cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3618740_d9
title: Additional file 19: of RNA-sequencing of the sturgeon Acipenser baeri provides insights into expression dynamics of morphogenic differentiation and developmental regulatory genes in early versus late developmental stages

description: List of unigenes associated with morphogenesis as screened from GO enrichment file and their expression profile. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.c.3618740_d8
title: Additional file 8: of RNA-sequencing of the sturgeon Acipenser baeri provides insights into expression dynamics of morphogenic differentiation and developmental regulatory genes in early versus late developmental stages

description: Interproscan domain statistics. (XLS 250 kb)
DOI: 10.6084/m9.figshare.c.3618740_d7
title: Additional file 20: of RNA-sequencing of the sturgeon Acipenser baeri provides insights into expression dynamics of morphogenic differentiation and developmental regulatory genes in early versus late developmental stages

description: List of the set of development regulatory unigenes screened from the GO enrichment file and their expression dynamics. (XLSX 133 kb)
DOI: 10.6084/m9.figshare.c.3618740_d5
title: Additional file 7: of RNA-sequencing of the sturgeon Acipenser baeri provides insights into expression dynamics of morphogenic differentiation and developmental regulatory genes in early versus late developmental stages

description: Unigenes interpro annotation results file. (XLS 35 kb)
DOI: 10.6084/m9.figshare.c.3618740_d4
title: Additional file 1: of RNA-sequencing of the sturgeon Acipenser baeri provides insights into expression dynamics of morphogenic differentiation and developmental regulatory genes in early versus late developmental stages

description: Result file of the de novo assembly of sequenced reads into unigenes. (XLSX 41231 kb)
DOI: 10.6084/m9.figshare.c.3618740_d3
title: Additional file 15: of RNA-sequencing of the sturgeon Acipenser baeri provides insights into expression dynamics of morphogenic differentiation and developmental regulatory genes in early versus late developmental stages

description: GO enrichment analysis of DEGs screened between T1 and T22. (XLSX 147 kb)
DOI: 10.6084/m9.figshare.c.3618488_d2
title: MOESM3 of Functional disruption of human leukocyte antigen II in human embryonic stem cell

description: Additional file 3: Table S2. List of RT-PCR primers.
DOI: 10.6084/m9.figshare.c.3618488_d3
title: MOESM1 of Functional disruption of human leukocyte antigen II in human embryonic stem cell

description: Additional file 1: Table S1. Potential Talen off-targets analysis.
DOI: 10.6084/m9.figshare.c.3618485_d1
title: MOESM1 of Bioinformatics identification of potentially involved microRNAs in Tibetan with gastric cancer based on microRNA profiling

description: Additional file 1: Table S1. The significant KEGG and GO_BP terms of differentially expressed microRNAs. KEGG, Kyoto Encyclopedia of Genes and Genomes; GO Gene Ontology; BP, biological processes.
DOI: 10.6084/m9.figshare.c.3618473_d1
title: Additional file 1: of Characterization of common carp (Cyprinus carpio L.) interferon regulatory factor 5 (IRF5) and its expression in response to viral and bacterial challenges

description: Intron sequences of the ccIRF5 gene. Intron sizes are 495, 804, 225, 131, 88, 761, 518, and 766Â bp. (TXT 3 kb)
DOI: 10.6084/m9.figshare.c.3618458_d8
title: Additional file 5: Table S4. of Fine mapping and RNA-Seq unravels candidate genes for a major QTL controlling multiple fiber quality traits at the T1 region in upland cotton

description: Correlation coefficient among fiber quality traits in F2 population. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3618458_d9
title: Additional file 7: Table S6. of Fine mapping and RNA-Seq unravels candidate genes for a major QTL controlling multiple fiber quality traits at the T1 region in upland cotton

description: The physical locations of markers and genes on the reference genomes. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3618458_d7
title: Additional file 8: Table S7. of Fine mapping and RNA-Seq unravels candidate genes for a major QTL controlling multiple fiber quality traits at the T1 region in upland cotton

description: Overview of Mapping Status by RNA-Seq. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3618458_d5
title: Additional file 4: Table S3. of Fine mapping and RNA-Seq unravels candidate genes for a major QTL controlling multiple fiber quality traits at the T1 region in upland cotton

description: Average value of fiber quality related traits for different trichome phenotype. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3618458_d6
title: Additional file 3: Table S2. of Fine mapping and RNA-Seq unravels candidate genes for a major QTL controlling multiple fiber quality traits at the T1 region in upland cotton

description: Phenotypic variation of fiber quality traits in 1434Â F2 population. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3618458_d4
title: Additional file 6: Table S5. of Fine mapping and RNA-Seq unravels candidate genes for a major QTL controlling multiple fiber quality traits at the T1 region in upland cotton

description: New SSR markers developed from G. raimondii genome sequence. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3618458_d1
title: Additional file 1: Table S1. of Fine mapping and RNA-Seq unravels candidate genes for a major QTL controlling multiple fiber quality traits at the T1 region in upland cotton

description: RT-PCR primer developed from G. hirsutum genome sequence. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3618353_d8
title: Additional file 7: of Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens

description: List of alternative spliced genes from MATS analysis, comparing CLL and B cell data. (XLSX 45Â kb)
DOI: 10.6084/m9.figshare.c.3618353_d7
title: Additional file 6: of Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens

description: Differentially expressed genes in M- and U-CLL specimens. (XLSX 78Â kb)
DOI: 10.6084/m9.figshare.c.3618353_d6
title: Additional file 5: of Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens

description: List of genes in each functional pathway from IPA analysis. (XLSX 27Â kb)
DOI: 10.6084/m9.figshare.c.3618008_d4
title: Additional file 4: Table S4. of The genetic diversity and structure of indica rice in China as detected by single nucleotide polymorphism analysis

description: Origination and classification of 471 germplasm accessions. (XLSX 36Â kb)
DOI: 10.6084/m9.figshare.c.3618008_d3
title: Additional file 1: Table S1. of The genetic diversity and structure of indica rice in China as detected by single nucleotide polymorphism analysis

description: Information on the 5060 SNPs. (XLSX 666Â kb)
DOI: 10.6084/m9.figshare.c.3618008_d1
title: Additional file 3: Table S3. of The genetic diversity and structure of indica rice in China as detected by single nucleotide polymorphism analysis

description: GO enrichment analysis of genes listed in TableÂ 2. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3617990_d5
title: Additional file 4: of Predicting chemical bioavailability using microarray gene expression data and regression modeling: A tale of three explosive compounds

description: Identified DE genes and other selected predictor genes, measured tissue residue of HMX, and the performance of 18 regression models using only DE genes as predictors for the 4-, 14- and 28-day exposures. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.c.3617990_d3
title: Additional file 2: of Predicting chemical bioavailability using microarray gene expression data and regression modeling: A tale of three explosive compounds

description: Identified DE genes (predictor genes), their expression data and measured tissue residue results for 4- and 14-day TNT-exposed earthworms. (XLSX 996 kb)
DOI: 10.6084/m9.figshare.c.3617990_d4
title: Additional file 5: of Predicting chemical bioavailability using microarray gene expression data and regression modeling: A tale of three explosive compounds

description: Functional annotation of 110 identified predictor genes for TNT, RDX and HMX residues using Blast2GO.(XLSX 29 kb)
DOI: 10.6084/m9.figshare.c.3617990_d1
title: Additional file 3: of Predicting chemical bioavailability using microarray gene expression data and regression modeling: A tale of three explosive compounds

description: Identified DE genes (predictor genes), their expression data and measured tissue residue results for 4- and 14-day RDX-exposed earthworms. (XLSX 1109 kb)
DOI: 10.15468/dl.z838gw
title: Occurrence Download

description: A dataset containing 4158 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cirsium nipponicum (Maxim.) Makino",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is Japan"
 ]
}

 The dataset includes 4158 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032627-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3616667_d3
title: Additional file 13: Table S9. of 
                     De novo comparative transcriptome analysis provides new insights into sucrose induced somatic embryogenesis in camphor tree (Cinnamomum camphora L.)

description: Differentially expressed DEGs associated with somatic embryogenesis. (XLSX 58 kb)
DOI: 10.6084/m9.figshare.c.3616667_d1
title: Additional file 11: Table S8. of 
                     De novo comparative transcriptome analysis provides new insights into sucrose induced somatic embryogenesis in camphor tree (Cinnamomum camphora L.)

description: KEGG enrichment analysis of DEGs. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.c.3616667_d2
title: Additional file 9: Table S6. of 
                     De novo comparative transcriptome analysis provides new insights into sucrose induced somatic embryogenesis in camphor tree (Cinnamomum camphora L.)

description: List of DEGs singled out by comparing the libraries of IZE_Suc vs IZE, SE_5w vs IZE_Suc and SE_5w vs IZE. (XLSX 382 kb)
DOI: 10.6084/m9.figshare.c.3616625_d3
title: Additional file 3: Table S2. of Epigenetic signature of Gleason score and prostate cancer recurrence after radical prostatectomy

description: Correlations of gene expression levels and the epigenetic signature. (TXT 64 kb)
DOI: 10.6084/m9.figshare.c.3616625_d1
title: Additional file 2: Table S1. of Epigenetic signature of Gleason score and prostate cancer recurrence after radical prostatectomy

description: Correlations between methylation levels of CpG sites included in the epigenetic signature and mRNA expression levels of corresponding genes. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3616508_d18
title: Additional file 3: Table S2. of Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates

description: Unique genes in Bacillus amyloliquefaciens SQR9 in the pan genome formed by SQR9, Bacillus subtilis 168, and B. amyloliquefaciens FZB42, DSM7T, and B9601-Y2. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.c.3616508_d19
title: Additional file 7: Table S4. of Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates

description: Genomic island (GI) prediction of Bacillus amyloliquefaciens SQR9. GIs were predicted by IslandViewer and M-GCAT (Sheet 1). Sheet 2 shows the detailed information for all genes in the 11 predicted GIs. (XLSX 209 kb)
DOI: 10.6084/m9.figshare.c.3616508_d17
title: Additional file 12: Table S6. of Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates

description: Illumina RNA-Seq data of all significantly differentially expressed genes in different categories (Sheet 1, 24Â h post-inoculation; Sheet 2, 48Â h post-inoculation). (XLSX 275 kb)
DOI: 10.6084/m9.figshare.c.3616508_d10
title: Additional file 13: Table S7. of Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates

description: List of genes involved in rhizosphere adaptation (degradation of plant polysaccharides, cell motility and chemotaxis, biofilm formation, transporters, and detoxification), synthesis of secondary metabolisms, and plant growth promotion. (XLSX 59 kb)
DOI: 10.6084/m9.figshare.c.3616508_d9
title: Additional file 18: Table S10. of Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates

description: BLASTP results for each open reading frame in the pks4 cluster (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3616145_d18
title: Additional file 10: Table S9. of Genome-wide investigation and expression analyses of the pentatricopeptide repeat protein gene family in foxtail millet

description: The Ka/Ks ratios and the estimated divergence times for orthologous SiPPR proteins between foxtail millet and Arabidopsis. (XLSX 36Â kb)
DOI: 10.6084/m9.figshare.c.3616145_d15
title: Additional file 8: Table S7. of Genome-wide investigation and expression analyses of the pentatricopeptide repeat protein gene family in foxtail millet

description: The Ka/Ks ratios and the estimated divergence times for orthologous SiPPR proteins between foxtail millet and moss. (XLSX 29Â kb)
DOI: 10.6084/m9.figshare.c.3616145_d12
title: Additional file 3: Table S3. of Genome-wide investigation and expression analyses of the pentatricopeptide repeat protein gene family in foxtail millet

description: Blast2Go annotation details of SiPPR protein sequences. (XLSX 28Â kb)
DOI: 10.6084/m9.figshare.c.3616145_d13
title: Additional file 12: Table S11. of Genome-wide investigation and expression analyses of the pentatricopeptide repeat protein gene family in foxtail millet

description: The Ka/Ks ratios and the estimated divergence times for orthologous SiPPR proteins between foxtail millet and maize. (XLSX 34Â kb)
DOI: 10.6084/m9.figshare.c.3616145_d8
title: Additional file 4: Table S4. of Genome-wide investigation and expression analyses of the pentatricopeptide repeat protein gene family in foxtail millet

description: The physically mapped PPR genes of foxtail millet were compared with those in the chromosomes of other related grass genomes, including B. distachyon, rice, sorghum, and maize. (XLSX 133Â kb)
DOI: 10.6084/m9.figshare.c.3616154_d3
title: Additional file 3: Table S1. of Pitfalls of improperly procured adjacent non-neoplastic tissue for somatic mutation analysis using next-generation sequencing

description: Coverage summary of whole-exome sequencing (WES). (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3616145_d5
title: Additional file 15: Table S13. of Genome-wide investigation and expression analyses of the pentatricopeptide repeat protein gene family in foxtail millet

description: RNA-seq analysis of PPR gene expression under drought stress treatment (20Â % PEG 6000) in foxtail millet. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3616154_d2
title: Additional file 5: Table S3. of Pitfalls of improperly procured adjacent non-neoplastic tissue for somatic mutation analysis using next-generation sequencing

description: Detailed information of all somatic mutations in targeted amplicon sequencing (TAS), including coverage, VAF and estimated contamination level. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.c.3616145_d4
title: Additional file 9: Table S8. of Genome-wide investigation and expression analyses of the pentatricopeptide repeat protein gene family in foxtail millet

description: The Ka/Ks ratios and the estimated divergence times for orthologous SiPPR proteins between foxtail millet and Selaginella. (XLSX 38Â kb)
DOI: 10.6084/m9.figshare.c.3615806_d10
title: Additional file 1: Table S1. of Single-cell analysis of long non-coding RNAs in the developing human neocortex

description: Related to Figs.Â 1 and 3. Sample and sequencing statistics. Developmental stages, number of reads sequenced and aligned for each bulk RNA-seq and single-cell RNA-seq sample (separate tabs in xls file). Single-cell RNA-seq statistics also include number of unique genes and ERCC Spike-In Control species detected, and how many reads were assigned to either. (XLS 44 kb)
DOI: 10.6084/m9.figshare.c.3615806_d9
title: Additional file 10: Table S6. of Single-cell analysis of long non-coding RNAs in the developing human neocortex

description: Related to Fig.Â 3. Single cell expression table. A total of 276 single cells from human neocortex development and all genes (including known and novel lncRNAs) that pass the minimum expression threshold (Methods). Expression values are in size factor normalized counts, according to DESeq. (XLS 31786 kb)
DOI: 10.6084/m9.figshare.c.3615836_d1
title: Additional file 2: Table S1. of DectICO: an alignment-free supervised metagenomic classification method based on feature extraction and dynamic selection

description: The difference of the LOOCV accuracy between DectICO and the-sequence-composition-based method for each classifier. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3615806_d5
title: Additional file 4: Table S3. of Single-cell analysis of long non-coding RNAs in the developing human neocortex

description: Related to Figure S1. Table of novel lncRNAs not annotated in Ensembl release 75. Gene names and coordinates are in BED format. These lncRNAs were the set of novel lncRNAs annotated in the polyA full reference, which includes both multi-exon and single exon lncRNAs. (XLS 1429 kb)
DOI: 10.6084/m9.figshare.c.3615806_d4
title: Additional file 8: Table S5. of Single-cell analysis of long non-coding RNAs in the developing human neocortex

description: Related to Fig.Â 2c. Expression table of all bulk tissue samples showing genes enriched in either total RNA-seq or polyA RNA-seq. Both polyA and total RNA-seq data are represented for each tissue sample. Expression values are in TPM (Transcripts per Million). (XLS 58 kb)
DOI: 10.6084/m9.figshare.c.3615806_d2
title: Additional file 14: Table S7. of Single-cell analysis of long non-coding RNAs in the developing human neocortex

description: Related to Fig.Â 4. Table of 105 cell type-specific mRNAs (1st tab) and lncRNAs (2nd tab) and their expression enrichment scores, which are log2 transformed, for each of the seven cell type clusters. (XLS 42 kb)
DOI: 10.6084/m9.figshare.c.3615413_d2
title: Additional file 2: Table S1. of First identification of kdr allele F1534S in VGSC gene and its association with resistance to pyrethroid insecticides in Aedes albopictus populations from Haikou City, Hainan Island, China

description: kdr genotypes of Aedes albopictus populations from pyrethroid larval bioassay groups in Haikou City, Hainan Island, China. Table S2 Frequencies of kdr genotypes in relation to mosquito survival phenotype determined by the deltamethrin and DDT susceptibility adult bioassay in Aedes albopictus populations in Haikou City, Hainan Island, China (ZIP 28Â kb)
DOI: 10.6084/m9.figshare.c.3614888_d3
title: Additional file 5: of Required duration of mass ivermectin treatment for onchocerciasis elimination in Africa: a comparative modelling analysis

description: R script needed to run the simulations presented in this paper (EPIONCHO.R). (R 5 kb)
DOI: 10.6084/m9.figshare.c.3614888_d2
title: Additional file 4: of Required duration of mass ivermectin treatment for onchocerciasis elimination in Africa: a comparative modelling analysis

description: Source EPIONCHO code, written in programming language C (EPIONCHO.c). (C 30 kb)
DOI: 10.6084/m9.figshare.c.3614897_d1
title: MOESM1 of Molecular epidemiology, virulence determinants and antimicrobial resistance of Campylobacter spreading in retail chicken meat in Central China

description: Additional file 1. Table S1. The results of the durg resistance testing of each strain.
DOI: 10.6084/m9.figshare.c.3614861_d1
title: Additional file 2: of With or without reirradiation in advanced local recurrent nasopharyngeal carcinoma: a caseâ  control study

description: Dataset of included patients. (XLS 42 kb)
DOI: 10.6084/m9.figshare.c.3614840_d1
title: Additional file 1: of Phylogenomic analyses reveal a molecular signature linked to subterranean adaptation in rodents

description: Table S1. Median values of substitution rates for non-synonymous sites (dN) and synonymous sites (dS), non-synonymous to synonymous substitution (dN/dS) ratios, and overall GC content (GC) and GC content at the third codon position (GC3) in the various lineages. Table S2. The 731 GO terms with log(ω BMR/ω Mouse) and log(ω NMR/ω Guinea pig) values higher than zero. Table S3. The 35 GO terms with lower dN/dS in subterranean rodent lineages, as indicated by LRTs. Table S4. The genes with higher dN/dS values in the BMR compared with other species, as indicated by LRTs. Table S5. The genes with higher dN/dS values in the NMR compared with the other species, as indicated by LRTs. Table S6. The PSGs in the BMR. Table S7. The PSGs in the NMR. Table S8. A subset (n = 15) of PSGs in the BMR and NMR. Table S9. Summary of the over-represented GO terms in subterranean lineages. Table S10. Life history data from the AnAge database ( http://genomics.senescence.info/species/ ) for study taxa. (XLS 550 kb)
DOI: 10.6084/m9.figshare.c.3614816_d5
title: Additional file 4: of High expression of ID family and IGJ genes signature as predictor of low induction treatment response and worst survival in adult Hispanic patients with B-acute lymphoblastic leukemia

description: Table S4. Complete list of signaling pathways dysregulated in patients who achieved complete remission therapy. Signaling pathway analysis was done using MetaCore KPA using the set of 442 genes differentially expressed between good and poor response group. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3614816_d3
title: Additional file 3: of High expression of ID family and IGJ genes signature as predictor of low induction treatment response and worst survival in adult Hispanic patients with B-acute lymphoblastic leukemia

description: Table S3. Complete list of signaling pathways dysregulated in patients who failed to complete remission therapy. Signaling pathway analysis was done using MetaCore KPA using the set of 442 genes differentially expressed between good and poor response group. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3614453_d5
title: Additional file 3: of Fusing literature and full network data improves disease similarity computation

description: Benchmark.xls. The benchmark set of related disease pairs. (XLS 25 kb)
DOI: 10.6084/m9.figshare.c.3614453_d4
title: Additional file 5: of Fusing literature and full network data improves disease similarity computation

description: SimilarityNet.xls. The disease similarity network. (XLS 2552 kb)
DOI: 10.6084/m9.figshare.c.3614453_d2
title: Additional file 2: of Fusing literature and full network data improves disease similarity computation

description: DiseaseGeneAssocDisGeNET.xls. Disease-gene associations acquired from DisGeNET database. (XLS 1582 kb)
DOI: 10.6084/m9.figshare.c.3614453_d3
title: Additional file 4: of Fusing literature and full network data improves disease similarity computation

description: SimilarityPvalues.xls. P-values of similarities of disease pairs in the benchmark set and a random set. (XLS 170 kb)
DOI: 10.6084/m9.figshare.c.3614453_d1
title: Additional file 1: of Fusing literature and full network data improves disease similarity computation

description: DiseaseGeneAssocSIDD.xls. Disease-gene associations acquired from SIDD database. (XLS 888 kb)
DOI: 10.6084/m9.figshare.c.3613955_d1
title: Additional file 5: of Microvascular endothelial cells-derived microvesicles imply in ischemic stroke by modulating astrocyte and blood brain barrier function and cerebral blood flow

description: Availability of data for Evans blue dye extravasation in tMCAO mice after treated with OGD-EMVs and n-EMVs. (XLS 18 kb)