that HRM analysis could identify mutant T0 plants carrying various types of mutation, including single nucleotide substitutions and short insertion/deletions, with false positive/negative rates of 0-2.78%. Furthermore, T1 plants derived from single T0 plants could be correctly genotyped by HRM analysis using WT parents and T0 plants as controls. We hence recommend the adoption of HRM analysis in CRISPR/Cas9 mediated genetic studies and breeding in rice and other crop species.
DOI: 10.25582/data.2023-02.2733249/2297605
title: Data for EMSL Project 51287 from February 2023
DOI: 10.6084/m9.figshare.14328660.v1
title: HRM-facilitated rapid identification and genotyping of mutations induced by CRISPR/Cas9 mutagenesis in rice

description: Abstract The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) technology has recently emerged as a powerful genomic editing tool with great potential for crop breeding. However, commonly used protocols for screening of CRISPR/Cas9-induced mutations are laborious, time-consuming, and costly. In the present study we examined the applicability of high resolution melting (HRM) analysis fast screening CRISPR/Cas9-induced mutations in T0 plants and subsequent genotyping of T1 populations. Comparative analysis demonstrated that HRM analysis could identify mutant T0 plants carrying various types of mutation, including single nucleotide substitutions and short insertion/deletions, with false positive/negative rates of 0-2.78%. Furthermore, T1 plants derived from single T0 plants could be correctly genotyped by HRM analysis using WT parents and T0 plants as controls. We hence recommend the adoption of HRM analysis in CRISPR/Cas9 mediated genetic studies and breeding in rice and other crop species.
DOI: 10.6084/m9.figshare.14328673
title: QTL mapping for microtuber ABA content in a diploid potato population

description: Abstract Abscisic acid (ABA) is known to impact many areas of plant growth and development and is also assumed to facilitate plant stress regulation. ABA is also involved in the rapid suberization of wounds and is the essential dormancy release regulator. The direct application of DNA markers to plant populations enables the use of mapping to help determine the regulation of a quantitatively inherited trait isolated in a population. QTLs represent a chromosomal region that is linked to a marker gene and that significantly affects the quantitative trait under review. In the present study, we investigated the ABA content after harvest and after sprouting in a diploid population. The most noticeable QTLs related to ABA were found on chromosomes I and IV, and these QTLs fully explained 6.5% and 7% of the entire phenotypic variance, respectively. The acquired information advances our understanding of the inheritance of traits applicable for variety development.
DOI: 10.6084/m9.figshare.14328673.v1
title: QTL mapping for microtuber ABA content in a diploid potato population

description: Abstract Abscisic acid (ABA) is known to impact many areas of plant growth and development and is also assumed to facilitate plant stress regulation. ABA is also involved in the rapid suberization of wounds and is the essential dormancy release regulator. The direct application of DNA markers to plant populations enables the use of mapping to help determine the regulation of a quantitatively inherited trait isolated in a population. QTLs represent a chromosomal region that is linked to a marker gene and that significantly affects the quantitative trait under review. In the present study, we investigated the ABA content after harvest and after sprouting in a diploid population. The most noticeable QTLs related to ABA were found on chromosomes I and IV, and these QTLs fully explained 6.5% and 7% of the entire phenotypic variance, respectively. The acquired information advances our understanding of the inheritance of traits applicable for variety development.
DOI: 10.25582/data.2023-02.2732392/2297606
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-02.2733151/2297607
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2705766/2297608
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.11707263
title: MOESM2 of Transcriptome profiling of laser-captured germ cells and functional characterization of zbtb40 during 17alpha-methyltestosterone-induced spermatogenesis in orange-spotted grouper (Epinephelus coioides)

description: Additional file 2 : Table S1. The detailes of the top 20 KEGG enriched pathway. Table S2. The top 10 conserved sites among 14 species.
DOI: 10.6084/m9.figshare.11707263.v1
title: MOESM2 of Transcriptome profiling of laser-captured germ cells and functional characterization of zbtb40 during 17alpha-methyltestosterone-induced spermatogenesis in orange-spotted grouper (Epinephelus coioides)

description: Additional file 2 : Table S1. The detailes of the top 20 KEGG enriched pathway. Table S2. The top 10 conserved sites among 14 species.
DOI: 10.25582/data.2023-01.2706892/2297609
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2707181/2297610
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710823/2297611
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2711223/2297612
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710393/2297613
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2708389/2297614
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.11707311
title: MOESM2 of Exosomal circRNA-100338 promotes hepatocellular carcinoma metastasis via enhancing invasiveness and angiogenesis

description: Additional file 2: Figure S1E. The number of invaded cells (n)
DOI: 10.6084/m9.figshare.11707311.v1
title: MOESM2 of Exosomal circRNA-100338 promotes hepatocellular carcinoma metastasis via enhancing invasiveness and angiogenesis

description: Additional file 2: Figure S1E. The number of invaded cells (n)
DOI: 10.25582/data.2023-02.2733169/2297615
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2710000/2297616
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.14328762
title: MeMYB26, a drought-responsive transcription factor in cassava (Manihot esculenta Crantz)

description: Abstract Cassava (Manihot esculenta Crantz) is worldwide the sixth-largest food crop and highly drought resistant. The expression of the myeloblastosis (MYB) family protein MeMYB26 in cassava was previously reported to be significantly up-regulated under water deficit. To study the basic characterization, natural variations and potential functions of MeMYB26 for drought resistance in cassava, the protein was subjected to bioinformatics analysis, multiplex-PCR with next-generation sequencing and candidate association studies. The results indicated that MeMYB26 is a typical transcription factor, with two MYB DNA-binding and transcriptional activation domains. One stop-gained and five nonsynonymous variations in the genomic region of MeMYB26 were significantly associated with drought resistance traits. The results of the scale-free coexpression network showed that the MeMYB26 gene plays a critical role in plant stress resistance, growth and biomass development. It was concluded that MeMYB26 is a reliable candidate gene associated with drought tolerance and biomass storage in cassava.
DOI: 10.6084/m9.figshare.14328762.v1
title: MeMYB26, a drought-responsive transcription factor in cassava (Manihot esculenta Crantz)

description: Abstract Cassava (Manihot esculenta Crantz) is worldwide the sixth-largest food crop and highly drought resistant. The expression of the myeloblastosis (MYB) family protein MeMYB26 in cassava was previously reported to be significantly up-regulated under water deficit. To study the basic characterization, natural variations and potential functions of MeMYB26 for drought resistance in cassava, the protein was subjected to bioinformatics analysis, multiplex-PCR with next-generation sequencing and candidate association studies. The results indicated that MeMYB26 is a typical transcription factor, with two MYB DNA-binding and transcriptional activation domains. One stop-gained and five nonsynonymous variations in the genomic region of MeMYB26 were significantly associated with drought resistance traits. The results of the scale-free coexpression network showed that the MeMYB26 gene plays a critical role in plant stress resistance, growth and biomass development. It was concluded that MeMYB26 is a reliable candidate gene associated with drought tolerance and biomass storage in cassava.
DOI: 10.6084/m9.figshare.11707323
title: MOESM3 of Exosomal circRNA-100338 promotes hepatocellular carcinoma metastasis via enhancing invasiveness and angiogenesis

description: Additional file 3: Figure S2A. Relative expression of circRNA-100,338, Figure S2B. Relative expression of circRNA-100,338, Figure S2C. The number of invaded cells (n), Figure S2D. The number of invaded cells (n), Figure S2F. MMP9 activity (ng/mL), Figure S2G. MMP9 activity (ng/mL)
DOI: 10.6084/m9.figshare.11707323.v1
title: MOESM3 of Exosomal circRNA-100338 promotes hepatocellular carcinoma metastasis via enhancing invasiveness and angiogenesis

description: Additional file 3: Figure S2A. Relative expression of circRNA-100,338, Figure S2B. Relative expression of circRNA-100,338, Figure S2C. The number of invaded cells (n), Figure S2D. The number of invaded cells (n), Figure S2F. MMP9 activity (ng/mL), Figure S2G. MMP9 activity (ng/mL)
DOI: 10.25582/data.2023-01.2711276/2297617
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710067/2297618
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2706972/2297619
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.11707329
title: MOESM4 of Exosomal circRNA-100338 promotes hepatocellular carcinoma metastasis via enhancing invasiveness and angiogenesis

description: Additional file 4: Figure S3C. Relative circRNA-100,338 expression, Figure S3D. Proliferation of HUVEC cells, Figure S3E. Proliferation of HUVEC cells, Figure S3H. The number of migrated cells (n)
DOI: 10.25582/data.2023-01.2710549/2297620
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.11707329.v1
title: MOESM4 of Exosomal circRNA-100338 promotes hepatocellular carcinoma metastasis via enhancing invasiveness and angiogenesis

description: Additional file 4: Figure S3C. Relative circRNA-100,338 expression, Figure S3D. Proliferation of HUVEC cells, Figure S3E. Proliferation of HUVEC cells, Figure S3H. The number of migrated cells (n)
DOI: 10.25582/data.2023-01.2708839/2297621
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710678/2297622
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2715847/2297623
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.11707341
title: MOESM6 of Exosomal circRNA-100338 promotes hepatocellular carcinoma metastasis via enhancing invasiveness and angiogenesis

description: Additional file 6: Figure S5A. Relative expression of exosomal circRNA-100,338, Figure S5C. Tumor volume (cm3), Figure S5D. MVD (n), Figure S5E. MMP9 level by ELISA analysis (ng/mg protein), Figure S5F. The mean number of lung metastatic nodules (n), Figure S5G. Percentage of Ki67 in lung metastatic nodules (%)
DOI: 10.25582/data.2023-02.2732572/2297624
title: Data for EMSL Project 51287 from February 2023
DOI: 10.6084/m9.figshare.11707341.v1
title: MOESM6 of Exosomal circRNA-100338 promotes hepatocellular carcinoma metastasis via enhancing invasiveness and angiogenesis

description: Additional file 6: Figure S5A. Relative expression of exosomal circRNA-100,338, Figure S5C. Tumor volume (cm3), Figure S5D. MVD (n), Figure S5E. MMP9 level by ELISA analysis (ng/mg protein), Figure S5F. The mean number of lung metastatic nodules (n), Figure S5G. Percentage of Ki67 in lung metastatic nodules (%)
DOI: 10.25582/data.2023-01.2710373/2297625
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.11707350
title: MOESM8 of Exosomal circRNA-100338 promotes hepatocellular carcinoma metastasis via enhancing invasiveness and angiogenesis

description: Additional file 8.Â The proteins interacting with circRNA-100338 in HUVEC.
DOI: 10.25582/data.2023-01.2710498/2297626
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.11707353
title: MOESM9 of Exosomal circRNA-100338 promotes hepatocellular carcinoma metastasis via enhancing invasiveness and angiogenesis

description: Additional file 9: Figure S6C.
DOI: 10.6084/m9.figshare.11707353.v1
title: MOESM9 of Exosomal circRNA-100338 promotes hepatocellular carcinoma metastasis via enhancing invasiveness and angiogenesis

description: Additional file 9: Figure S6C.
DOI: 10.25582/data.2023-02.2732728/2297627
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2712152/2297628
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2733114/2297629
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2707461/2297630
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2709109/2297631
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2732318/2297632
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2716672/2297633
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.11707368
title: Additional file 2 of Co-opted transposons help perpetuate conserved higher-order chromosomal structures

description: Table S1. This file contains 4 supplementary tables for this paper. Table S1.1: List of orthologous mouse-human loops mapped with details. Table S1.2: List of orthologous mouse-human loops that are turnover events in mouse mapped with TE details. Table S1.3: List of orthologous mouse-human loops that are turnover events in human mapped with TE details. Table S1.4: List of orthologous mouse-human loops whose anchors are derived from TEs in both humans and mouse, mapped with TE details.
DOI: 10.25582/data.2023-01.2710169/2297634
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.11707368.v1
title: Additional file 2: of Co-opted transposons help perpetuate conserved higher-order chromosomal structures

description: Table S1. This file contains 4 supplementary tables for this paper. Table S1.1: List of orthologous mouse-human loops mapped with details. Table S1.2: List of orthologous mouse-human loops that are turnover events in mouse mapped with TE details. Table S1.3: List of orthologous mouse-human loops that are turnover events in human mapped with TE details. Table S1.4: List of orthologous mouse-human loops whose anchors are derived from TEs in both humans and mouse, mapped with TE details.
DOI: 10.6084/m9.figshare.11707368.v2
title: Additional file 2 of Co-opted transposons help perpetuate conserved higher-order chromosomal structures

description: Table S1. This file contains 4 supplementary tables for this paper. Table S1.1: List of orthologous mouse-human loops mapped with details. Table S1.2: List of orthologous mouse-human loops that are turnover events in mouse mapped with TE details. Table S1.3: List of orthologous mouse-human loops that are turnover events in human mapped with TE details. Table S1.4: List of orthologous mouse-human loops whose anchors are derived from TEs in both humans and mouse, mapped with TE details.
DOI: 10.25582/data.2023-01.2705692/2297635
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2711452/2297636
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.11707374
title: Additional file 3 of Co-opted transposons help perpetuate conserved higher-order chromosomal structures

description: Table S2. This file contains 5 supplementary tables for this paper. Table S2.1: Hi-C Experiments. Table S2.2: Hi-C2 Experiments. Table S2.3: Hi-C2 Region/Probe Information. Table S2.4: Targeted TEs and genotype information for all mutant clones. Table S2.5: Crossdomain interaction stats (related to Fig. 3C).
DOI: 10.6084/m9.figshare.11707374.v2
title: Additional file 3 of Co-opted transposons help perpetuate conserved higher-order chromosomal structures

description: Table S2. This file contains 5 supplementary tables for this paper. Table S2.1: Hi-C Experiments. Table S2.2: Hi-C2 Experiments. Table S2.3: Hi-C2 Region/Probe Information. Table S2.4: Targeted TEs and genotype information for all mutant clones. Table S2.5: Crossdomain interaction stats (related to Fig. 3C).
DOI: 10.25582/data.2023-02.2732228/2297637
title: Data for EMSL Project 51287 from February 2023
DOI: 10.6084/m9.figshare.11707374.v1
title: Additional file 3: of Co-opted transposons help perpetuate conserved higher-order chromosomal structures

description: Table S2. This file contains 5 supplementary tables for this paper. Table S2.1: Hi-C Experiments. Table S2.2: Hi-C2 Experiments. Table S2.3: Hi-C2 Region/Probe Information. Table S2.4: Targeted TEs and genotype information for all mutant clones. Table S2.5: Crossdomain interaction stats (related to Fig. 3C).
DOI: 10.6084/m9.figshare.11707377
title: Additional file 4 of Co-opted transposons help perpetuate conserved higher-order chromosomal structures

description: Table S3.1. KS-test statistic to test distribution of various nucleotide substitutions (crossmatch). Table S3.2. KS-test statistic to test distribution of various nucleotide substitutions (needle).
DOI: 10.25582/data.2023-01.2711007/2297638
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.11707377.v1
title: Additional file 4: of Co-opted transposons help perpetuate conserved higher-order chromosomal structures

description: Table S3.1. KS-test statistic to test distribution of various nucleotide substitutions (crossmatch). Table S3.2. KS-test statistic to test distribution of various nucleotide substitutions (needle).
DOI: 10.6084/m9.figshare.11707377.v2
title: Additional file 4 of Co-opted transposons help perpetuate conserved higher-order chromosomal structures

description: Table S3.1. KS-test statistic to test distribution of various nucleotide substitutions (crossmatch). Table S3.2. KS-test statistic to test distribution of various nucleotide substitutions (needle).
DOI: 10.25582/data.2023-02.2732327/2297639
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-02.2732613/2297640
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2708852/2297641
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710212/2297642
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2706089/2297643
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2711506/2297644
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2706115/2297645
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710210/2297646
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2706508/2297647
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.14853087
title: Additional file 4 of Serum metabolomics in chickens infected with Cryptosporidium baileyi

description: Additional file 4: Table S3. Differential metabolites between experimental and mock serum samples responsive to C. bailey infection identified by UPLC-MS in this study.
DOI: 10.15156/bio/sh341505.07fu
title: SH341505.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.