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Sample GSM3018259 Query DataSets for GSM3018259
Status Public on Feb 21, 2018
Title HEC-TM-OHT96h-shSCN9A_R1
Sample type RNA
Source name Mammary epithelial cells immortalized with hTERT expressing anti SCN9A shRNA treated with 4-OHT during 96 hours
Organism Homo sapiens
Characteristics cell type: Human mammary epithelial cells (HECs; Lonza)
treatment: expressing anti SCN9A shRNA treated with 4-OHT during 96 hours
Treatment protocol HECs were treated daily for 24 or 96 hours with 4-OHT (Sigma-Aldrich) at 250 nM, or with 65 mM KCl (Sigma-Aldrich),for 24 hours
Growth protocol Human mammary epithelial cells (HECs; Lonza) were cultured in mammary epithelial cell growth medium (Promocell) with penicillin/ streptomycin 100 U/ml (Life Technologies). The cells were maintained in a humidified atmosphere at 37°C under 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from HEC-TM cells using NucleoSpin® RNA (Macherey Nalgen) following the manufacturer's recommendations
Label Cy3
Label protocol cRNAs were synthesized and labeled with the Cy3 dye from 100 ng of total RNA using the one-color Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's recommandations, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. After fragmentation 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent GE Whole Human Genome Oligo Microarrays (Agilent-026652) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried briefly in acetonitrile.
Scan protocol Microarrays were scanned with an Agilent DNA microarray scanner G2565CA (Agilent Technologies).Fluorescent signals were extracted and normalized with the Feature Extraction software version (Agilent Technologies),
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Submission date Feb 20, 2018
Last update date Feb 21, 2018
Contact name jean-michel flaman
Phone +33687477812
Organization name Inserm 1052
Department CRCL
Street address 28 rue Laennec
City Lyon
ZIP/Postal code 69373
Country France
Platform ID GPL13497
Series (1)
GSE110884 The SCN9A channel and plasma membrane depolarization promote cellular senescence through Rb pathway

Data table header descriptions
VALUE Data were normalized to the 75th percentile signal intensity and the baseline was adjusted on control HEC-TM non treated condition using GeneSpring GX 12.6 software (Agilent Technologies)

Data table
GE_BrightCorner 0.04113865
DarkCorner 0.047008038
A_23_P146146 -0.30454445
A_23_P42935 0.2879033
A_23_P117082 -0.7971144
A_23_P2683 -0.005818367
A_24_P358131 0.45115948
A_33_P3367647 -0.31868172
A_23_P157316 -0.08709812
A_32_P14850 0.34714222
A_23_P158596 -0.59088993
A_23_P350107 -0.21561241
A_23_P388190 0.06668377
A_23_P106544 0.14698315
A_33_P3219745 -0.333354
A_32_P85539 0.21676302
A_23_P94998 -0.101961136
A_33_P3235677 -0.33809566
A_23_P417014 0.2852478
A_23_P103905 -0.4061556

Total number of rows: 34183

Table truncated, full table size 819 Kbytes.

Supplementary file Size Download File type/resource
GSM3018259_HEC-TM-OHT96h-shSCN9A_R1.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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