cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6945152.v1
title: 16S rRNA sequencing result: bacteria abundance in genus level

description: Bacteria abundance of silkworm (strain QB and P50) in genus level
DOI: 10.6084/m9.figshare.6945206.v1
title: Taxonomy analysis of shotgun sequencing results

description: Taxonomy analysis of silkworm gut microbiota based on shotgun metagenomic sequencing data.
DOI: 10.6084/m9.figshare.6945128
title: OTU table of 16s rRNA sequencing

description: OTU table with taxonomy informations generated by QIIME software.
DOI: 10.6084/m9.figshare.6945122
title: non-redundent gene set.fa

description: non-redundent gene set of silkworm gut microbiota shotgun sequencing data, including sample MS1P50 and MS1QB.
DOI: 10.6084/m9.figshare.6945056
title: Annotation results.xlsx

description: Shotgun metagenomic data of silkworm gut microbiota annotated with Nr, KEGG, COG, CAZy, ARDB, and SignalP database.
DOI: 10.6084/m9.figshare.6945122.v1
title: non-redundent gene set.fa

description: non-redundent gene set of silkworm gut microbiota shotgun sequencing data, including sample MS1P50 and MS1QB.
DOI: 10.6084/m9.figshare.6945056.v1
title: Annotation results.xlsx

description: Shotgun metagenomic data of silkworm gut microbiota annotated with Nr, KEGG, COG, CAZy, ARDB, and SignalP database.
DOI: 10.6084/m9.figshare.6945026
title: Neoseiulus californicus treated by LC30/LC10/the applicaiton concentration (100μg/mL) of SYP-9625 and CK.txt

description: There is the two sex life table data of Neoseiulus californicus fed on Tetranychus cinnabarinus treated by LC30/LC10/CK of SYP-9625 and the two sex life table data of Neoseiulus californicus exposed to the applicaiton concentration (100μg/mL) of SYP-9625 summarized by Yajing Tian and Jingqi Ouyang.
DOI: 10.6084/m9.figshare.6945002
title: Phage therapy BBD - Isolated bacteriophages - Annotation Table

description: Table shows the gene annotations of sequences obtained from a coral black band disease bacteriophage lysate. Assembled sequences are available for the three largest contigs. All other data is available on request. For further information, see publication (An attempt to treat black band disease of corals with lytic phages isolated from cultures of the cyanobacterium <i>R. reptotaenium</i>).<br><b></b>
DOI: 10.6084/m9.figshare.6945026.v1
title: Neoseiulus californicus females treated by LC30/LC10/CK of SYP-9625.txt

description: There is the two sex life table data of Neoseiulus californicus females fed on Tetranychus cinnabarinus treated by LC30/LC10/CK of SYP-9625 summarized by Yajing Tian and Jingqi Ouyang.
DOI: 10.6084/m9.figshare.6945026.v3
title: Neoseiulus californicus treated by LC30/LC10/the applicaiton concentration (100μg/mL) of SYP-9625 and CK.txt

description: There is the two sex life table data of Neoseiulus californicus fed on Tetranychus cinnabarinus treated by LC30/LC10/CK of SYP-9625 and the two sex life table data of Neoseiulus californicus exposed to the applicaiton concentration (100μg/mL) of SYP-9625 summarized by Yajing Tian and Jingqi Ouyang.
DOI: 10.6084/m9.figshare.6945002.v1
title: Phage therapy BBD - Isolated bacteriophages - Annotation Table

description: Table shows the gene annotations of sequences obtained from a coral black band disease bacteriophage lysate. For further information, see publication. Access link:<br>
DOI: 10.6084/m9.figshare.6945026.v2
title: Neoseiulus californicus treated by LC30/LC10/the applicaiton concentration (100μg/mL) of SYP-9625 and CK.txt

description: There is the two sex life table data of Neoseiulus californicus fed on Tetranychus cinnabarinus treated by LC30/LC10/CK of SYP-9625 and the two sex life table data of Neoseiulus californicus exposed to the applicaiton concentration (100μg/mL) of SYP-9625 summarized by Yajing Tian and Jingqi Ouyang.
DOI: 10.6084/m9.figshare.6945002.v2
title: Phage therapy BBD - Isolated bacteriophages - Annotation Table

description: Table shows the gene annotations of sequences obtained from a coral black band disease bacteriophage lysate. For further information, see publication (An attempt to treat black band disease of corals with lytic phages isolated from cultures of the cyanobacterium <i>R. reptotaenium</i>).<br><b></b>
DOI: 10.6084/m9.figshare.6945002.v3
title: Phage therapy BBD - Isolated bacteriophages - Annotation Table

description: Table shows the gene annotations of sequences obtained from a coral black band disease bacteriophage lysate. Assembled sequences are available for the three largest contigs. All other data is available on request. For further information, see publication (An attempt to treat black band disease of corals with lytic phages isolated from cultures of the cyanobacterium <i>R. reptotaenium</i>).<br><b></b>
DOI: 10.6084/m9.figshare.6944966
title: Additional file 6: of Functional insights into the infective larval stage of Anisakis simplex s.s., Anisakis pegreffii and their hybrids based on gene expression patterns

description: Anisakis allergome. 1) Count file and results of differential expression for the 74 allergen families detected in A. simplex s.s., A. pegreffi and hybrids. 2) Blast results obtained in the search performed using 509 known allergens as queries against the reference Anisakis transcriptome. Nine hundred and thirty seven consensus sequences of the reference transcriptome were detected to significantly match to the queries and were classified into 74 allergen families of which we include additional information. This summarization is also available in AnisakisDB as a dynamic table from where sequences and annotations can be easily navigated and retrieved. (XLS 351 kb)
DOI: 10.6084/m9.figshare.6944966.v1
title: Additional file 6: of Functional insights into the infective larval stage of Anisakis simplex s.s., Anisakis pegreffii and their hybrids based on gene expression patterns

description: Anisakis allergome. 1) Count file and results of differential expression for the 74 allergen families detected in A. simplex s.s., A. pegreffi and hybrids. 2) Blast results obtained in the search performed using 509 known allergens as queries against the reference Anisakis transcriptome. Nine hundred and thirty seven consensus sequences of the reference transcriptome were detected to significantly match to the queries and were classified into 74 allergen families of which we include additional information. This summarization is also available in AnisakisDB as a dynamic table from where sequences and annotations can be easily navigated and retrieved. (XLS 351 kb)
DOI: 10.6084/m9.figshare.6944960
title: Additional file 5: of Functional insights into the infective larval stage of Anisakis simplex s.s., Anisakis pegreffii and their hybrids based on gene expression patterns

description: Differential expression of ES transcripts. 1) Count file used as input in the differential expression test performed at the ES gene level; 2) Summarization of the 356 ES genes accompanied by logFC values and their FDR support obtained from the 3 performed differential expression analyses and additional information relative to consensus sequences grouped to each gene description, as well as associated GOs terms and identification of SignalP domain. This summarization is also available in AnisakisDB as a dynamic table from where sequences and annotations can be navigated and retrieved. (XLSX 91 kb)
DOI: 10.6084/m9.figshare.6944960.v1
title: Additional file 5: of Functional insights into the infective larval stage of Anisakis simplex s.s., Anisakis pegreffii and their hybrids based on gene expression patterns

description: Differential expression of ES transcripts. 1) Count file used as input in the differential expression test performed at the ES gene level; 2) Summarization of the 356 ES genes accompanied by logFC values and their FDR support obtained from the 3 performed differential expression analyses and additional information relative to consensus sequences grouped to each gene description, as well as associated GOs terms and identification of SignalP domain. This summarization is also available in AnisakisDB as a dynamic table from where sequences and annotations can be navigated and retrieved. (XLSX 91 kb)
DOI: 10.6084/m9.figshare.6944954
title: Additional file 4: of Functional insights into the infective larval stage of Anisakis simplex s.s., Anisakis pegreffii and their hybrids based on gene expression patterns

description: Differentially enriched metabolic pathways and GOs. Annotation of metabolic pathways and and GOs integrating results of differential enrichment using GOseq. (XLSX 232 kb)
DOI: 10.6084/m9.figshare.6944954.v1
title: Additional file 4: of Functional insights into the infective larval stage of Anisakis simplex s.s., Anisakis pegreffii and their hybrids based on gene expression patterns

description: Differentially enriched metabolic pathways and GOs. Annotation of metabolic pathways and and GOs integrating results of differential enrichment using GOseq. (XLSX 232 kb)
DOI: 10.6084/m9.figshare.6944945
title: Additional file 3: of Functional insights into the infective larval stage of Anisakis simplex s.s., Anisakis pegreffii and their hybrids based on gene expression patterns

description: Differential expression analyses at the whole transcriptome level. Results obtained from the analyses of differential expression; 1) Hybrids vs A. pegreffi; 2) Hybrids vs A. simplex s.s.; 3) A. pegreffii vs A. simplex s.s. Rows summarizing significant differentially expressed transcripts supported by FDR
DOI: 10.6084/m9.figshare.6944945.v1
title: Additional file 3: of Functional insights into the infective larval stage of Anisakis simplex s.s., Anisakis pegreffii and their hybrids based on gene expression patterns

description: Differential expression analyses at the whole transcriptome level. Results obtained from the analyses of differential expression; 1) Hybrids vs A. pegreffi; 2) Hybrids vs A. simplex s.s.; 3) A. pegreffii vs A. simplex s.s. Rows summarizing significant differentially expressed transcripts supported by FDR
DOI: 10.6084/m9.figshare.6944858
title: Additional file 5: of Transcriptomic signatures reveal immune dysregulation in human diabetic and idiopathic gastroparesis

description: Table S5. Differentially expressed genes common in diabetic gastroparesis and diabetic controls and idiopathic gastroparesis and controls. (XLSX 107 kb)
DOI: 10.6084/m9.figshare.6944858.v1
title: Additional file 5: of Transcriptomic signatures reveal immune dysregulation in human diabetic and idiopathic gastroparesis

description: Table S5. Differentially expressed genes common in diabetic gastroparesis and diabetic controls and idiopathic gastroparesis and controls. (XLSX 107 kb)
DOI: 10.6084/m9.figshare.6944852
title: Additional file 4: of Transcriptomic signatures reveal immune dysregulation in human diabetic and idiopathic gastroparesis

description: Table S4. Differentially expressed genes in idiopathic gastroparesis and idiopathic controls. (XLSX 155 kb)
DOI: 10.6084/m9.figshare.6944852.v1
title: Additional file 4: of Transcriptomic signatures reveal immune dysregulation in human diabetic and idiopathic gastroparesis

description: Table S4. Differentially expressed genes in idiopathic gastroparesis and idiopathic controls. (XLSX 155 kb)
DOI: 10.6084/m9.figshare.6944846
title: Additional file 5: of CTCF maintains regulatory homeostasis of cancer pathways

description: Mouse and human tumor metadata and differential expression results of RNA-seq data. Sample information regarding all mouse and human tumor samples included in analyses. Results from the differential expression analysis of mouse liver tumors and human uterine and breast cancer dataset (performed using DESeq2). Gene set enrichment analysis for mouse concordant genes. Intersection results of MEF and tumor DE analyses. Format: xls. File size: 20.7Â MB. (XLS 20148 kb)
DOI: 10.6084/m9.figshare.6944846.v1
title: Additional file 5: of CTCF maintains regulatory homeostasis of cancer pathways

description: Mouse and human tumor metadata and differential expression results of RNA-seq data. Sample information regarding all mouse and human tumor samples included in analyses. Results from the differential expression analysis of mouse liver tumors and human uterine and breast cancer dataset (performed using DESeq2). Gene set enrichment analysis for mouse concordant genes. Intersection results of MEF and tumor DE analyses. Format: xls. File size: 20.7Â MB. (XLS 20148 kb)
DOI: 10.6084/m9.figshare.6944831
title: Additional file 3: of Transcriptomic signatures reveal immune dysregulation in human diabetic and idiopathic gastroparesis

description: Table S3. Differentially expressed genes in diabetic gastroparesis and non-diabetic controls. (XLSX 127 kb)
DOI: 10.6084/m9.figshare.6944834
title: Additional file 4: of CTCF maintains regulatory homeostasis of cancer pathways

description: Proteome quantification. Normalized protein abundances from the TMT proteomics dataset along with the results from the differential abundance analysis. Format: xls. File size: 2.9Â MB. (XLS 2840 kb)
DOI: 10.6084/m9.figshare.6944834.v1
title: Additional file 4: of CTCF maintains regulatory homeostasis of cancer pathways

description: Proteome quantification. Normalized protein abundances from the TMT proteomics dataset along with the results from the differential abundance analysis. Format: xls. File size: 2.9Â MB. (XLS 2840 kb)
DOI: 10.6084/m9.figshare.6944831.v1
title: Additional file 3: of Transcriptomic signatures reveal immune dysregulation in human diabetic and idiopathic gastroparesis

description: Table S3. Differentially expressed genes in diabetic gastroparesis and non-diabetic controls. (XLSX 127 kb)
DOI: 10.6084/m9.figshare.6944822
title: Additional file 9: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

description: Table S9. Range of expression estimates, and absolute difference between largest and smallest estimate, after randomly down-sampling the LPS-stimulated BMDM datasets. (XLSX 8074 kb)
DOI: 10.6084/m9.figshare.6944822.v1
title: Additional file 9: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

description: Table S9. Range of expression estimates, and absolute difference between largest and smallest estimate, after randomly down-sampling the LPS-stimulated BMDM datasets. (XLSX 8074 kb)
DOI: 10.6084/m9.figshare.6944810
title: Additional file 3: of CTCF maintains regulatory homeostasis of cancer pathways

description: Differential expression results of RNA-seq data. Results from the differential expression analysis of the RNA-seq dataset using DESeq2. Also, results from the gene set enrichment analyses for both Gene Ontology sets and KEGG pathways. Format: xls. File size: 13.5Â MB. (XLS 13174 kb)
DOI: 10.6084/m9.figshare.6944807
title: Additional file 2: of Transcriptomic signatures reveal immune dysregulation in human diabetic and idiopathic gastroparesis

description: Table S2. Differentially expressed genes in diabetic gastroparesis and diabetic controls. (XLSX 93 kb)
DOI: 10.6084/m9.figshare.6944810.v1
title: Additional file 3: of CTCF maintains regulatory homeostasis of cancer pathways

description: Differential expression results of RNA-seq data. Results from the differential expression analysis of the RNA-seq dataset using DESeq2. Also, results from the gene set enrichment analyses for both Gene Ontology sets and KEGG pathways. Format: xls. File size: 13.5Â MB. (XLS 13174 kb)
DOI: 10.6084/m9.figshare.6944807.v1
title: Additional file 2: of Transcriptomic signatures reveal immune dysregulation in human diabetic and idiopathic gastroparesis

description: Table S2. Differentially expressed genes in diabetic gastroparesis and diabetic controls. (XLSX 93 kb)
DOI: 10.6084/m9.figshare.6944795
title: Additional file 8: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

description: Table S8. Number of detectably expressed genes after randomly down-sampling the LPS-stimulated BMDM datasets. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.6944792
title: Additional file 2: of CTCF maintains regulatory homeostasis of cancer pathways

description: Differential binding results of ChIP-seq datasets. Results from the differential binding analyses of the CTCF ChIP-seq dataset using csaw, and of the H3K4me3 and H3K27ac datasets using DiffBind. Format: xls. File size: 20.5Â MB. (XLS 20040 kb)
DOI: 10.6084/m9.figshare.6944795.v1
title: Additional file 8: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

description: Table S8. Number of detectably expressed genes after randomly down-sampling the LPS-stimulated BMDM datasets. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.6944792.v1
title: Additional file 2: of CTCF maintains regulatory homeostasis of cancer pathways

description: Differential binding results of ChIP-seq datasets. Results from the differential binding analyses of the CTCF ChIP-seq dataset using csaw, and of the H3K4me3 and H3K27ac datasets using DiffBind. Format: xls. File size: 20.5Â MB. (XLS 20040 kb)
DOI: 10.6084/m9.figshare.6944780
title: Additional file 1: of CTCF maintains regulatory homeostasis of cancer pathways

description: Validation of Ctcf deletion. Quantification of Ctcf deletion by qRT-PCR and quantitative western blot experiments on wild-type and Ctcf +/â MEFs. Format: xls. File size: 61Â KB. (XLS 40 kb)
DOI: 10.6084/m9.figshare.6944780.v1
title: Additional file 1: of CTCF maintains regulatory homeostasis of cancer pathways

description: Validation of Ctcf deletion. Quantification of Ctcf deletion by qRT-PCR and quantitative western blot experiments on wild-type and Ctcf +/â MEFs. Format: xls. File size: 61Â KB. (XLS 40 kb)
DOI: 10.6084/m9.figshare.6944771
title: Additional file 7: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

description: Table S7. Proportion of RNA-seq reads retained by down-sampling the LPS-stimulated BMDM datasets. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.6944771.v1
title: Additional file 7: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

description: Table S7. Proportion of RNA-seq reads retained by down-sampling the LPS-stimulated BMDM datasets. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.6944759
title: Additional file 6: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

description: Table S6. Chicken RNA-seq meta-dataset, after the second (and final) iteration of Kallisto. (XLSX 23600 kb)
DOI: 10.6084/m9.figshare.6944759.v1
title: Additional file 6: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

description: Table S6. Chicken RNA-seq meta-dataset, after the second (and final) iteration of Kallisto. (XLSX 23600 kb)
DOI: 10.6084/m9.figshare.6944747
title: Additional file 2: of Statistical relationship between metabolic decomposition and chemical uptake predicts bioconcentration factor data for diverse chemical exposures

description: Table S1 includes log10 Kow values and log10 BCF values for various chemicals as measured or derived from measurements taken in adult zebrafish. Table S2 Table S2 includes log10 Kow values and log10 BCF values for various chemicals as measured or derived from measurements taken in embryonic zebrafish. Table S3 Table S3 includes log10 Kow values and log10 BCF values for various chemicals as measured or derived from measurements taken in various other fish species. (XLSX 81Â kb)
DOI: 10.6084/m9.figshare.6944747.v1
title: Additional file 2: of Statistical relationship between metabolic decomposition and chemical uptake predicts bioconcentration factor data for diverse chemical exposures

description: Table S1 includes log10 Kow values and log10 BCF values for various chemicals as measured or derived from measurements taken in adult zebrafish. Table S2 Table S2 includes log10 Kow values and log10 BCF values for various chemicals as measured or derived from measurements taken in embryonic zebrafish. Table S3 Table S3 includes log10 Kow values and log10 BCF values for various chemicals as measured or derived from measurements taken in various other fish species. (XLSX 81Â kb)
DOI: 10.6084/m9.figshare.6944741
title: Additional file 5: of Evolutionary stability of topologically associating domains is associated with conserved gene regulation

description: Table S2. Ortholog genes in human and mouse with gene expression correlation across tissues. (TSV 1036 kb)
DOI: 10.6084/m9.figshare.6944741.v1
title: Additional file 5: of Evolutionary stability of topologically associating domains is associated with conserved gene regulation

description: Table S2. Ortholog genes in human and mouse with gene expression correlation across tissues. (TSV 1036 kb)
DOI: 10.6084/m9.figshare.6944738
title: Additional file 5: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

description: Table S5. Transcripts not detectably expressed (at &gt;â 1 TPM) in any tissue, after the first iteration of Kallisto. (XLSX 91 kb)
DOI: 10.6084/m9.figshare.6944738.v1
title: Additional file 5: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

description: Table S5. Transcripts not detectably expressed (at &gt;â 1 TPM) in any tissue, after the first iteration of Kallisto. (XLSX 91 kb)
DOI: 10.6084/m9.figshare.6944726
title: Additional file 4: of Evolutionary stability of topologically associating domains is associated with conserved gene regulation

description: Table S1. Matching tissues and samples with CAGE expression data in human and mouse. (TSV 2 kb)
DOI: 10.6084/m9.figshare.6944726.v1
title: Additional file 4: of Evolutionary stability of topologically associating domains is associated with conserved gene regulation

description: Table S1. Matching tissues and samples with CAGE expression data in human and mouse. (TSV 2 kb)
DOI: 10.6084/m9.figshare.6944720
title: Additional file 4: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

description: Table S4. Number of genes with detectable expression, per tissue, after the first iteration of Kallisto. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6944720.v1
title: Additional file 4: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

description: Table S4. Number of genes with detectable expression, per tissue, after the first iteration of Kallisto. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6944708
title: Additional file 3: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

description: Table S3. Exponents of the log-log plots after plotting the reverse cumulative distribution of TPM per gene on a log-log scale. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.6944708.v1
title: Additional file 3: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

description: Table S3. Exponents of the log-log plots after plotting the reverse cumulative distribution of TPM per gene on a log-log scale. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.6944693
title: Additional file 2: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

description: Table S2. Independent datasets sequencing the same tissue/cell type. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.6944693.v1
title: Additional file 2: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

description: Table S2. Independent datasets sequencing the same tissue/cell type. (XLSX 8 kb)