|
| Status |
Public on Sep 21, 2016 |
| Title |
Sample_DUX4-14h |
| Sample type |
SRA |
| |
|
| Source name |
Cultured myoblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Facioscapulohumeral dystrophy (FSHD)
tissue: Immortalized primary myoblasts
treatment: Doxycyline
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from myoblasts using TRIzol reagent as per manufacturer's instructions and cleaned up using Qiagen Rneasy columns, including the optional, on-column DNAse digestion step.
The Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Samples were multiplexed using Illumina barcodes to run 2-6 samples per sequencing lane.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Illumina CASAVA software was used for basecalling and sample de-multiplexing.
Reads were mapped to the hg19 human genome assembly using Bowtie v1.0.0 and RSEM v1.2.4. RSEM was modified to call Bowtie with the -v 2 mapping strategy. RSEM was then invoked with the arguments --bowtie-m 100 --bowtie-chunkmbs 500 --calc-ci --output-genome- bam on the gene annotation file.
Sample 1 to 6 are used to generate the processed csv files with EdgeR-based expression estimates and fold change values (with dox vs withoutdox) for coding genes.
Genome_build: hg19
|
| |
|
| Submission date |
Aug 11, 2016 |
| Last update date |
May 15, 2019 |
| 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 |
GPL18460 |
| Series (1) |
| GSE85461 |
Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells |
|
| Relations |
| BioSample |
SAMN05559940 |
| SRA |
SRX2012539 |
