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Sample GSM5641628 Query DataSets for GSM5641628
Status Public on Nov 01, 2022
Title aa154-424_c1_doxIFNg2_S17
Sample type SRA
 
Source name DUX4_aa154-424 RNA-Seq, Dox + IFNg treated
Organism Homo sapiens
Characteristics treatment: Dox + IFNg treated
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, Dox + IFNg treated
countsAA154-424.csv
aa154-424_c1_doxIFNg2_S17
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
E-mail(s) stapscot@fredhutch.org
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
Relations
BioSample SAMN22441773
SRA SRX12705909

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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