cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16681507.v1
title: Additional file 3 of AKT signaling is associated with epigenetic reprogramming via the upregulation of TET and its cofactor, alpha-ketoglutarate during iPSC generation

description: Additional file 3: Automated shell script used for quantification of DNA methylation for Linux.
DOI: 10.6084/m9.figshare.16681510
title: Additional file 4 of AKT signaling is associated with epigenetic reprogramming via the upregulation of TET and its cofactor, alpha-ketoglutarate during iPSC generation

description: Additional file 4: Read me for automated shell script used for quantification of DNA m ethylation.
DOI: 10.6084/m9.figshare.16681510.v1
title: Additional file 4 of AKT signaling is associated with epigenetic reprogramming via the upregulation of TET and its cofactor, alpha-ketoglutarate during iPSC generation

description: Additional file 4: Read me for automated shell script used for quantification of DNA m ethylation.
DOI: 10.6084/m9.figshare.16681582.v1
title: Additional file 1 of Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome

description: Additional file 1. DEGs between bailed-out polyps and colonies. Result of a DE analysis between bailed-out polyps (N = 9) and normal colonies (N = 9) under ambient conditions. Transcripts are presented as transcriptID^annotation. P-values and FDR for expression differences between the two groups are presented for each transcript. Expression levels are presented as TPM after trimmed mean of M values (TMM) cross-sample normalization. RNAseq libraries are presented as treatment (Hyperthermal/Hyper-illumination/Hyposalinity)_coral morphotype (Colony/Polyp)_biological replicate (rep1/rep2/rep3).
DOI: 10.6084/m9.figshare.16681582
title: Additional file 1 of Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome

description: Additional file 1. DEGs between bailed-out polyps and colonies. Result of a DE analysis between bailed-out polyps (N = 9) and normal colonies (N = 9) under ambient conditions. Transcripts are presented as transcriptID^annotation. P-values and FDR for expression differences between the two groups are presented for each transcript. Expression levels are presented as TPM after trimmed mean of M values (TMM) cross-sample normalization. RNAseq libraries are presented as treatment (Hyperthermal/Hyper-illumination/Hyposalinity)_coral morphotype (Colony/Polyp)_biological replicate (rep1/rep2/rep3).
DOI: 10.6084/m9.figshare.16681585
title: Additional file 2 of Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome

description: Additional file 2. GO enrichment among DEGs between bailed-out polyps and colonies. Enriched biological processes among DEGs between bailed-out polyps and normal colonies under ambient conditions. All biological processes with Bonferroni-adjusted p-values &lt; 0.05 are listed with corresponding fold enrichment values.
DOI: 10.6084/m9.figshare.16681585.v1
title: Additional file 2 of Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome

description: Additional file 2. GO enrichment among DEGs between bailed-out polyps and colonies. Enriched biological processes among DEGs between bailed-out polyps and normal colonies under ambient conditions. All biological processes with Bonferroni-adjusted p-values &lt; 0.05 are listed with corresponding fold enrichment values.
DOI: 10.6084/m9.figshare.16681588
title: Additional file 3 of Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome

description: Additional file 3. ORFs of three ACE-like genes in P. acuta. Corresponding transcript IDs are provided in parentheses.
DOI: 10.6084/m9.figshare.16681588.v1
title: Additional file 3 of Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome

description: Additional file 3. ORFs of three ACE-like genes in P. acuta. Corresponding transcript IDs are provided in parentheses.
DOI: 10.6084/m9.figshare.16681591.v1
title: Additional file 4 of Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome

description: Additional file 4. ORFs of three ECE-like genes in P. acuta. Corresponding transcript IDs are provided in parentheses.
DOI: 10.6084/m9.figshare.16681591
title: Additional file 4 of Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome

description: Additional file 4. ORFs of three ECE-like genes in P. acuta. Corresponding transcript IDs are provided in parentheses.
DOI: 10.6084/m9.figshare.16681594
title: Additional file 5 of Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome

description: Additional file 5. DEGs in bailed-out polyps and colonies in the hyperthermal experiment. Results of DE analyses in bailed-out polyps (N = 3) and colonies (N = 3) in response to hyperthermal treatment. Transcripts are presented as transcriptID^annotation. P-values and FDR for expression difference before and after the treatment are presented for each transcript. Expression levels are presented as TPM after TMM cross-sample normalization. RNAseq libraries are presented as coral morphotype (Colony/Polyp)_sampling time (pre/after)_biological replicate (rep1/rep2/rep3).
DOI: 10.6084/m9.figshare.16681594.v1
title: Additional file 5 of Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome

description: Additional file 5. DEGs in bailed-out polyps and colonies in the hyperthermal experiment. Results of DE analyses in bailed-out polyps (N = 3) and colonies (N = 3) in response to hyperthermal treatment. Transcripts are presented as transcriptID^annotation. P-values and FDR for expression difference before and after the treatment are presented for each transcript. Expression levels are presented as TPM after TMM cross-sample normalization. RNAseq libraries are presented as coral morphotype (Colony/Polyp)_sampling time (pre/after)_biological replicate (rep1/rep2/rep3).
DOI: 10.6084/m9.figshare.16681597
title: Additional file 6 of Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome

description: Additional file 6. GO enrichment among DEGs in the hyperthermal experiment. Enriched biological processes among DEGs identified simultaneously in bailed-out polyps and colonies, specific to bailed-out polyps, or specific to colonies are listed separately. All biological processes with Bonferroni-adjusted p-values &lt; 0.05 are listed with corresponding fold enrichment values.
DOI: 10.6084/m9.figshare.16681597.v1
title: Additional file 6 of Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome

description: Additional file 6. GO enrichment among DEGs in the hyperthermal experiment. Enriched biological processes among DEGs identified simultaneously in bailed-out polyps and colonies, specific to bailed-out polyps, or specific to colonies are listed separately. All biological processes with Bonferroni-adjusted p-values &lt; 0.05 are listed with corresponding fold enrichment values.
DOI: 10.6084/m9.figshare.16681600
title: Additional file 7 of Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome

description: Additional file 7. DEGs in bailed-out polyps and colonies in the hyposaline experiment. Results of DE analyses in bailed-out polyps (N = 3) and colonies (N = 3) in response to hyposaline treatment. Transcripts are presented as transcriptID^annotation. P-value and FDR for expression difference before and after the treatment are presented for each transcript. Expression levels are presented as TPM after TMM cross-sample normalization. RNAseq libraries are presented as coral morphotype (Colony/Polyp)_sampling time (pre/after)_biological replicate (rep1/rep2/rep3).
DOI: 10.6084/m9.figshare.16681600.v1
title: Additional file 7 of Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome

description: Additional file 7. DEGs in bailed-out polyps and colonies in the hyposaline experiment. Results of DE analyses in bailed-out polyps (N = 3) and colonies (N = 3) in response to hyposaline treatment. Transcripts are presented as transcriptID^annotation. P-value and FDR for expression difference before and after the treatment are presented for each transcript. Expression levels are presented as TPM after TMM cross-sample normalization. RNAseq libraries are presented as coral morphotype (Colony/Polyp)_sampling time (pre/after)_biological replicate (rep1/rep2/rep3).
DOI: 10.6084/m9.figshare.16681603
title: Additional file 8 of Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome

description: Additional file 8. GO enrichment among DEGs in the hyposaline experiment. Enriched biological processes among DEGs identified simultaneously in bailed-out polyps and colonies, specific to bailed-out polyps, or specific to colonies are listed separately. All biological processes with Bonferroni-adjusted p-values &lt; 0.05 are listed with corresponding fold enrichment values.
DOI: 10.6084/m9.figshare.16681603.v1
title: Additional file 8 of Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome

description: Additional file 8. GO enrichment among DEGs in the hyposaline experiment. Enriched biological processes among DEGs identified simultaneously in bailed-out polyps and colonies, specific to bailed-out polyps, or specific to colonies are listed separately. All biological processes with Bonferroni-adjusted p-values &lt; 0.05 are listed with corresponding fold enrichment values.
DOI: 10.6084/m9.figshare.16681613
title: Additional file 2 of Wolbachia-driven selective sweep in a range expanding insect species

description: Additional file 2. The wEle1 draft genome assembly (Nscaffold = 893; N50 = 5523 bp; longest scaffold = 53,331 bp,genome size = 1.4 MB) as a fasta file.
DOI: 10.6084/m9.figshare.16681613.v1
title: Additional file 2 of Wolbachia-driven selective sweep in a range expanding insect species

description: Additional file 2. The wEle1 draft genome assembly (Nscaffold = 893; N50 = 5523 bp; longest scaffold = 53,331 bp,genome size = 1.4 MB) as a fasta file.
DOI: 10.6084/m9.figshare.20004635
title: Additional file 2 of InflamNat: web-based database and predictor of anti-inflammatory natural products

description: Additional file 2. Physicochemical properties and cell-based anti-inflammatory activity of InflamNat Compounds.
DOI: 10.6084/m9.figshare.22626037
title: Additional file 4 of Student standardized patients versus occupational standardized patients for improving clinical competency among TCM medical students: a 3-year prospective randomized study

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.22626040
title: Additional file 5 of Student standardized patients versus occupational standardized patients for improving clinical competency among TCM medical students: a 3-year prospective randomized study

description: Supplementary Material 5
DOI: 10.6084/m9.figshare.20004635.v1
title: Additional file 2 of InflamNat: web-based database and predictor of anti-inflammatory natural products

description: Additional file 2. Physicochemical properties and cell-based anti-inflammatory activity of InflamNat Compounds.
DOI: 10.6084/m9.figshare.10049081
title: MOESM15 of Eriodictyol can modulate cellular auxin gradients to efficiently promote in vitro cotton fibre development

description: Additional file 15: Table S3. List of primers used in this study.
DOI: 10.6084/m9.figshare.10049081.v1
title: MOESM15 of Eriodictyol can modulate cellular auxin gradients to efficiently promote in vitro cotton fibre development

description: Additional file 15: Table S3. List of primers used in this study.
DOI: 10.6084/m9.figshare.10049084
title: MOESM1 of Eriodictyol can modulate cellular auxin gradients to efficiently promote in vitro cotton fibre development

description: Additional file 1: Table S1. Statistics for the paired clean reads and read mapping for 6 treatments with 3 replications.
DOI: 10.6084/m9.figshare.10049084.v1
title: MOESM1 of Eriodictyol can modulate cellular auxin gradients to efficiently promote in vitro cotton fibre development

description: Additional file 1: Table S1. Statistics for the paired clean reads and read mapping for 6 treatments with 3 replications.
DOI: 10.6084/m9.figshare.10049099
title: MOESM1 of Prediction of sgRNA on-target activity in bacteria by deep learning

description: Additional file 1 More detailed tables. Statistical significance of Spearman correlation coefficients in this paper and more details about 5-fold cross-validation. Table S1. Performance of all modes including DeepCRISPR, CNN_Lin, DeepCas9, CNN_2layers, CNN_3layers, CNN_4layers, CNN_5layers, and CNN_7layers. Table S2. The Spearman correlation coefficients and significances between eukaryotic sgRNA activity and predictions based on our prokaryotic models and eukaryotic models. Table S3. Significance between on-target activity and six melting temperatures, four RNA fold scores, and four POSs. Table S4. Detailed information of 5-fold cross-validation for several network architectures.
DOI: 10.6084/m9.figshare.10049099.v1
title: MOESM1 of Prediction of sgRNA on-target activity in bacteria by deep learning

description: Additional file 1 More detailed tables. Statistical significance of Spearman correlation coefficients in this paper and more details about 5-fold cross-validation. Table S1. Performance of all modes including DeepCRISPR, CNN_Lin, DeepCas9, CNN_2layers, CNN_3layers, CNN_4layers, CNN_5layers, and CNN_7layers. Table S2. The Spearman correlation coefficients and significances between eukaryotic sgRNA activity and predictions based on our prokaryotic models and eukaryotic models. Table S3. Significance between on-target activity and six melting temperatures, four RNA fold scores, and four POSs. Table S4. Detailed information of 5-fold cross-validation for several network architectures.
DOI: 10.6084/m9.figshare.7421699
title: Additional file 1: of Genomic identification and functional analysis of essential genes in Caenorhabditis elegans

description: List of alleles studied. The alleles used for WGS are listed in the 2nd column. (XLS 44 kb)
DOI: 10.6084/m9.figshare.10049111
title: MOESM3 of Prediction of sgRNA on-target activity in bacteria by deep learning

description: Additional file 3 CNN architectures for comparison. CNN architectures from CNN_2layers to CNN_7layers.
DOI: 10.6084/m9.figshare.10049111.v1
title: MOESM3 of Prediction of sgRNA on-target activity in bacteria by deep learning

description: Additional file 3 CNN architectures for comparison. CNN architectures from CNN_2layers to CNN_7layers.
DOI: 10.6084/m9.figshare.10049108
title: MOESM7 of Eriodictyol can modulate cellular auxin gradients to efficiently promote in vitro cotton fibre development

description: Additional file 7: Table S2. Comparison of the expression profiles of novel and annotated gene between control and ERI samples.
DOI: 10.6084/m9.figshare.10049108.v1
title: MOESM7 of Eriodictyol can modulate cellular auxin gradients to efficiently promote in vitro cotton fibre development

description: Additional file 7: Table S2. Comparison of the expression profiles of novel and annotated gene between control and ERI samples.
DOI: 10.60859/frfv-5174
title: NG00150
DOI: 10.6084/m9.figshare.10049120
title: MOESM4 of Prediction of sgRNA on-target activity in bacteria by deep learning

description: Additional file 4 Eukaryotic datasets. Eleven independent eukaryotic test and training set of DeepCRISPR, DeepCas9, TSAM, and our CNN_5layers.
DOI: 10.6084/m9.figshare.10049120.v1
title: MOESM4 of Prediction of sgRNA on-target activity in bacteria by deep learning

description: Additional file 4 Eukaryotic datasets. Eleven independent eukaryotic test and training set of DeepCRISPR, DeepCas9, TSAM, and our CNN_5layers.
DOI: 10.6084/m9.figshare.10049126
title: MOESM5 of Prediction of sgRNA on-target activity in bacteria by deep learning

description: Additional file 5 Melting temperatures. The melting temperatures of 43 nt-long target DNA sequences.
DOI: 10.6084/m9.figshare.10049126.v1
title: MOESM5 of Prediction of sgRNA on-target activity in bacteria by deep learning

description: Additional file 5 Melting temperatures. The melting temperatures of 43 nt-long target DNA sequences.
DOI: 10.6084/m9.figshare.10049144
title: MOESM7 of Prediction of sgRNA on-target activity in bacteria by deep learning

description: Additional file 7 Set 1 dataset. Set 1 samples including 44,163, 45,070, and 48,112 sgRNAs for Cas9, eSpCas9 and Cas9 (â łrecA), respectively.
DOI: 10.6084/m9.figshare.10049144.v1
title: MOESM7 of Prediction of sgRNA on-target activity in bacteria by deep learning

description: Additional file 7 Set 1 dataset. Set 1 samples including 44,163, 45,070, and 48,112 sgRNAs for Cas9, eSpCas9 and Cas9 (â łrecA), respectively.
DOI: 10.6084/m9.figshare.10049150
title: MOESM8 of Prediction of sgRNA on-target activity in bacteria by deep learning

description: Additional file 8 RNA fold scores. Four physicochemical properties characterizing 20 nt-long guide sequences fold.
DOI: 10.6084/m9.figshare.10049150.v1
title: MOESM8 of Prediction of sgRNA on-target activity in bacteria by deep learning

description: Additional file 8 RNA fold scores. Four physicochemical properties characterizing 20 nt-long guide sequences fold.
DOI: 10.6084/m9.figshare.10049156
title: MOESM9 of Prediction of sgRNA on-target activity in bacteria by deep learning

description: Additional file 9 All sgRNAs POSs. POSs calculated by CROP-IT, CCTop, MITScore, and CFD-Score.
DOI: 10.6084/m9.figshare.10049156.v1
title: MOESM9 of Prediction of sgRNA on-target activity in bacteria by deep learning

description: Additional file 9 All sgRNAs POSs. POSs calculated by CROP-IT, CCTop, MITScore, and CFD-Score.
DOI: 10.6084/m9.figshare.20004699
title: Additional file 3 of Age, sex, residence, and region-specific differences in prevalence and patterns of multimorbidity among older Chinese: evidence from Chinese Longitudinal Healthy Longevity Survey

description: Additional file 3: Table S1. Analysis results of the association rules in the total population. Table S2. Analysis results of the association rules for 65–79-year-olds. Table S3. Analysis results of the association rules for 80–89-year-olds. Table S4. Analysis results of the association rules for ≥90-year-olds. Table S5. Analysis results of the association rules for males. Table S6. Analysis results of the association rules for females. Table S7. Analysis results of the association rules in urban areas. Table S8. Analysis results of the association rules in rural areas. Table S9. Analysis results of the association rules in the East. Table S10. Analysis results of the association rules in the West. Table S11. Analysis results of the association rules in the South. Table S12. Analysis results of the association rules in the North. Table S13. Analysis results of the association rules in the Central.
DOI: 10.6084/m9.figshare.20004699.v1
title: Additional file 3 of Age, sex, residence, and region-specific differences in prevalence and patterns of multimorbidity among older Chinese: evidence from Chinese Longitudinal Healthy Longevity Survey

description: Additional file 3: Table S1. Analysis results of the association rules in the total population. Table S2. Analysis results of the association rules for 65–79-year-olds. Table S3. Analysis results of the association rules for 80–89-year-olds. Table S4. Analysis results of the association rules for ≥90-year-olds. Table S5. Analysis results of the association rules for males. Table S6. Analysis results of the association rules for females. Table S7. Analysis results of the association rules in urban areas. Table S8. Analysis results of the association rules in rural areas. Table S9. Analysis results of the association rules in the East. Table S10. Analysis results of the association rules in the West. Table S11. Analysis results of the association rules in the South. Table S12. Analysis results of the association rules in the North. Table S13. Analysis results of the association rules in the Central.
DOI: 10.6084/m9.figshare.20004638
title: Additional file 3 of InflamNat: web-based database and predictor of anti-inflammatory natural products

description: Additional file 3. Molecular Targets of InflamNat Compounds.
DOI: 10.6084/m9.figshare.22623037
title: Additional file 1 of Low-dose arecoline regulates distinct core signaling pathways in oral submucous fibrosis and oral squamous cell carcinoma

description: Additional file 1: Suppl. Table 1. Summary of DEGs in NFs samples with or without low-dose arecoline treatment.
DOI: 10.6084/m9.figshare.22623043
title: Additional file 3 of Low-dose arecoline regulates distinct core signaling pathways in oral submucous fibrosis and oral squamous cell carcinoma

description: Additional file 3: Suppl. Table 3. 10 common DEGs in NFs and CAL27 cells after low-dose arecoline treatment.
DOI: 10.6084/m9.figshare.10049240
title: MOESM10 of Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.)

description: Additional file 10: Table S11. Relative expression of RsHSF genes under different treatments determined by RT-qPCR.
DOI: 10.6084/m9.figshare.10049240.v1
title: MOESM10 of Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.)

description: Additional file 10: Table S11. Relative expression of RsHSF genes under different treatments determined by RT-qPCR.
DOI: 10.6084/m9.figshare.10049246
title: MOESM11 of Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.)

description: Additional file 11: Table S12. The accession number of RNAseq data.
DOI: 10.6084/m9.figshare.10049246.v1
title: MOESM11 of Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.)

description: Additional file 11: Table S12. The accession number of RNAseq data.
DOI: 10.6084/m9.figshare.10049249
title: MOESM1 of Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.)

description: Additional file 1: Table S1. Amino acid sequences of the HSF proteins from NODAI Radish genome database. Table S2. CDS sequences of the HSF genes from NODAI Radish genome database. Table S3. DNA sequences of the HSF genes from NODAI Radish genome database.