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Sample GSM4860129 Query DataSets for GSM4860129
Status Public on Jul 19, 2023
Title Lung_TiO2_Low_Day30_rep4
Sample type RNA
 
Source name Rat, Lung, TiO2, Exposed to Low dose, Day 30, replicate 4
Organism Rattus norvegicus
Characteristics strain: Sprague Dawley
tissue: accessory lobe of lung
gender: female
age: 13 weeks-old (at the onset of instillation)
treatment: rat exposed to TiO2 (1.5 mg/m3) 30 days post exposure
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 TiO2 (Low dose: 1.5 mg/m3, Medium dose: 5 mg/m3, High dose: 15 mg/m3).
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, 6 exposed rats to medium 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.
 
Hybridization protocol 600 ng of Cy3-CTP-labelled cRNA (Specific Activity > 6 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 within 3 hours 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 TiO2 (1.5 mg/m3) 30 days post exposure
Data processing Agilent Feature Extraction Software (v 12.0.1.1) was used for background subtraction and data were normalized using the GeneSpring software (v 14.9)
 
Submission date Oct 26, 2020
Last update date Jul 19, 2023
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 (1)
GSE160117 Gene expression modification in lungs of rats exposed to TiO2 by inhalation

Data table header descriptions
ID_REF
VALUE Data were normalized by shift to 75.0 percentile

Data table
ID_REF VALUE
GE_BrightCorner -0.26458025
DarkCorner -0.5133524
ERCC-00085_231 -0.59595346
A_43_P20870 0.019038677
A_44_P1163786 -0.27117825
A_44_P1146259 0.5818758
A_44_P200636 0.08354139
A_44_P267993 0.071492195
A_44_P651091 -0.5982151
A_64_P030162 0.57622766
A_44_P152233 0.005742073
A_43_P14012 0.22027636
A_64_P100406 0.007957935
A_44_P1129942 -0.047745705
A_44_P1116327 0.22478676
A_64_P134445 0.27164268
A_42_P512838 -0.32739353
A_44_P661269 0.19836092
ERCC-00120_69 -0.7846613
A_44_P1107408 -0.72994614

Total number of rows: 45738

Table truncated, full table size 1104 Kbytes.




Supplementary file Size Download File type/resource
GSM4860129_Lung_TiO2_Low_Day30_rep4.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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