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Sample GSM8008016 Query DataSets for GSM8008016
Status Public on Jan 15, 2024
Title MRC5_CTRL_R3
Sample type RNA
Source name MRC5 fibroblast treated with DMSO
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 0.16949391
A_23_P117082 0.31203914
A_23_P2683 0.13804881
A_24_P358131 -0.1967799
A_23_P157316 -0.6585374
A_32_P14850 -0.0067498684
A_23_P158596 -0.07998085
A_23_P350107 -0.07295576
A_23_P388190 0.07811959
A_23_P106544 0.11831379
A_32_P85539 0.01825872
A_23_P94998 -0.072193146
A_23_P103905 0.022804856
A_24_P497186 -0.06965923
A_23_P118536 0.05313933
A_23_P434289 -0.4217267
A_33_P3326898 -0.77900434
A_24_P67898 -0.114448845
A_24_P28657 0.12644702
A_33_P3344292 -0.5026789

Total number of rows: 22412

Table truncated, full table size 544 Kbytes.

Supplementary file Size Download File type/resource
GSM8008016_SG12034169_252665248543_S001_GE1_1105_Oct12_1_1.txt.gz 2.2 Mb (ftp)(http) TXT

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