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Status |
Public on Nov 04, 2011 |
Title |
C2C12 cells ZBED6 siRNA 96h rep3 |
Sample type |
RNA |
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Source name |
C2C12 cells ZBED6 siRNA 96h rep3
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Organism |
Mus musculus |
Characteristics |
cell line: C2C12 cell type: myoblast
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Treatment protocol |
Cells were seeded in complete DMEM lacking antibiotics and reverse transfected with siRNA by lipofectamine 2000 (Invitrogen). ZBED6 silencing and validation of silencing was done by qPCR and western blotting as described (Markljung et al. 2009). Briefly, C2C12 cells were treated with ZBED6 or scrambled siRNAs for two days and four days in biological triplicates. Total RNA from each sample was extracted for qRT-PCR validation and microarray analysis.
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Growth protocol |
The C2C12 cells used for these studies were between passages 10 and 18. Cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with L-glutamine (ATCC), supplemented with 10 % heat-inactivated fetal bovine serum and penicillin (0.2 U/mL)/streptomycin (0.2 μg/ml)/L-glutamine (0.2 μg/ml) (Gibco) at 37°C in a 5 % CO2 humidified atmosphere. At 70-80 % confluency, cells were trypsinized and seeded at 100,000 cells per well in 12-well plates (Falcon) for the transfection experiments.
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Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
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Label |
biotin
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Label protocol |
Biotinylated probes were prepared from 250 ng of total RNA, using the Ambion Illumina TotalPrep RNA Amplification kit
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Hybridization protocol |
Standard Illumina hybridization protocol
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Scan protocol |
Standard Illumina scanning protocol
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Description |
LAN016
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Data processing |
The data were normalised using the lumi package implemented in the software FlexArray v. 1.4.1 using Robust spline normalization
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Submission date |
Nov 03, 2011 |
Last update date |
Nov 04, 2011 |
Contact name |
Carl-Johan Rubin |
E-mail(s) |
carl-johan.rubin@imbim.uu.se
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Organization name |
Uppsala University
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Department |
Dedp. Med. Biochem. & Microbiol.
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Lab |
Leif Andersson
|
Street address |
Husargatan 3
|
City |
Uppsala |
ZIP/Postal code |
75237 |
Country |
Sweden |
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Platform ID |
GPL6885 |
Series (1) |
GSE33430 |
Unraveling the role of ZBED6 in transcriptional regulation by whole transcriptome analysis after RNAi in mouse myoblasts |
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