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Status |
Public on Jul 31, 2019 |
Title |
JP16 |
Sample type |
SRA |
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Source name |
Whole Blood
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Organism |
Homo sapiens |
Characteristics |
disease subtype: Control anti-jo1 status: Negative
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated from whole blood in Tempus tubes using MagMAX™ for stabilised blood tubes RNA Isolation Kit (Ambion). 1μg of total RNA used with an Illumina TruSeq® Stranded mRNA library preparation kit, 0.5μg total RNA with NEBNext® Multiplex Small RNA Library Prep sets for Illumina with size selection using 6% PolyAcrylamide gel
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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Description |
mRNA_star_PM_vis_CONTROL_Wald_DESeq2.xls mRNA_star_DM_vis_CONTROL_Wald_DESeq2.xls mRNA_star_IBM_vis_CONTROL_Wald_DESeq2.xls mRNA_all_jo1_vs_controls_DESeq2.xls
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Data processing |
FastQC was used to produce quality reports for each sample Reads were trimmed using Trimmomatic Reads were mapped to the human genome (hg38, gencode v25) using STAR Reads were counted using htseq Differential gene expression was analysed using DESeq2. Genome_build: hg38 Supplementary_files_format_and_content: Excel file of DESeq2 mRNA output for polymyositis compared to controls.The table columns are gene ids, raw counts, normalised counts, mean values from all normalised samples (baseMean), log2 fold change, standard error for log2 fold change (lfcSE), statistic value for the null hypothesis (stat), p-value, false discovery rate (padj), chromosome name (seqnames), start and end position of the gene, strand, gene name and gene description. Supplementary_files_format_and_content: Excel file of DESeq2 mRNA output for dermatomyositis compared to controls.The table columns are gene ids, raw counts, normalised counts, mean values from all normalised samples (baseMean), log2 fold change, standard error for log2 fold change (lfcSE), statistic value for the null hypothesis (stat), p-value, false discovery rate (padj), chromosome name (seqnames), start and end position of the gene, strand, gene name and gene description. Supplementary_files_format_and_content: Excel file of DESeq2 mRNA output for inclusion body myositis compared to controls.The table columns are gene ids, raw counts, normalised counts, mean values from all normalised samples (baseMean), log2 fold change, standard error for log2 fold change (lfcSE), statistic value for the null hypothesis (stat), p-value, false discovery rate (padj), chromosome name (seqnames), start and end position of the gene, strand, gene name and gene description. Supplementary_files_format_and_content: Excel file of DESeq2 mRNA output for anti-Jo1 positive polymyositis and dermatomyositis compared to controls.The table columns are gene ids, raw counts, normalised counts, mean values from all normalised samples (baseMean), log2 fold change, standard error for log2 fold change (lfcSE), statistic value for the null hypothesis (stat), p-value, false discovery rate (padj), chromosome name (seqnames), start and end position of the gene, strand, gene name and gene description. Supplementary_files_format_and_content: Excel file of DESeq2 microRNA output for polymyositis compared to controls.. The table columns are mature microRNA ids, raw counts, normalised counts, mean values from all normalised samples (baseMean), log2 fold change, standard error for log2 fold change (lfcSE), statistic value for the null hypothesis (stat), p-value, false discovery rate (padj), chromosome name (seqnames), start and end position of the microRNA, microRNA length (width), strand, mature microRNA ID, mature microRNA name and microRNA gene ID. Supplementary_files_format_and_content: Excel file of DESeq2 microRNA output for dermatomyositis compared to controls.. The table columns are mature microRNA ids, raw counts, normalised counts, mean values from all normalised samples (baseMean), log2 fold change, standard error for log2 fold change (lfcSE), statistic value for the null hypothesis (stat), p-value, false discovery rate (padj), chromosome name (seqnames), start and end position of the microRNA, microRNA length (width), strand, mature microRNA ID, mature microRNA name and microRNA gene ID. Supplementary_files_format_and_content: Excel file of DESeq2 microRNA output for inclusion body myositis compared to controls.. The table columns are mature microRNA ids, raw counts, normalised counts, mean values from all normalised samples (baseMean), log2 fold change, standard error for log2 fold change (lfcSE), statistic value for the null hypothesis (stat), p-value, false discovery rate (padj), chromosome name (seqnames), start and end position of the microRNA, microRNA length (width), strand, mature microRNA ID, mature microRNA name and microRNA gene ID. Supplementary_files_format_and_content: Excel file of DESeq2 microRNA output for anti-Jo1 positive polymyositis and dermatomyositis compared to controls.. The table columns are mature microRNA ids, raw counts, normalised counts, mean values from all normalised samples (baseMean), log2 fold change, standard error for log2 fold change (lfcSE), statistic value for the null hypothesis (stat), p-value, false discovery rate (padj), chromosome name (seqnames), start and end position of the microRNA, microRNA length (width), strand, mature microRNA ID, mature microRNA name and microRNA gene ID.
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Submission date |
Jan 31, 2019 |
Last update date |
Jul 31, 2019 |
Contact name |
Joanna Parkes |
E-mail(s) |
jparkes@binghamton.edu
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Organization name |
Binghamton University
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Department |
School of Pharmacy and Pharmaceutical Sciences
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Street address |
Pharmacy Building
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City |
Johnson City |
State/province |
NY |
ZIP/Postal code |
13790 |
Country |
USA |
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Platform ID |
GPL20301 |
Series (1) |
GSE125977 |
MicroRNA and mRNA profiling in the idiopathic inflammatory myopathies |
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Relations |
BioSample |
SAMN10855124 |
SRA |
SRX5318493 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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