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Sample GSM8008012 Query DataSets for GSM8008012
Status Public on Jan 15, 2024
Title MRC5_CSC_R2
Sample type RNA
Source name MRC5 fibroblast treated with CSC during 6 days
Organism Homo sapiens
Characteristics cell type: Normal human fibroblast cells
Treatment protocol MRC5 cells were cultured with DMSO or Cigaret Smoke Condensate (CSC) at 40µg/ml during 6 days
Growth protocol MRC5 normal human fibroblasts (ATCC) were cultured in Dulbecco′s modified Eagle′s medium (DMEM, Life Technologies) with GlutaMax and supplemented with 10% FBS (Sigma-Aldrich) and 1% penicillin/streptomycin (ThermoFisher Scientific). Cells were maintained at 37°C under a 5% CO2 atmosphere. All experiments were carried out on cells at early passages (between 22 and 28).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from MRC5 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 1.65 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 Whole Human Genome Microarrays 4x44K v2 (Agilent Technologies) 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 Jan 09, 2024
Last update date Jan 15, 2024
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)
GSE252801 Gene expression profiling of human fibroblast MRC5 cells exposed to cigarette smoke condensate (CSC)

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

Data table
A_23_P42935 -0.36088157
A_23_P117082 0.22861648
A_23_P2683 -0.2331527
A_24_P358131 0.15418655
A_23_P157316 -0.12681532
A_32_P14850 0.14333367
A_23_P158596 1.0084457
A_23_P350107 0.08754286
A_23_P388190 -0.121430084
A_23_P106544 -0.47699547
A_32_P85539 -0.1310657
A_23_P94998 -0.1735754
A_23_P103905 0.22263491
A_24_P497186 -0.6633272
A_23_P118536 -0.3484305
A_23_P434289 -0.27596712
A_33_P3326898 0.52314067
A_24_P67898 0.47160405
A_24_P28657 -0.6504776
A_33_P3344292 0.5268984

Total number of rows: 22412

Table truncated, full table size 532 Kbytes.

Supplementary file Size Download File type/resource
GSM8008012_SG12034169_252665248542_S001_GE1_1105_Oct12_1_2.txt.gz 2.1 Mb (ftp)(http) TXT

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