|
| Status |
Public on Mar 19, 2014 |
| Title |
2315tube |
| Sample type |
SRA |
| |
|
| Source name |
cultured myotube from FSHD1 patient
|
| Organism |
Homo sapiens |
| Characteristics |
subject: FSHD1 patient 1
cell type: differentiated human primary myotube cells
|
| Treatment protocol |
Myoblasts were fused at 80% confluence in DMEM/F-12 Glutamax media (#) containing 2% KnockOut serum replacement formulation (#10828 GIBCO) for 36 hours.
|
| Growth protocol |
Human primary myoblasts cell lines were received from the University of Rochester biorepository (http://www.urmc.rochester.edu/fields-center/). Myoblasts were cultured in DMEM/F-10 media (#31550 GIBCO, Grand Island, NY) in the presence of 20% heat inactivated fetal bovine serum (FBS #10270 GIBCO), 1% penicillin/streptomycin (#15140 GIBCO) and was supplemented with 10ng/ml rhFGF (#G5071 Promega, Madison, Wisconsin) and 1μM dexamethasone (#D2915 SIGMA, St. Louis, Missouri).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Samples for RNA sequencing were harvested in QIAzol lysis reagent (#79306 Qiagen N.V., The Netherlands). RNA was isolated by miRNeasy Mini Kit (#217004 Qiagen) including DNase treatment according to the manufacturer instructions.
mRNA purification, mRNA fragmentation and cDNA synthesis were performed with the TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base calls and quality scores were generated using Illumina's Real-Time Analysis software v1.8.7. Binary base call files were converted to text formatted qseq files via OLB 1.9.0, which were then filtered and converted to fastq format by CASAVA 1.7, using the default Chastity threshold of 0.6.
Read counts for the genes are collected by Bioconductor Biostrings and IRanges packages. Reads that are mapped ambiguously to M locations are counted as 1/M at each occurrence.
Genome_build: hg19
Supplementary_files_format_and_content: read counts
Raw data not provided due to patient privacy concerns.
|
| |
|
| Submission date |
Sep 20, 2013 |
| Last update date |
Apr 05, 2017 |
| Contact name |
Stephen Tapscott |
| E-mail(s) |
stapscot@fredhutch.org
|
| Organization name |
Fred Hutch Cancer Research Center
|
| Department |
Human Biology
|
| Lab |
Tapscott
|
| Street address |
1100 Fairview N. Ave
|
| City |
Seattle |
| State/province |
WASHINGTON |
| ZIP/Postal code |
98103 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE51041 |
DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis. |
|
| Relations |
| BioSample |
SAMN02360478 |
