cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14745423
title: ZSCAN16-AS1 expedites hepatocellular carcinoma progression via modulating the miR-181c-5p/SPAG9 axis to activate the JNK pathway

description: Hepatocellular carcinoma (HCC) is generally known as one of the most common cancers in the world. Nowadays, interventional therapies such as transcatheter arterial chemoembolization (TACE) have emerged as an efficient therapy for HCC patients. Accumulating evidence has unveiled that long non-coding RNAs (lncRNAs) are crucial regulators in HCC progression. Nonetheless, the biological function of lncRNA zinc finger and SCAN domain containing 16 antisense RNA 1 (ZSCAN16-AS1) in HCC has not been systematically clarified. RT-qPCR was used to test ZSCAN16-AS1 expression in HCC cells. The biological functions of RP11-757 G1.5 on HCC cell proliferation, migration, invasion and apoptosis were investigated by colony formation, EdU, CCK-8 and transwell assays, as well as flow cytometry analysis. RNA immunoprecipitation (RIP), RNA pull-down and luciferase reporter assays were utilized to explore the specific mechanism of ZSCAN16-AS1. ZSCAN16-AS1 was significantly up-regulated in HCC cells. ZSCAN16-AS1 silence inhibited HCC cell proliferation, migration and invasion, while it accelerated HCC cell apoptosis. ZSCAN16-AS1 worked as a competing endogenous RNA (ceRNA) to regulate sperm associated antigen 9 (SPAG9) expression through sponging miR-181 c-5p. Moreover, SPAG9 could activate the c-Jun-N-terminal kinase (JNK) pathway. Taken together, our study elucidated that ZSCAN16-AS1 expedited HCC progression via modulating the miR-181 c-5p/SPAG9 axis to activate the JNK pathway, which might be a highly potential HCC therapy and treatment target.
DOI: 10.6084/m9.figshare.22602146
title: Additional file 2 of X chromosome associations with chronic obstructive pulmonary disease and related phenotypes: an X chromosome-wide association study

description: Additional file 2: Table S1. XWAS Meta-analysis All Top Suggested Associations At 10-6 Or Less If Present, Otherwise Top Suggested Associations At 10–5 Or Less
DOI: 10.6084/m9.figshare.3146710.v12
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [Data Record 1: qPCR validations]

description: <b>DESCRIPTION</b><br>qPCR was used to assess the enrichment of ChIP and MeDIP experiments and to validate the integrity of sequencing libraries<br><br><b>FILES</b><br>Validation of ChIP-seq library enrichment:<br><b>20130426-CA1-1h-K27ac-K79me3-K4me3-H3-lib_qPCR.xlsx</b> – this file contains tables with qPCR values from validations of ChIP-seq libraries for samples from CA1 neuronal or non-neuronal cells (+ or -, respectively) taken 1 hour (1h) after naïve (N), context (Ct) or context-shock (FC) and immunoprecipitated for H3K27ac, H3K79me3, H3K4me3 or H3. The target genes were NeuN, Chd4, GAPDH, InterG and cFOS.<br><b>20130715-ACCnaiveK76me3K27ac_qPCR.xlsx</b> – this file contains tables with qPCR values from validations of ChIP-seq libraries for naïve (N) samples from ACC neuronal or non-neuronal cells (+ or -, respectively) and immunoprecipitated for H3K79me3 or H3K27ac. The target genes were NeuN, Chd4 and GAPDH.<br><b>20131125-CA1-Naive_qPCR.xlsx</b> – this file contains tables with qPCR values from validations of ChIP-seq libraries for naïve (N) samples from CA1 neuronal or non-neuronal cells (+ or -, respectively) and immunoprecipitated for H3K27ac, H3K27me3, H3K79me3, H3K4me3, H3 or H3K4me1. The target genes were TFF1, GAPDH, InterG and NeuN.<br><b>20150122-CA1-K9ac_qPCR.xlsx</b> – this file contains tables with qPCR values from validations of ChIP-seq libraries for samples from ACC neuronal or non-neuronal cells (+ or -, respectively) taken 1 hour (1h) after naïve (N), context (Ct) or context-shock (FC) and immunoprecipitated for H3K9ac. The target genes were cFosF2R2, cFosF3R3, GAPDH, InterG and NeuN.<br><br>Validation of MedIP-seq library enrichment:<br><b>20150729-MeDIP-LIB-ACC_qPCR.xlsx</b> – this file contains tables with qPCR values from validations of MedIP-seq libraries for samples from ACC taken 1 hour (1h) after naïve (N), context (Ct) or context-shock (CS). The target genes were Cobl, Loxhd1, Vrk1 and GAPDHenh (-).<br><b>20150802-ACC-lib_qPCR.xlsx</b> – this file contains tables with qPCR values from validations of MedIP-seq libraries for samples from ACC taken 1 hour (1h) or 4 weeks (4w) after naïve (N), context (C) or context-shock (CS). The target genes were Fgfr2, Nova1 and Reelin.<br><br><b>DATA GENERATION</b><br>qPCR experiments were run on Roche LightCycler 480, and the machine was used to export the Ct values. The resulting output was imported into pyQPCR (version 0.10dev) using dilutions of inputs as standards, along with the following parameters:<br>Calculation type: Absolute quantification<br>Confidence interval: 90.00%<br>Machine: Roche LightCycler 480<br>Maximum E(Ct): 0.30<br>Minimum Ct: 35.00<br><br>
DOI: 10.6084/m9.figshare.3146692.v4
title: (4) DHPTMs

description: Differential Histone Post-translational modifications
DOI: 10.6084/m9.figshare.3146689.v5
title: [Data Record 3]: CRM predictions

description: Neuronal and non-neuronal cis-regulatory modules were predicted, together with their activity, using a discriminative random forest classifier RFECS that was trained on a published set of positive and negative transcription factor binding sites and histone post-translational modifications
DOI: 10.6084/m9.figshare.3146698.v9
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [Data Record 8: DEEs and DEGs]

description: <b>DESCRIPTION</b><br>This data record contains tables of differentially expressed genes (DEG) and exons (DEE), where each table contains comparisons between the conditions naive and context (N-C) and naive and context-shock (N-CS) for each time point (1h or 4w) and tissue (CA1 or ACC).<br><br><b>TABLES</b><br>DEG tables<br>Columns "ensemblID", "gene_name" and "description" refer to the ENSEMBL ID, gene symbol and gene description, respectively. Columns "chromosome", "start", "end" and "strand" indicate the position of the gene (with strand being "1" for positive strand or "-1" for negative strand). Column "biotype" refers to the type of gene (protein-coding, antisense, non-coding etc.). Finally, column "baseMean" refers to the mean expression of the gene in all samples, column "log2FoldChange" refers to the log2 fold change between the samples in the different conditions, and columns "pvlaue" and "padj" refer to the raw and Benjamini-Hochberg-adjusted p-values, respectively.<br>DEE tables<br>Column "ensemblID" still refers to the ENSEMBL gene ID, but some genes may appear multiple times, as they contain multiple exons, and the column "exonID" indicates the exon number in the gene. Columns “pvalue”, “padj”, “meanBase” and “log2FoldChange” correspond to the same columns in the DEG tables (with the exception of “meanBase”, which is equivalent to “baseMean” in the DEG tables).<br><br><b>DATA GENERATION</b><br>The code used to do differential expression analyses of genes and exons can be found in Figshare (https://dx.doi.org/10.6084/m9.figshare.3146749).<br><br>
DOI: 10.6084/m9.figshare.3146695.v5
title: [Data Record 5]: DMRs

description: List of DHPTMs
DOI: 10.6084/m9.figshare.3146692.v5
title: (4) DHPTMs

description: This file contains a table for each analysis of Differential Histone Post-translational modifications. Each table contains the following information:<br>1) coordinates of the target regions (chromosome, start and end positions, with strand information included for analyses for marks H3K4me3, H3K9ac, H3K27me3 and H3K79me3 based on transcription start sites and gene regions, and no strand information for marks H3K4me1 and H3K27ac based on peaks)<br>2) baseMean - average number of reads in region across all samples<br>3) log2FoldChange - log2 fold change between number of reads in treatment condition and in control condition<br>4) lfcSE - standard error of the log2 fold change<br>5) stat - Wald statistic used to calculate the p-value<br>6) pvalue - p-value associated with a particular region<br>7) padj - p-value adjusted using Benjamini & Hochberg adjustment<br>
DOI: 10.6084/m9.figshare.3146698.v11
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [Data Record 8: DEEs and DEGs]

description: <b>DESCRIPTION</b><br>This data record contains tables of differentially expressed genes (DEG) and exons (DEE), where each table contains comparisons between the conditions naive and context (N-C) and naive and context-shock (N-CS) for each time point (1h or 4w) and tissue (CA1 or ACC).<br><br><b>TABLES</b><br>DEG tables<br>Columns "ensemblID", "gene_name" and "description" refer to the ENSEMBL ID, gene symbol and gene description, respectively. Columns "chromosome", "start", "end" and "strand" indicate the position of the gene (with strand being "1" for positive strand or "-1" for negative strand). Column "biotype" refers to the type of gene (protein-coding, antisense, non-coding etc.). Finally, column "baseMean" refers to the mean expression of the gene in all samples, column "log2FoldChange" refers to the log2 fold change between the samples in the different conditions, and columns "pvlaue" and "padj" refer to the raw and Benjamini-Hochberg-adjusted p-values, respectively.<br>DEE tables<br>Column "ensemblID" still refers to the ENSEMBL gene ID, but some genes may appear multiple times, as they contain multiple exons, and the column "exonID" indicates the exon number in the gene. Columns “pvalue”, “padj”, “meanBase” and “log2FoldChange” correspond to the same columns in the DEG tables (with the exception of “meanBase”, which is equivalent to “baseMean” in the DEG tables).<br><br><b>DATA GENERATION</b><br>The code used to do differential expression analyses of genes and exons can be found in Figshare (https://dx.doi.org/10.6084/m9.figshare.3146749).<br><br>
DOI: 10.6084/m9.figshare.3146695.v6
title: [Data Record 5]: DMRs

description: # Description: List of all differentially methylated regions (DMRs). Each tab of this document contains a different compared condition for each time point (1h or 4w), tissue (CA1 or ACC) and cell type (Neu or Non), where tabs with the suffix "_raw" contain all DMRs for adjusted p-value threshold of 0.5. The compared conditions concern the different sets of mouse, N-C compares naïve (N) to context only (C) mice, N-CS compares naive (N) to context shock (CS) mice, and C-CS compares context only (C) to context shock (CS) mice. The columns 'chromosome', 'DMR start' and 'DMR end' contain the position in the genome where the DMR was detected (mm10 assembly). The column 'logFC' shows the fold change of the comparison between the conditions in log 2. Columns 'pvalue' and 'p-adjust' contain the pvalue and the adjusted p-value according to the FDR test. <br># Description: List of annotated differentially methylated regions (DMRs). Each tab of this document contains a different compared condition for each time point (1h or 4w), tissue (CA1 or ACC) and cell type (Neu or Non). The compared conditions concerns the different sets of mouse, N-C compares naïve (N) to context only (C) mice, N-CS compares naive (N) to context shock (CS) mice, and C-CS compares context only (C) to context shock (CS) mice. All tabs without the suffix "_raw" contain a list of DMRs for adjusted p-value 0.1 in C-CS tests or for adjusted p-value 0.05 in N-C and N-CS tests. The first column 'Gene name' contains the gene symbol name for the closest gene. The column 'Gene type' contains the type of transcript annotated in Ensembl database. The column 'TranscriptId' contains the Ensembl ID. The column 'Gene structure' contains the location of the DMR concerning the structure of the closest gene. The columns 'chromosome', 'DMR start' and 'DMR end' contain the position in the genome where the DMR was detected (mm10 assembly). The column 'logFC' shows the fold change of the comparison between the conditions in log 2. Columns 'pvalue' and 'p-adjust' contain the pvalue and the adjusted p-value according to the FDR test.
DOI: 10.6084/m9.figshare.3146710.v13
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [Data Record 1: qPCR validations]

description: <b>DESCRIPTION</b><br>qPCR was used to assess the enrichment of ChIP and MeDIP experiments and to validate the integrity of sequencing libraries<br><br><b>FILES</b><br>Validation of ChIP-seq library enrichment:<br><b>20130426-CA1-1h-K27ac-K79me3-K4me3-H3-lib_qPCR.xlsx</b> – this file contains tables with qPCR values from validations of ChIP-seq libraries for samples from CA1 neuronal or non-neuronal cells (+ or -, respectively) taken 1 hour (1h) after naïve (N), context (Ct) or context-shock (FC) and immunoprecipitated for H3K27ac, H3K79me3, H3K4me3 or H3. The target genes were NeuN, Chd4, GAPDH, InterG and cFOS.<br><b>20130715-ACCnaiveK76me3K27ac_qPCR.xlsx</b> – this file contains tables with qPCR values from validations of ChIP-seq libraries for naïve (N) samples from ACC neuronal or non-neuronal cells (+ or -, respectively) and immunoprecipitated for H3K79me3 or H3K27ac. The target genes were NeuN, Chd4 and GAPDH.<br><b>20131125-CA1-Naive_qPCR.xlsx</b> – this file contains tables with qPCR values from validations of ChIP-seq libraries for naïve (N) samples from CA1 neuronal or non-neuronal cells (+ or -, respectively) and immunoprecipitated for H3K27ac, H3K27me3, H3K79me3, H3K4me3, H3 or H3K4me1. The target genes were TFF1, GAPDH, InterG and NeuN.<br><b>20150122-CA1-K9ac_qPCR.xlsx</b> – this file contains tables with qPCR values from validations of ChIP-seq libraries for samples from ACC neuronal or non-neuronal cells (+ or -, respectively) taken 1 hour (1h) after naïve (N), context (Ct) or context-shock (FC) and immunoprecipitated for H3K9ac. The target genes were cFosF2R2, cFosF3R3, GAPDH, InterG and NeuN.<br><br>Validation of MedIP-seq library enrichment:<br><b>20150729-MeDIP-LIB-ACC_qPCR.xlsx</b> – this file contains tables with qPCR values from validations of MedIP-seq libraries for samples from ACC taken 1 hour (1h) after naïve (N), context (Ct) or context-shock (CS). The target genes were Cobl, Loxhd1, Vrk1 and GAPDHenh (-).<br><b>20150802-ACC-lib_qPCR.xlsx</b> – this file contains tables with qPCR values from validations of MedIP-seq libraries for samples from ACC taken 1 hour (1h) or 4 weeks (4w) after naïve (N), context (C) or context-shock (CS). The target genes were Fgfr2, Nova1 and Reelin.<br><br><b>DATA GENERATION</b><br>qPCR experiments were run on Roche LightCycler 480, and the machine was used to export the Ct values. The resulting output was imported into pyQPCR (version 0.10dev) using dilutions of inputs as standards, along with the following parameters:<br>Calculation type: Absolute quantification<br>Confidence interval: 90.00%<br>Machine: Roche LightCycler 480<br>Maximum E(Ct): 0.30<br>Minimum Ct: 35.00<br><br>
DOI: 10.6084/m9.figshare.3146698.v10
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [Data Record 10: DEEs and DEGs]

description: <b>DESCRIPTION</b><br>This data record contains tables of differentially expressed genes (DEG) and exons (DEE), where each table contains comparisons between the conditions naive and context (N-C) and naive and context-shock (N-CS) for each time point (1h or 4w) and tissue (CA1 or ACC).<br><br><b>TABLES</b><br>DEG tables<br>Columns "ensemblID", "gene_name" and "description" refer to the ENSEMBL ID, gene symbol and gene description, respectively. Columns "chromosome", "start", "end" and "strand" indicate the position of the gene (with strand being "1" for positive strand or "-1" for negative strand). Column "biotype" refers to the type of gene (protein-coding, antisense, non-coding etc.). Finally, column "baseMean" refers to the mean expression of the gene in all samples, column "log2FoldChange" refers to the log2 fold change between the samples in the different conditions, and columns "pvlaue" and "padj" refer to the raw and Benjamini-Hochberg-adjusted p-values, respectively.<br>DEE tables<br>Column "ensemblID" still refers to the ENSEMBL gene ID, but some genes may appear multiple times, as they contain multiple exons, and the column "exonID" indicates the exon number in the gene. Columns “pvalue”, “padj”, “meanBase” and “log2FoldChange” correspond to the same columns in the DEG tables (with the exception of “meanBase”, which is equivalent to “baseMean” in the DEG tables).<br><br><b>DATA GENERATION</b><br>The code used to do differential expression analyses of genes and exons can be found in Figshare (https://dx.doi.org/10.6084/m9.figshare.3146749).<br><br>
DOI: 10.6084/m9.figshare.3146689.v6
title: [Data Record 3]: CRM predictions

description: <b>DESCRIPTION</b><br>Neuronal and non-neuronal cis-regulatory modules in tissues ACC and CA1 were predicted, together with their activity, using a discriminative random forest classifier RFECS that was trained on a published set of positive and negative transcription factor binding sites and histone post-translational modifications<br><br><b>TABLE DESCRIPTION</b><br> List of all predicted cis-regulatory modules (CRMs; in other words enhancers and other non-genic regulatory regions) in neuronal or non-neuronal data from the ACC or CA1 of naive mice. The tables includes the CRM coordinates and the RFECS probabilities for each CRM.<br>
DOI: 10.6084/m9.figshare.3146710.v15
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [Data Record 2: qPCR validations]

description: <b>DESCRIPTION</b><br>qPCR was used to validate the integrity of sequencing libraries of different ChIP-seq samples, as well as validate particular differentially methylated genes<br><br><b>FILES</b><br>Validation of ChIP-seq library enrichment:<br><b>20130426-CA1-1h-K27ac-K79me3-K4me3-H3-lib_qPCR.xlsx</b> – this file contains tables with qPCR values from validations of ChIP-seq libraries for samples from CA1 neuronal or non-neuronal cells (+ or -, respectively) taken 1 hour (1h) after naïve (N), context (Ct) or context-shock (FC) and immunoprecipitated for H3K27ac, H3K79me3, H3K4me3 or H3. The target genes were NeuN, Chd4, GAPDH, InterG and cFOS.<br><b>20130715-ACCnaiveK76me3K27ac_qPCR.xlsx</b> – this file contains tables with qPCR values from validations of ChIP-seq libraries for naïve (N) samples from ACC neuronal or non-neuronal cells (+ or -, respectively) and immunoprecipitated for H3K79me3 or H3K27ac. The target genes were NeuN, Chd4 and GAPDH.<br><b>20131125-CA1-Naive_qPCR.xlsx</b> – this file contains tables with qPCR values from validations of ChIP-seq libraries for naïve (N) samples from CA1 neuronal or non-neuronal cells (+ or -, respectively) and immunoprecipitated for H3K27ac, H3K27me3, H3K79me3, H3K4me3, H3 or H3K4me1. The target genes were TFF1, GAPDH, InterG and NeuN.<br><b>20150122-CA1-K9ac_qPCR.xlsx</b> – this file contains tables with qPCR values from validations of ChIP-seq libraries for samples from ACC neuronal or non-neuronal cells (+ or -, respectively) taken 1 hour (1h) after naïve (N), context (Ct) or context-shock (FC) and immunoprecipitated for H3K9ac. The target genes were cFosF2R2, cFosF3R3, GAPDH, InterG and NeuN.<br><br>Validation of differentially methylated genes:<br><b>20150729-MeDIP-LIB-ACC_qPCR.xlsx</b> – this file contains tables with qPCR values for samples taken from ACC tissue 1 hour (1h) after naïve (N), context (Ct) or context-shock (CS). The target genes were <i>Loxhd1</i>, <i>Vrk1</i>, <i>GAPDH</i>(-) and <i>Cobl</i>.<br><b>20150802-ACC-lib_qPCR.xlsx</b> – this file contains tables with qPCR values for samples taken from ACC tissue 1 hour (1h) or 4 weeks (4w) after naïve (N), context (C) or context-shock (CS). The target genes were <i>Fgfr2</i>, <i>Nova1</i> and <i>Reelin</i>.<br><br><b>DATA GENERATION</b><br>qPCR experiments were run on Roche LightCycler 480, and the machine was used to export the Ct values. The resulting output was imported into pyQPCR (version 0.10dev) using dilutions of inputs as standards, along with the following parameters:<br>Calculation type: Absolute quantification<br>Confidence interval: 90.00%<br>Machine: Roche LightCycler 480<br>Maximum E(Ct): 0.30<br>Minimum Ct: 35.00<br><br>
DOI: 10.6084/m9.figshare.3146692.v6
title: [Data Record 4]: DHPTMs

description: This file contains a table for each analysis of Differential Histone Post-translational modifications. Each table contains the following information:<br>1) coordinates of the target regions (chromosome, start and end positions, with strand information included for analyses for marks H3K4me3, H3K9ac, H3K27me3 and H3K79me3 based on transcription start sites and gene regions, and no strand information for marks H3K4me1 and H3K27ac based on peaks)<br>2) baseMean - average number of reads in region across all samples<br>3) log2FoldChange - log2 fold change between number of reads in treatment condition and in control condition<br>4) lfcSE - standard error of the log2 fold change<br>5) stat - Wald statistic used to calculate the p-value<br>6) pvalue - p-value associated with a particular region<br>7) padj - p-value adjusted using Benjamini & Hochberg adjustment<br>
DOI: 10.6084/m9.figshare.3146695.v7
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [Data Record 5: DMRs]

description: This data record contains lists of differentially methylated regions (DMRs). Each tab of this document contains a different compared condition for each time point (1h or 4w), tissue (CA1 or ACC) and cell type (Neu or Non), where tabs with the suffix "_raw" contain all DMRs for adjusted p-value threshold of 0.5, and all other tabs contain annotated DMRs for adjusted p-value 0.1 in C-CS tests or for adjusted p-value 0.05 in N-C and N-CS tests. The compared conditions concern the different sets of mouse, N-C compares naïve (N) to context only (C) mice, N-CS compares naive (N) to context shock (CS) mice, and C-CS compares context only (C) to context shock (CS) mice. For the annotated DMRs, the lists contain columns "Gene name", "Gene type", "Transcript ID" and "Gene structure", corresponding to the gene name, type (protein_coding, long non-coding, miRNA etc.), ENSEMBL transcript ID and structure (intronic, downstream, etc.) for the nearest gene to each DMR. The columns 'chromosome', 'DMR start' and 'DMR end' contain the position in the genome where the DMR was detected (mm10 assembly). The column 'logFC' shows the fold change of the comparison between the conditions in log 2. Columns 'pvalue' and 'p-adjust' contain the pvalue and the adjusted p-value according to the FDR test.