GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3018260 Query DataSets for GSM3018260
Status Public on Feb 21, 2018
Title HEC-TM-OHT96h-shSCN9A_R2
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 -0.13655281
DarkCorner -0.0062379837
A_23_P146146 0.035436153
A_23_P42935 0.18700027
A_23_P117082 -0.8377924
A_23_P2683 0.06145096
A_24_P358131 0.45723534
A_33_P3367647 0.037251472
A_23_P157316 -0.35230112
A_32_P14850 0.473773
A_23_P158596 -0.37458992
A_23_P350107 -0.11718464
A_23_P388190 0.0182333
A_23_P106544 0.21116543
A_33_P3219745 0.038524628
A_32_P85539 0.05124998
A_23_P94998 -0.100541115
A_33_P3235677 0.03880596
A_23_P417014 0.4183793
A_23_P103905 -0.3228569

Total number of rows: 34183

Table truncated, full table size 820 Kbytes.

Supplementary file Size Download File type/resource
GSM3018260_HEC-TM-OHT96h-shSCN9A_R2.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap