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Sample GSM3587224

Query DataSets for GSM3587224

Status

Public on Jul 31, 2019

Title

JP22

Sample type

SRA

Source name

Whole Blood

Organism

Homo sapiens

Characteristics

disease subtype: Dermatomyositis
anti-jo1 status: Negative

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

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Description

mRNA_star_DM_vis_CONTROL_Wald_DESeq2.xls

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.

Submission date

Jan 31, 2019

Last update date

Jul 31, 2019

Contact name

Joanna Parkes

E-mail(s)

jparkes@binghamton.edu

Organization name

Binghamton University

Department

School of Pharmacy and Pharmaceutical Sciences