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Sample GSM1260126 Query DataSets for GSM1260126
Status Public on Nov 08, 2013
Title SiFFL1_220709_20110630
Sample type RNA
 
Source name HeLa_control FFL siRNA
Organism Homo sapiens
Characteristics cell line: HeLa H9
transfected with: control FFL siRNA
Treatment protocol For siRNAs, cells were transfected 48h using Lipofectamine and Plus reagent (InVitrogen), at a concentration of 50nM, and cells were homogeneized in Trizol. For IPs, cells were extracted in HNTG buffer (20 mM HEPES, pH 7.9, 150 mM NaCl, 1% Triton, 10% glycerol, 1 mM MgCl2, 1 mM EGTA, and protease inhibitors) for 30 min at 4°C. Cellular debris were removed by centrifugation (10 min at 9000 g). Extracts were put on antibody-coated beads for 2h at 4°C (M2 -Sigma). Beads were washed twice in HNTG and three times in PBS, and pelleted materials were Trizol.
Growth protocol HeLa H9 cells were grown to sub-confluency in DMEM, 10% FCS, at 37°C.
Extracted molecule total RNA
Extraction protocol RNAs from beads or cell extracts were homogenized in Trizol and purified with RNeasy mini kit (Qiagen).
Label biotin
Label protocol Tilling Samples were prepared and hybridized to Tiling Array according to Affymetrix specifications (Tilling with WT Amplified Double-Stranded cDNA Synthesis Kit). HuGene Samples were prepared and hybridized according to Affymetrix specifications : WTGene termlabel manuelrev1
 
Hybridization protocol Tilling Samples were prepared and hybridized to Tiling Array according to Affymetrix specifications (Tilling with WT Amplified Double-Stranded cDNA Synthesis Kit). HuGene Samples were prepared and hybridized according to Affymetrix specifications : WTGene termlabel manuelrev1
Scan protocol The arrays were scanned using an Affymetrix GeneChip Scanner according to manufacturer's instruction : GeneChip® Expression Wash, Stain and Scan User Manual For Cartridge Arrays rev.1
Description result file: SiARSvsFFL_signal.txt
Data processing The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (v. 1.1) using parameters: one side upper, 90 bp bandwidth and perfect match only.
SiARSvsFFL_signal.txt contains the signal intensities coming from the TAS Software (2 SiARS2 arrays versus 2 SiFFL arrays) and the 'AffyParamSiARSVsSiFFL.txt' file contains parameter settings and input file information for the TAS analysis.
 
Submission date Nov 06, 2013
Last update date Nov 08, 2013
Contact name Edouard BERTRAND
Organization name CNRS
Street address 1919 Route de Mendes
City Montpellier
ZIP/Postal code 34293
Country France
 
Platform ID GPL4910
Series (1)
GSE52131 CBC-ARS2 stimulates 3'-end maturation of multiple RNA families and favors cap-proximal processing

Supplementary file Size Download File type/resource
GSM1260126_siFFL1_220709-20110630_Hs35b_P01R_v01_.CEL.gz 21.5 Mb (ftp)(http) CEL
Processed data are available on Series record

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