|
| Status |
Public on Nov 01, 2022 |
| Title |
aa154-424_c1_IFNg1_S13 |
| Sample type |
SRA |
| |
|
| Source name |
DUX4_aa154-424 RNA-Seq, IFNg treated
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: 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, IFNg treated
countsAA154-424.csv
aa154-424_c1_IFNg1_S13
|
| 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 |
SAMN22441777 |
| SRA |
SRX12705905 |
