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Status |
Public on Nov 01, 2022 |
Title |
aa154-424_c1_doxIFNg1_S16 |
Sample type |
SRA |
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Source name |
DUX4_aa154-424 RNA-Seq, Dox + IFNg treated
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Organism |
Homo sapiens |
Characteristics |
treatment: Dox + IFNg treated genotype: MB135 myoblasts with inducibile DUX4-aa154-424 cell type: MB135 myoblasts passages: p12-p15
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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)
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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.
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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)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
NextSeq 2000 |
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Description |
MB135 myoblasts with inducibile DUX4_aa154-424 RNA-Seq, Dox + IFNg treated countsAA154-424.csv aa154-424_c1_doxIFNg1_S16
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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.
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Submission date |
Oct 20, 2021 |
Last update date |
Nov 01, 2022 |
Contact name |
Stephen Tapscott |
E-mail(s) |
stapscot@fredhutch.org
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Organization name |
Fred Hutchinson Cancer Research Center
|
Street address |
1100 Fairview Ave N, Room C3-123
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City |
Seattle |
State/province |
Washington |
ZIP/Postal code |
98109 |
Country |
USA |
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Platform ID |
GPL30173 |
Series (1) |
GSE186244 |
Human DUX4 and mouse Dux interact with STAT1 and broadly inhibit interferon-stimulated gene induction |
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Relations |
BioSample |
SAMN22441774 |
SRA |
SRX12705908 |