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Sample GSM7783272 Query DataSets for GSM7783272
Status Public on Oct 01, 2023
Title NT_R1
Sample type RNA
 
Source name HMECT cells
Organism Homo sapiens
Characteristics source: Cell culture
transduction: control vector pWZL
Treatment protocol HMECT were transduced with a retrovirus pWZL control vector or pWZL RSK3 encoding vector. After one week of selection with neomycin, cells were treated or not with TGFβ (PeproTech) at the concentration of 0.5 ng/mL for 48h before RNA extraction.
Growth protocol Immortalized human Mammary Epithelial Cells (HMECT) were grown in Mammary Epithelial Cell Growth Medium (MECGM, C-39115 Promocell) with 1% penicillin/streptomycin (Life Technologies). Cells were maintained at 37°C under a 5% CO2 atmosphere.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from HMECT cells in culture 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 1.65 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 Mouse GE 4x44K v2 Microarrays (Agilent-026655) 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 10.5.1.1 (Agilent Technologies),
Data processing The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
 
Submission date Sep 15, 2023
Last update date Oct 01, 2023
Contact name jean-michel flaman
E-mail(s) jean-michel.flaman@lyon.unicancer.fr
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)
GSE243320 RSK3 switches cell fate: from stress-induced senescence to malignant progression

Data table header descriptions
ID_REF
VALUE Data were normalized to the 75th percentile signal intensity and the baseline was adjusted on control condition NT using GeneSpring GX 12.6 software (Agilent Technologies). The normalized data are indicated in log2FC.

Data table
ID_REF VALUE
A_23_P42935 0.25242567
A_23_P117082 0.0
A_23_P2683 0.0
A_24_P358131 0.25397396
A_23_P157316 0.24210739
A_32_P14850 0.04473877
A_23_P158596 0.23990726
A_23_P350107 0.080495834
A_23_P388190 -0.06275463
A_23_P106544 0.0
A_32_P85539 0.02053833
A_23_P94998 0.14777088
A_23_P417014 0.0
A_23_P103905 0.03584671
A_24_P497186 0.0
A_23_P118536 -0.036468506
A_23_P434289 0.0
A_33_P3326898 0.06150675
A_24_P67898 0.28110027
A_24_P28657 0.0

Total number of rows: 26277

Table truncated, full table size 570 Kbytes.




Supplementary file Size Download File type/resource
GSM7783272_SG12034169_252665247863_S001_GE1_1105_Oct12_1_1.txt.gz 2.2 Mb (ftp)(http) TXT

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