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Sample GSM556534 Query DataSets for GSM556534
Status Public on Dec 31, 2015
Title CS1
Sample type RNA
 
Source name CS1
Organism Rattus norvegicus
Characteristics strain: Sprague Dawley
developmental stage: adult
sex: male
treatment group: solvent
tissue: substantia nigra pars compacta
Treatment protocol Rotenone (Sigma, Lyon, France) was dissolved in a solution of dimethylsulfoxide (DMSO) / polyethylene glycol (PEG) (1/1) containing the non-ionic surfactant polyol Pluronic® F-127 (Interchim, Montluçon, France) used as a dispersing reagent at the final concentration of 0.05%. Prior to the implantation, Alzet® osmotic mini-pumps (2ML4, Charles River Laboratories, Saint Germain sur l’Arbresle, France) were filled with the solvent or rotenone and incubated overnight at 37°C in a sterile saline solution (NaCl 0.9%, wt/vol) according to manufacturer’s instructions. Rats were anaesthetized by an intraperitoneal injection of ketamine (75 mg/kg) and xylazine (10 mg/kg). Osmotic pumps were implanted subcutaneously and diffused either the solvent (SOLV, control group, n = 3) or 0.5 mg/kg/day rotenone (ROT group, n = 3) for 28 days. The final delivery of rotenone was calculated with respect to average body weight at the time of the implantation. In order to monitor potential side effects of pesticide exposure, body weight was recorded daily for each rat throughout the experimentation.
Growth protocol Male Sprague Dawley rats aged of 5 months were housed with ad libitum access to food and water in a temperature- (24 + 1°C) and humidity- (60%) controlled room under a 12 h / 12 h light-dark schedule (lights on at 08.00 h).
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from laser-capture microdissected rat substantia nigra pars compacta (SNpc) using the RNeasy mini-kit (QIAGEN, Courtaboeuf, France) according to manufacturer’s instructions, including the additional step of DNase treatment. Total RNA (2 ug) was amplified and labeled by a round of in vitro transcription using a MessageAmp aRNA kit (Ambion, Cambridgeshire, U.K.) following the manufacturers protocol. Before amplification, spikes of different concentrations of synthetic mRNA were added to all tubes. These positive controls were used to verify the quality of the process. Amplified RNA (aRNA) was measured with an ultraviolet spectrophotometer and the quality verified on picochips using the Agilent bioanalyzer.
Label biotin
Label protocol Biotin-labeled aRNA (10 ug) was fragmented with 5 uL of fragmentation buffer (GE Healthcare, Amersham, Saclay, France) in a final volume of 20 uL.
 
Hybridization protocol Fragmented aRNA was added to Amersham hybridization solution (Amersham) (final volume 260 uL) and injected onto CodeLink Uniset mouse 35K bioarrays containing 35,000 mouse oligonucleotide gene probes (Amersham). The arrays were hybridized overnight at 37-C at 300 rpm on a rotary mixer in an incubator, washed at 46-C for 1 hour in stringent TNT buffer (100 mM Tris, 150 mM NaCl, 0.02% Tween 20; all from Sigma- Aldrich, Saint Quentin-Fallavier, France), incubated in 3.4 mL of streptavidin-Cy5 (Amersham) solution for 30 minutes, washed 4 times in 240 mL of TNT buffer, rinsed twice in 240 mL of water containing 0.2% Triton X-100, and dried by centrifugation at 600 rpm.
Scan protocol The arrays were scanned with a Genepix 4000B scanner (Axon Instruments, Dipsi Industrie, Chatillon, France) using Genepix software with the laser set at 635 nm, the power at 100%, and the photomultiplier tube voltage at 60%. The scanned image files were analyzed using CodeLink expression software version 4.0, which produces both raw and normalized hybridization signals for each spot on the array.
Description Cumulative low doses of the organic pesticide rotenone in the adult rat substantia nigra pars compacta
Data processing The CodeLink software (version 4) normalizes the overall raw hybridization signal intensity on each array to the median of the array (median intensity is one after normalization).
 
Submission date Jun 15, 2010
Last update date Dec 31, 2015
Contact name frédéric leprêtre
E-mail(s) frederic.lepretre@univ-lille.fr
Organization name Lille University
Department CHU of Lille, CBP
Lab plateforme de génomique fonctionnelle et structurale
Street address Boulevard du Pr Leclercq
City lille
ZIP/Postal code 59037
Country France
 
Platform ID GPL2896
Series (1)
GSE22364 Cumulative low doses of the organic pesticide rotenone in the adult rat substantia nigra pars compacta

Data table header descriptions
ID_REF
VALUE median normalized signal intensity

Data table
ID_REF VALUE
325066 0.267064016621656
325004 15.579495299185
325088 46.1637919991268
284060 31.6761818599896
325053 43.8967106283197
284025 45.4755761532484
325018 82.30054024036
325102 61.4023962933287
284088 2.87323932083939
325067 15.5534037380459
284053 52.7743958174586
325032 16.4505785908264
284004 5.86120898846335
284102 15.6431924668221
325081 376.590851558463
284067 296.256858385508
325046 11.4857744773365
284018 30.0706712667436
325011 38.1058929561873
325095 37.6753520559115

Total number of rows: 33911

Table truncated, full table size 799 Kbytes.




Supplementary file Size Download File type/resource
GSM556534.txt.gz 1.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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