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Sample GSM7783275 Query DataSets for GSM7783275
Status Public on Oct 01, 2023
Title Ctrl TGFb_R1
Sample type RNA
Source name HMECT cells
Organism Homo sapiens
Characteristics source: Cell culture
transduction: control vector pWZL
treatment: TGFb
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 (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 Sep 15, 2023
Last update date Oct 01, 2023
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)
GSE243320 RSK3 switches cell fate: from stress-induced senescence to malignant progression

Data table header descriptions
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
A_23_P42935 0.40978718
A_23_P117082 0.10593033
A_23_P2683 -0.16899681
A_24_P358131 -0.039546967
A_23_P157316 0.5877714
A_32_P14850 0.34795284
A_23_P158596 0.15738201
A_23_P350107 0.07203865
A_23_P388190 -0.14159584
A_23_P106544 -0.45852757
A_32_P85539 0.62064743
A_23_P94998 -0.4119234
A_23_P417014 -0.2799797
A_23_P103905 0.1225996
A_24_P497186 0.3622837
A_23_P118536 -0.068241596
A_23_P434289 0.0817976
A_33_P3326898 0.20351171
A_24_P67898 0.36767197
A_24_P28657 -0.8017626

Total number of rows: 26277

Table truncated, full table size 626 Kbytes.

Supplementary file Size Download File type/resource
GSM7783275_SG12034169_252665247863_S001_GE1_1105_Oct12_1_2.txt.gz 2.2 Mb (ftp)(http) TXT

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