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Status |
Public on Nov 08, 2013 |
Title |
SiFFL1_220709_20110630 |
Sample type |
RNA |
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Source name |
HeLa_control FFL siRNA
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Organism |
Homo sapiens |
Characteristics |
cell line: HeLa H9 transfected with: control FFL siRNA
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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.
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Growth protocol |
HeLa H9 cells were grown to sub-confluency in DMEM, 10% FCS, at 37°C.
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Extracted molecule |
total RNA |
Extraction protocol |
RNAs from beads or cell extracts were homogenized in Trizol and purified with RNeasy mini kit (Qiagen).
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Label |
biotin
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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
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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
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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
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Description |
result file: SiARSvsFFL_signal.txt
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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.
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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 |
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Platform ID |
GPL4910 |
Series (1) |
GSE52131 |
CBC-ARS2 stimulates 3'-end maturation of multiple RNA families and favors cap-proximal processing |
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