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Sample GSM5641631 Query DataSets for GSM5641631
Status Public on Nov 01, 2022
Title aa154-424_c1_unt2_S11
Sample type SRA
Source name DUX4_aa154-424 RNA-Seq, Untreated
Organism Homo sapiens
Characteristics treatment: Untreated
genotype: MB135 myoblasts with inducibile DUX4-aa154-424
cell type: MB135 myoblasts
passages: p12-p15
Treatment protocol IFNg treated samples were 200ng/mL interferon gamma for 16 hours, DOX+IFNg samples were pre-treated with 1ug/mL doxicycline for 4 hours and then 200ng/mL interferon gamma for 16 hours (20 hours total treatment)
Growth protocol Myoblasts were cultured in F-10 media supplemented with 15% Fetal Bovine Serum, 10ng/mL rhFGF Basic, 1uM dexamethasone, and 2ug/mL puromycin. Cells were passaged at ~70% confluence with a 1:5 split ratio.
Extracted molecule polyA RNA
Extraction protocol RNA was isolated from cell lysates using Macherey-Nagel's Nucleospin RNA kit (p/n 740955.250)
Libraries were constructed using Illumina's TruSeq stranded mRNA kit (p/n 20020595)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
Description MB135 myoblasts with inducibile DUX4_aa154-424 RNA-Seq, Untreated
Data processing Sequencing data was processed with Illumina Pipeline software (Casava version 1.9)
Reads quality and adapter trimmed using Trimmomatic v0.39 with the following arguments: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were aligned to genome using Rsubread v.2.0.1 with the following arguments: type = "rna", input_format = "gzFASTQ", output_format = "BAM",
Transcripts were counted from the aligned bam files using the Gencode V35 annotation file and featureCounts() from the Rsubread package, v2.0.1 with the following arguments: annot.ext = "gencode.v35.annotation.gtf", isGTFAnnotationFile = TRUE, useMetaFeatures = TRUE, isPairedEnd = TRUE,requireBothEndsMapped = TRUE)
Genome_build: GRCh38, patch 13
Supplementary_files_format_and_content: CSV with raw read counts.
Submission date Oct 20, 2021
Last update date Nov 01, 2022
Contact name Stephen Tapscott
Organization name Fred Hutchinson Cancer Research Center
Street address 1100 Fairview Ave N, Room C3-123
City Seattle
State/province Washington
ZIP/Postal code 98109
Country USA
Platform ID GPL30173
Series (1)
GSE186244 Human DUX4 and mouse Dux interact with STAT1 and broadly inhibit interferon-stimulated gene induction
BioSample SAMN22441770
SRA SRX12705912

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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