|
| Status |
Public on Jan 03, 2011 |
| Title |
HL1_siSrf1_smallRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
mouse cardiomyocytes (HL1-cells)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: cardiomyocytes
cell line: HL-1
sirna: Srf si2
|
| Treatment protocol |
For Srf knockdown HL-1 cells were transfected with two different siRNAs. Therefore cells were grown for at least two days without addition of antibiotics to 70-80% confluence. 3 × 105 cells were seeded into 6-well plates with 2ml media resulting in 70-80% confluence after 4h. 9μl of 20μM siRNA was mixed with 270μl of DMEM media and 16μl of Lipofectamin™ 2000 was mixed with 470μl DMEM media. Both mixtures were combined, incubated for 20min at room temperature and added drop wise to the cells. Cells were harvested for total RNA preparation 48h after transfection.
|
| Growth protocol |
HL-1 cells were provided by Prof. William C. Claycomb and cultured as described (Claycomb et al. (1998) HL1 cells: a cardiac muscle cell line that contracts and retains phenozypic characteristics of the adult cardiomyocytes. Proc Natl Acad Sci USA 95(6):2979-2984.). The cells were harvested for experiments at their maximum concentration.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNAs were isolated from total RNA of HL-1 cells and prepared for miRNA sequencing using Illumina Kit FG-102-1009 according to manufacturer’s protocol. Small RNA Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Total RNA was isolated using TRIzol reagent.
|
| Data processing |
Image analysis and base calling was done using the open source Firecrest and Bustard applications (Solexa Pipeline 1.4.0). For each of these samples, we determined the abundance value for each sequence in the library. The numbers in the VALUE column represent the expression level of the corresponding sequence for the library.
|
| |
|
| Submission date |
Nov 17, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Silke Sperling |
| E-mail(s) |
silke.sperling@charite.de
|
| Phone |
++49 (0)30 450540123
|
| Organization name |
Experimental and Clinical Research Center (ECRC), Charité / MDC for Molecular Medicine
|
| Department |
Cardiovascular Genetics
|
| Lab |
Cardiovascular Genetics
|
| Street address |
Lindenberger Weg 80
|
| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
| |
|
| Platform ID |
GPL9185 |
| Series (2) |
| GSE19066 |
Small RNA sequencing in mouse cardiomyocytes after siRNA mediated knockdown of Srf |
| GSE26397 |
The Cardiac Transcription Network Modulated by Gata4, Mef2a, Nkx2.5 and Srf, Histone Modifications and MicroRNAs |
|
| Relations |
| SRA |
SRX018667 |
| BioSample |
SAMN00010813 |
