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Sample GSM826887 Query DataSets for GSM826887
Status Public on Nov 04, 2011
Title C2C12 cells negative control siRNA 48h rep3
Sample type RNA
 
Source name C2C12 cells negative control siRNA 48h rep3
Organism Mus musculus
Characteristics cell line: C2C12
cell type: myoblast
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.
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.
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.
Label biotin
Label protocol Biotinylated probes were prepared from 250 ng of total RNA, using the Ambion Illumina TotalPrep RNA Amplification kit
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description LAN007
Data processing The data were normalised using the lumi package implemented in the software FlexArray v. 1.4.1 using Robust spline normalization
 
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
Organization name Uppsala University
Department Dedp. Med. Biochem. & Microbiol.
Lab Leif Andersson
Street address Husargatan 3
City Uppsala
ZIP/Postal code 75237
Country Sweden
 
Platform ID GPL6885
Series (1)
GSE33430 Unraveling the role of ZBED6 in transcriptional regulation by whole transcriptome analysis after RNAi in mouse myoblasts

Data table header descriptions
ID_REF
VALUE Robust spline normalization
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1250052 7.922127 0.00877193
ILMN_3122480 7.766338 0.5551379
ILMN_2599935 8.298788 0
ILMN_2675543 7.75267 0.735589
ILMN_2686883 7.781635 0.3809524
ILMN_2751818 7.775524 0.452381
ILMN_2728634 7.830676 0.0914787
ILMN_3040515 7.809501 0.1879699
ILMN_2711608 7.752067 0.7418546
ILMN_1232875 7.802537 0.2230576
ILMN_1258507 7.748496 0.783208
ILMN_2746142 7.78549 0.3483709
ILMN_1252690 7.849036 0.05388471
ILMN_2655499 7.750769 0.7606516
ILMN_1252870 7.826443 0.1115288
ILMN_1248179 7.719511 0.9899749
ILMN_2649955 8.410295 0
ILMN_2628708 8.083161 0
ILMN_3024781 7.758525 0.6616541
ILMN_2705628 7.78385 0.3609022

Total number of rows: 25697

Table truncated, full table size 722 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Raw data are available on Series record

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