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Sample GSM3108647 Query DataSets for GSM3108647
Status Public on Dec 01, 2020
Title Lung_403_High_Day30_rep4
Sample type RNA
 
Source name Rat, Lung, NM-403, High, Day 30
Organism Rattus norvegicus
Characteristics strain: Sprague Dawley
tissue: accessory lobe of lung
gender: female
age: 13 weeks-old (at the onset of inhalation)
treatment: NM-403
dose: High
time: Day 30
Treatment protocol 13 week old female Sprague Dawley rats were exposed by nose-only inhalation 6 hours/day, 5 days/week for 4 weeks to two doses of NM-403 carbon nanotube.
Growth protocol Accessory lobe of rat lungs were stored in RNA later at -20°C before use
Extracted molecule total RNA
Extraction protocol Total RNA were disrupted using gentleMACS™ Dissociator (Miltenyi Biotech) and extracted from accessory lobe of lungs with Nucleospin® RNA midi kit (Macherey-Nagel) according to the manufacturer’s instructions. RNA quality was determined by spectrophotometry (A260nm/A280nm > 1.8) and by capillary electrophoresis using Agilent 2100 Bioanalyser (RIN > 7, Agilent RNA 6000 NanoRNA 6000 Nano® Kit, Santa Clara, CA, USA).
Label Cy3
Label protocol For each of the 72 samples (6 control, 6 exposed rats to low dose and 6 exposed rats to high dose per time group), 100 ng of RNA were labelled with Cyanine 3-CTP using Low Input Quick Amp Labelling kits (One-Color Microarray-Based Gene Expression Analysis, version 6.7, Agilent Technologies) and purified (RNeasy Mini kit, QIAGEN) according to the manufacturer's instruction . Dye incorporation and cRNA yield and quality were checked by spectrophotometry and by electrophoresis (Agilent 2100 Bioanalyser).
 
Hybridization protocol 600 ng of Cy3-CTP-labelled cRNA (Specific Activity > 10 pmol Cy3 per µg cRNA) were fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25X Agilent Fragmentation Buffer and 10X Agilent Blocking Agent following the manufacturer’s instructions. On cRNA fragmentation completion, 25 µL of 2X Agilent Hybridization Buffer were added to the fragmentation mixture. The subsequent purified labelled cRNAs were hybridized to Agilent G4853A SurePrint G3 Rat v2 GE 8*60K microarrays (Agilent Technologies) at 65°C overnight (17h) in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with Agilent Gene Expression Wash Buffer 1 and 1 min with 37°C Agilent Gene Expression Wash buffer 2.
Scan protocol Slides were scanned immediately after washing using Agilent high-resolution scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.
Description Gene expression in lung of rat exposed to NM-403 (1.5 mg/m3) 30 days post exposure
Rat, Lung, NM-403, High, Day 30, replicate 4
Data processing Agilent Feature Extraction Software (v 11.0.1.1) was used for background subtraction and data were normalized using the GeneSpring software (v 14.9)
Data were normalized by shift to 75.0 percentile and filtered by flags and by expression based on the signal intensity values (to remove very low signal values and those that have reached saturation)
 
Submission date Apr 23, 2018
Last update date Dec 01, 2020
Contact name Carole Seidel
E-mail(s) carole.seidel@inrs.fr
Organization name INRS
Street address Rue du Morvan
City Vandoeuvre les Nancy
ZIP/Postal code 54519
Country France
 
Platform ID GPL22740
Series (2)
GSE113531 Inhaled multi-walled carbon nanotubes-induced gene expression profile in rat lung (NM-403)
GSE113532 Inhaled multi-walled carbon nanotubes-induced gene expression profile in rat lung

Data table header descriptions
ID_REF
VALUE normalized signal

Data table
ID_REF VALUE
GE_BrightCorner 0.36869383
A_44_P200636 -0.11631298
A_44_P152233 -0.13129187
A_43_P14012 -0.09843254
A_42_P512838 0.17845058
A_64_P073043 -0.2963562
A_43_P21945 -0.17569685
A_43_P14440 0.21415138
A_64_P135547 0.2426095
A_44_P1028858 0.114882946
A_44_P489793 -0.07354021
A_64_P133567 -0.12480068
A_64_P138625 0.20032978
A_42_P675041 -0.09847927
A_44_P1087533 0.007920265
A_44_P504750 -0.4452958
A_43_P15687 0.32558155
A_44_P1060432 0.09031296
A_42_P841704 0.048546314
A_44_P1370646 -0.013921738

Total number of rows: 14687

Table truncated, full table size 357 Kbytes.




Supplementary file Size Download File type/resource
GSM3108647_Lung_403_High_Day30_rep4.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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