|
| Status |
Public on Oct 31, 2017 |
| Title |
Emerin null differentiation day 3 |
| Sample type |
SRA |
| |
|
| Source name |
Emerin-null H2K myogenic precursor cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: H2K
cell type: myogenic precursor cells
genotype: Emerin-null
|
| Treatment protocol |
Cells were collected according to miRNeasy mini kit/ Qiazol protocol
|
| Growth protocol |
Proliferating myogenic progenitors were cultured in plates coated with gelatin at 37°C and 10% CO2 in DMEM containing 20% HI-FBS, 2% L-glutamine, 2% Chick embryo extract , 1% Pen/Strep and 20 units/ml γ-interferon . Differentiating cells were cultured in plates coated with gelatin in proliferative conditions for 24 h, then switched to differentiation media consisting of DMEM supplemented with 5% horse serum and 2% L-glutamine and grown at 37°C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen miRNeasy mini kit/ Qiazol according to manufacterer's instructions
Library construction and sequencing was performed using the Illumina HiScan-SQ at Functional Genomics Facility at The University of Chicago.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
[processed data files:]
WT vs Emerin null day 3 differentiation.xlsx
Emerin null differentiation day 2 to 3 transition.diff
Emerin null differentiaton day 3 to 4 transition.diff
Emerin null proliferation vs day 3 differentiation.diff
|
| Data processing |
Quality control of raw sequence was performed with FastQC.
Reads were mapped to the mouse genome (mm10) with Tophat according to established protocols
Differential expression analysis was done using Cuffdiff according to established protocols.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx files include expression values for individual genes for Wildtype and emerin-null myogenic precursor cells during proliferation and different days of differentiaton. They also include log2 fold change value for each gene in emerin-null myogenic precursors compared with respect to wildtype myogenic precursor cells and P-values for statistical significance. Cuffdiff files contain similar information using different samples for each analysis.
|
| |
|
| Submission date |
Oct 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ashvin Iyer |
| E-mail(s) |
aiyer@mail.usciences.edu
|
| Phone |
732-501-5702
|
| Organization name |
University of the Sciences
|
| Department |
Pharmaceutical Sciences
|
| Street address |
1325B Johnston Drive
|
| City |
Bethlehem |
| State/province |
Pennsylvania |
| ZIP/Postal code |
18017 |
| Country |
USA |
| |
|
| Platform ID |
GPL16173 |
| Series (1) |
| GSE104560 |
Expression profiling of differentiating emerin-null myogenic progenitor identifies molecular pathways implicated in their impaired differentiation |
|
| Relations |
| BioSample |
SAMN07735571 |
| SRA |
SRX3241612 |
