cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3610958_d11.v1
title: Additional file 9: Table S5. of Mapping the landscape of metabolic goals of a cell

description: shows metabolic fluxes inferred from flux ratios for 11 evolved E. coli strains. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3610958_d9.v1
title: Additional file 4: Table S2. of Mapping the landscape of metabolic goals of a cell

description: shows non-zero minimal/maximal optimization coefficients computed by objective variability analysis (OVA) for each reaction from simulated succinate-limited E. coli fluxes. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3610151_d1.v1
title: Additional file 1: of Long noncoding RNA C17orf91 is a potential prognostic marker and functions as an oncogene in ovarian cancer

description: Primers used in present study. (XLS 17Â kb)
DOI: 10.6084/m9.figshare.c.3609995_d7.v1
title: Additional file 3: Table S2. of A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit β-carotene accumulation in melon fruit

description: SNP differentiating between bulks. *: same base as reference genome; SNP type: M, mismatch; I, insertion; D, deletion; AA change: SNP causes amino acid changes; for example, R108H means that SNP at CDS position 108 causes amino acid changes from R to H (“R” in green bulk to “H” in orange bulk). (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3609995_d8.v1
title: Additional file 4: Table S3. of A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit Î˛-carotene accumulation in melon fruit

description: List of genes included in the significant SNP area. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.c.3609995_d6.v1
title: Additional file 6: Table S5. of A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit Î˛-carotene accumulation in melon fruit

description: List of genes exhibited significant up or down regulation in two fruit developmental stages. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3608810_d8.v1
title: Additional file 7: of Genome-wide analysis of gene expression reveals gene regulatory networks that regulate chasmogamous and cleistogamous flowering in Pseudostellaria heterophylla (Caryophyllaceae)

description: KEGG Enrichment analysis of differentially expressed transcripts. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3608810_d7.v1
title: Additional file 2: of Genome-wide analysis of gene expression reveals gene regulatory networks that regulate chasmogamous and cleistogamous flowering in Pseudostellaria heterophylla (Caryophyllaceae)

description: Transcripts annotated by GO, KEGG, and eggNOG. (XLSX 4808Â kb)
DOI: 10.6084/m9.figshare.c.3608810_d6.v1
title: Additional file 4: of Genome-wide analysis of gene expression reveals gene regulatory networks that regulate chasmogamous and cleistogamous flowering in Pseudostellaria heterophylla (Caryophyllaceae)

description: 24 floral genes of quantitative real time PCR for validation of RNA-Seq data. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3608810_d5.v1
title: Additional file 6: of Genome-wide analysis of gene expression reveals gene regulatory networks that regulate chasmogamous and cleistogamous flowering in Pseudostellaria heterophylla (Caryophyllaceae)

description: GO Enrichment analysis of differentially expressed transcripts. (XLSX 26Â kb)
DOI: 10.6084/m9.figshare.c.3608810_d4.v1
title: Additional file 5: of Genome-wide analysis of gene expression reveals gene regulatory networks that regulate chasmogamous and cleistogamous flowering in Pseudostellaria heterophylla (Caryophyllaceae)

description: Differentially expressed transcripts between CH and CL flowers. In total, 396 genes were identified as differentially expressed (|log2FC| &gt; 2, p-value
DOI: 10.6084/m9.figshare.c.3608810_d2.v1
title: Additional file 8: of Genome-wide analysis of gene expression reveals gene regulatory networks that regulate chasmogamous and cleistogamous flowering in Pseudostellaria heterophylla (Caryophyllaceae)

description: KEGG pathways classification for differentially expressed transcripts between CH (A) and CL (B) flowers. Red dot represented transcripts up-regulated in CH flowers, green dot represented transcript up-regulated in CL flowers. (XLSX 36Â kb)
DOI: 10.6084/m9.figshare.c.3608810_d1.v1
title: Additional file 3: of Genome-wide analysis of gene expression reveals gene regulatory networks that regulate chasmogamous and cleistogamous flowering in Pseudostellaria heterophylla (Caryophyllaceae)

description: Putative homologues of Pseudostellaria heterophylla genes involved in flowering process identified by BLAST search with Arabidopsis genes. (XLSX 56Â kb)
DOI: 10.6084/m9.figshare.c.3607706_d1.v1
title: Additional file 1: of The correlation between radiographic and pathologic grading of lumbar facet joint degeneration

description: Date set (XLS 33 kb)
DOI: 10.6084/m9.figshare.c.3607640_d3.v1
title: Additional file 3: Figure S1. of Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in Brachypodium distachyon

description: A phylogenetic tree of B. distachyon, Arabidopsis and rice AP2/ERF proteins constructed by MP method using MEGA5.0. Then groups are marked I to X. Figure S2. Conserved motifs identified from the AP2/ERF genes in B. distachyon. (ZIP 3757 kb)
DOI: 10.6084/m9.figshare.c.3607610_d11.v1
title: Additional file 15: of Transcriptome adaptation of the bovine mammary gland to diets rich in unsaturated fatty acids shows greater impact of linseed oil over safflower oil on gene expression and metabolic pathways

description: Differentially expressed genes with functions in cell death and apoptosis in linseed oil treatment. (XLS 35Â kb)
DOI: 10.6084/m9.figshare.c.3607640_d2.v1
title: Additional file 2: of Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in Brachypodium distachyon

description: The detailed sequence information of all the BdAP2/ERF genes, including genomic, transcript, CDS and protein as well as 2Â kb upstream sequence. (RAR 245 kb)
DOI: 10.6084/m9.figshare.c.3606632_d13.v1
title: Additional file 19: Table S10. of Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals

description: COGs with significantly altered abundance in â  Ca. Homeothermaceaeâ   versus related Bacteroidales families. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.c.3606632_d12.v1
title: Additional file 6: Table S3. of Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals

description: Cell wall associated PFAMs identified in â  Ca. Homeothermaceaeâ   genomes. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3605822_d2.v1
title: MOESM2 of Integrated isotope-assisted metabolomics and 13C metabolic flux analysis reveals metabolic flux redistribution for high glucoamylase production by Aspergillus niger

description: Additional file 2 . The best-fit flux distribution and minimal weighted residual from the parameter estimations.
DOI: 10.6084/m9.figshare.c.3605792_d5.v1
title: Additional file 2: Table S2. of The complete genome sequence and analysis of a plasmid-bearing myxobacterial strain Myxococcus fulvus 124B02 (M 206081)

description: Comparison of COG assignments of the genes between M. fulvus 124B02 and M. fulvus HW-1. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3605792_d3.v1
title: Additional file 4: Table S4. of The complete genome sequence and analysis of a plasmid-bearing myxobacterial strain Myxococcus fulvus 124B02 (M 206081)

description: Strain-specific genes in the family of DNA replication, recombination and repair in M. fulvus 124B02, compared with DSM 14675. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3605792_d4.v1
title: Additional file 1: Table S1. of The complete genome sequence and analysis of a plasmid-bearing myxobacterial strain Myxococcus fulvus 124B02 (M 206081)

description: Comparison of COG assignments of the genes between M. fulvus 124B02 and M. stipitatus DSM 14675. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3605792_d2.v1
title: Additional file 5: Table S5. of The complete genome sequence and analysis of a plasmid-bearing myxobacterial strain Myxococcus fulvus 124B02 (M 206081)

description: Homologues of pMF1.19 and pMF1.20 in M. fulvus 124B02. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3605792_d1.v1
title: Additional file 3: Table S3. of The complete genome sequence and analysis of a plasmid-bearing myxobacterial strain Myxococcus fulvus 124B02 (M 206081)

description: Comparison of COG assignments of the genes between M. fulvus 124B02 and M. xanthus DK1622. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3605681_d5.v1
title: Additional file 5: of Development of EMS-induced mutation population for amylose and resistant starch variation in bread wheat (Triticum aestivum) and identification of candidate genes responsible for amylose variation

description: Normalized threshold cycle (ΔCт) of two SBEII isoforms (SBEIIa and SBEIIb) during seed development. The data was taken at three stages of seed development (21, 28, and 35 days after anthesis, DAA) in two mutant lines, ‘TAC 75’(amylose content - 64 %) and ‘TAC 6’(amylose content– 6.8 %), in comparison to the parent variety, ‘C 306’ (amylose content - 26 %). The data was taken in two biological replications, each represented as mean ± SD from three technical replicates. Wheat ADP Ribosylation Factor (ARF) was used as an internal control gene for normalization. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3605681_d3.v1
title: Additional file 4: of Development of EMS-induced mutation population for amylose and resistant starch variation in bread wheat (Triticum aestivum) and identification of candidate genes responsible for amylose variation

description: Normalized threshold cycle (ΔCт) of chromosome specific alleles of GBSSI (GBSSI–7A, GBSSI–4A, and GBSSI–7D) during seed development. The data was taken at three stages of seed development (21, 28, and 35 days after anthesis, DAA) in two mutant lines, ‘TAC 75’(amylose content - 64 %) and ‘TAC 6’(amylose content– 6.8 %), in comparison to the parent variety, ‘C 306’ (amylose content - 26 %). The data was taken in two biological replications, each represented as mean ± SD from three technical replicates. Wheat ADP Ribosylation Factor (ARF) was used as an internal control gene for normalization. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3605681_d2.v1
title: Additional file 1: of Development of EMS-induced mutation population for amylose and resistant starch variation in bread wheat (Triticum aestivum) and identification of candidate genes responsible for amylose variation

description: Evaluation of 1035 (M3) mutant lines for amylose variation using five-time diluted standard Iodine-Potassium Iodide (I2â  KI) solution. Time taken to develop blue color was recorded using a digital electronic stopwatch, while color intensity was scored as zero for no color development, + for light blue color, and ++ for deep blue color. All the data was given as a mean of three seeds. (XLSX 58 kb)
DOI: 10.6084/m9.figshare.c.3605681_d1.v1
title: Additional file 3: of Development of EMS-induced mutation population for amylose and resistant starch variation in bread wheat (Triticum aestivum) and identification of candidate genes responsible for amylose variation

description: Normalized threshold cycle (ΔCт) of 20 starch metabolic genes during seed development. The data was taken at three stages of seed development (21, 28, and 35 days after anthesis, DAA) in two mutant lines, ‘TAC 75’(amylose content - 64 %) and ‘TAC 6’(amylose content– 6.8 %), in comparison to the parent variety, ‘C 306’ (amylose content - 26 %). The data was taken in two biological replications, each represented as mean ± SD from three technical replicates. Wheat ADP Ribosylation Factor (ARF) was used as an internal control gene for normalization. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.c.3605645_d1.v1
title: Additional file 1 of COMODI: an ontology to characterise differences in versions of computational models in biology

description: Example combine archive. (OMEX 4 kb)
DOI: 10.57967/hf/3819
title: Diffuse_Map_Surfaces
DOI: 10.6084/m9.figshare.c.3604559_d1.v1
title: Additional file 1: of Epigenomic profiling of prostate cancer identifies differentially methylated genes in TMPRSS2:ERG fusion-positive versus fusion-negative tumors

description: List of 3101 top-ranked differentially methylated CpG sites.
DOI: 10.6084/m9.figshare.c.3604532_d2.v1
title: Additional file 2: Tables S1â  S16. of Global histone modification profiling reveals the epigenomic dynamics during malignant transformation in a four-stage breast cancer model

description: Table S1. Differential expression genes between L and P6 cell lines. Table S2. Differential expression genes between LT and P6 cell lines. Table S3. Differential expression genes between LTR and P6 cell lines. Table S4. DEGs between LT and L cell lines. Table S5. DEGs between LTR and LT cell lines. Table S6. DEGs between TCGA breast cancer and normal tissues (â Ľthreefolds). Table S7. Genes overlapped between DEGs of TCGA and transformed cell lines. Table S8. Genes localized in H3K9me3 small LOCKs of HMC-p6. Table S9. Genes localized in decreased H3K9me2 boundaries in HMC-LT. Table S10. Genes localized in decreased H3K9me2 boundaries in HMC-LTR. Table S11. Uniprot cancer-related genes in the boundaries of decreased H3K9me2 LOCKs (compared to HMC-p6). Table S12. Genes overlapped between LT_NC/LT_shKDM3A and LT/P6 DEGs. Table S13. DEGs between LT_NC and LT_shKDM3a cells. Table S14. Genes overlapped between LTR_NC/LTR_siKDM3A and LTR/P6 DEGs. Table S15. DEGs between LTR_NC and LTR_siKDM3a cells. Table S16. Primer and siRNA sequences. (XLS 1135 kb)
DOI: 10.6084/m9.figshare.c.3604520_d1.v1
title: Additional file 3: of Hepatic resection provided long-term survival for patients with intermediate and advanced-stage resectable hepatocellular carcinoma

description: Figure S2. Kaplan-Meier Curve showing DFS of surgery plus TACE and surgery alone. (ZIP 396 KB)
DOI: 10.6084/m9.figshare.c.3603080_d6.v1
title: Additional file 5: Table S2. of Porcine methionine sulfoxide reductase B3: molecular cloning, tissue-specific expression profiles, and polymorphisms associated with ear size in Sus scrofa

description: The molecular weights and isoelectric points of multiple phosphorylation states. (XLS 23Â kb)
DOI: 10.6084/m9.figshare.c.3603080_d4.v1
title: Additional file 1: Table S1. of Porcine methionine sulfoxide reductase B3: molecular cloning, tissue-specific expression profiles, and polymorphisms associated with ear size in Sus scrofa

description: Amino acids encoded by the porcine MSRB3 gene. (XLS 23Â kb)
DOI: 10.22002/6f7e5-94618
title: Supporting data and codes for "Sliding and healing of frictional interfaces that appear stationary"

description: These data and software supplement the following publication:
Sirorattanakul, K., Larochelle, S., Rubino, V., Lapusta, N., Rosakis, A. J. Sliding and healing of frictional interfaces that appear stationary, Under review in Nature.
Any questions can be directed to Krittanon Sirorattanakul (Pond) at krittanon.pond@gmail.com.
DOI: 10.6084/m9.figshare.c.3602216_d3.v1
title: Additional file 8: of Genomic copy number variation association study in Caucasian patients with nonsyndromic cryptorchidism

description: CNV calls for Group 2 controls passed sample QC. Each column in Additional file 8 represents CNV location, SNPs numbers contained within the CNV, the length of the CNV, copy number (cn) of the CNV call, sample id, the starting marker identifier and the ending marker identifier in the CNV, and confidence score in PennCNV calling. (XLSX 1952Â kb)
DOI: 10.6084/m9.figshare.c.3602216_d2.v1
title: Additional file 6: of Genomic copy number variation association study in Caucasian patients with nonsyndromic cryptorchidism

description: CNV calls for Group 1 controls passed sample QC. Each column in Additional file 6 represents CNV location, SNPs numbers contained within the CNV, the length of the CNV, copy number (cn) of the CNV call, sample id, the starting marker identifier and the ending marker identifier in the CNV, and confidence score in PennCNV calling. (XLSX 1544Â kb)
DOI: 10.6084/m9.figshare.c.3602156_d10.v1
title: Additional file 10: Table S8. of Transcriptome profiling analysis for two Tibetan wild barley genotypes in responses to low nitrogen

description: Gene accession numbers and sequences of 1469 DEGs. (XLS 2369Â kb)
DOI: 10.6084/m9.figshare.c.3602156_d9.v1
title: Additional file 4: Table S3. of Transcriptome profiling analysis for two Tibetan wild barley genotypes in responses to low nitrogen

description: The FPKM value of 1469 DEGs in XZ149 and XZ56. (XLSX 464Â kb)
DOI: 10.6084/m9.figshare.c.3602156_d8.v1
title: Additional file 3: Table S2. of Transcriptome profiling analysis for two Tibetan wild barley genotypes in responses to low nitrogen

description: Summary of mapping reads of the RNA-Seq. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.c.3602156_d6.v1
title: Additional file 7: Table S6. of Transcriptome profiling analysis for two Tibetan wild barley genotypes in responses to low nitrogen

description: DEGs encoding kinases under low N stress in XZ149 and XZ56. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.c.3602150_d6.v1
title: Additional file 3: of 
                     De novo transcriptome sequencing and analysis of Coccinella septempunctata L. in non-diapause, diapause and diapause-terminated states to identify diapause-associated genes

description: S3-Significantly enriched KEGG pathways in D vs. ND and DT vs. D. (XLSX 16.6 kb)
DOI: 10.6084/m9.figshare.c.3600731_d13.v1
title: Additional file 7: of Effect of differentiation on microRNA expression in bovine skeletal muscle satellite cells by deep sequencing

description: Summary of base edit in three libraries. Note: The data in this supplementary file can be seen in the Excel spreadsheet.
DOI: 10.6084/m9.figshare.c.3600731_d11.v1
title: Additional file 13: of Effect of differentiation on microRNA expression in bovine skeletal muscle satellite cells by deep sequencing

description: Predicted target genes for novel miRNA. Note: The data in this supplementary file can be seen in the Excel spreadsheet.
DOI: 10.6084/m9.figshare.c.3600731_d10.v1
title: Additional file 12: of Effect of differentiation on microRNA expression in bovine skeletal muscle satellite cells by deep sequencing

description: Predicted target genes for up-regulation miRNA. Note: The data in this supplementary file can be seen in the Excel spreadsheet.
DOI: 10.6084/m9.figshare.c.3600731_d6.v1
title: Additional file 1: of Effect of differentiation on microRNA expression in bovine skeletal muscle satellite cells by deep sequencing

description: Primers and sequences for RT-qPCR analysis (XLS 12 kb)
DOI: 10.6084/m9.figshare.c.3600731_d7.v1
title: Additional file 9: of Effect of differentiation on microRNA expression in bovine skeletal muscle satellite cells by deep sequencing

description: Novel miRNAs identified in this study. Note: The data in this supplementary file can be seen in the Excel spreadsheet.
DOI: 10.6084/m9.figshare.c.3600731_d5.v1
title: Additional file 3: of Effect of differentiation on microRNA expression in bovine skeletal muscle satellite cells by deep sequencing

description: The known miRNA expression profiles between two libraries. Note: The data in this supplementary file can be seen in the Excel spreadsheet.
DOI: 10.6084/m9.figshare.c.3600164_d2.v1
title: Additional file 1: of Strand-specific RNA-Seq transcriptome analysis of genotypes with and without low-phosphorus tolerance provides novel insights into phosphorus-use efficiency in maize

description: Statistics of RNA sequences in roots (A) and shoots (B) in maize inbred lines 31778 and CCM454. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.c.3600134_d7.v1
title: Additional file 1: of Novel regional age-associated DNA methylation changes within human common disease-associated loci

description: BED file of a-DMRs with UCSC browser header. (BED 1Â kb)
DOI: 10.6084/m9.figshare.c.3600134_d6.v1
title: Additional file 7: of Novel regional age-associated DNA methylation changes within human common disease-associated loci

description: BED file of combined 14 ageing studies. (BED 2508Â kb)
DOI: 10.6084/m9.figshare.c.3600164_d1.v1
title: Additional file 5: of Strand-specific RNA-Seq transcriptome analysis of genotypes with and without low-phosphorus tolerance provides novel insights into phosphorus-use efficiency in maize

description: List of genes with significant expression differences in the shoots of inbred lines 31778 and CCM454 under sufficient condition. (XLSX 417Â kb)
DOI: 10.6084/m9.figshare.c.3600134_d3.v1
title: Additional file 2: of Novel regional age-associated DNA methylation changes within human common disease-associated loci

description: Supplementary Tables S1â  7. (XLSX 1125Â kb)
DOI: 10.6084/m9.figshare.c.3600044_d10.v1
title: Additional file 7: of The contribution of transposable elements to size variations between four teleost genomes

description: TE sequence 1: new repeats identified in zebrafish. (FAS 390Â kb)
DOI: 10.6084/m9.figshare.c.3598652_d11.v1
title: Additional file 9: of Genome-wide patterns of copy number variation in the Chinese yak genome

description: Over-representation / under-representation of molecular function, cellular component and biological process terms. (XLS 30 kb)
DOI: 10.6084/m9.figshare.c.3598652_d10.v1
title: Additional file 1: of Genome-wide patterns of copy number variation in the Chinese yak genome

description: Basic information relating to yak used in this study, their types, geographical distributions and resequencing data used in the CNV analysis. (XLS 45 kb)
DOI: 10.6084/m9.figshare.c.3598652_d8.v1
title: Additional file 4: of Genome-wide patterns of copy number variation in the Chinese yak genome

description: List of all CNVRs in the yak genome. (XLSX 784 kb)
DOI: 10.6084/m9.figshare.c.3598652_d9.v1
title: Additional file 2: of Genome-wide patterns of copy number variation in the Chinese yak genome

description: List of all 98,441 CNV events in this study. (XLSX 2719 kb)
DOI: 10.6084/m9.figshare.c.3598652_d7.v1
title: Additional file 5: of Genome-wide patterns of copy number variation in the Chinese yak genome

description: Primer sequences and confirmation results for qPCR. (XLS 39 kb)
DOI: 10.6084/m9.figshare.c.3598652_d6.v1
title: Additional file 11: of Genome-wide patterns of copy number variation in the Chinese yak genome

description: Population-differentiated CNVRs with annotated protein coding genes when comparing yak living at high and low altitudes. (XLS 35 kb)
DOI: 10.6084/m9.figshare.c.3598652_d4.v1
title: Additional file 3: of Genome-wide patterns of copy number variation in the Chinese yak genome

description: Summary of CNV events in different individuals. (XLS 35 kb)
DOI: 10.6084/m9.figshare.c.3598652_d3.v1
title: Additional file 10: of Genome-wide patterns of copy number variation in the Chinese yak genome

description: Population-differentiated CNVRs with annotated protein coding genes when comparing wild and domestic yak. (XLS 40 kb)
DOI: 10.6084/m9.figshare.c.3598652_d1.v1
title: Additional file 6: of Genome-wide patterns of copy number variation in the Chinese yak genome

description: Statistics for yak segmental duplication. (XLS 28 kb)
DOI: 10.6084/m9.figshare.c.3598598_d1.v1
title: Additional file 1 of Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment

description: Supplementary Dataset 1: RF index for each mutation. (XLS 364 kb)
DOI: 10.6084/m9.figshare.c.3598547_d6.v1
title: Additional file 3: Table S2. of Reference genes for accurate gene expression analyses across different tissues, developmental stages and genotypes in rice for drought tolerance

description: Weighted rank score of gene members of commonly used reference gene families. (XLSX 18 kb)