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Sample GSM4661761 Query DataSets for GSM4661761
Status Public on Jul 09, 2020
Title CNF1_D03_2.0mg/kg CNF1
Sample type RNA
 
Source name 3 day post-instillation in 2.0mg/kg CNF1-exposed rat lung
Organism Rattus norvegicus
Characteristics strain: Sprague-Dawley (Crl:CD[SD])
Sex: male
treatment: 2.0mg/kg CNF1
time: Day3
tissue: lung
Treatment protocol 0.5, 1.0 and 2.0 mg/mL of CNF (CNF1, CNF2, and CNF3) and MWCNT suspensions were prepared with distilled water with preservatives as each vehicle control. Each rat received a single intratracheal instillation dose (1 mg/kg) of the CNFs, MWCNT, and vehicles. Rats were dissected at 1, 3, 7, 30, and 90 days post-instillation. Lungs were perfused with physiological saline, excised, and used for whole genome microarray analysis.
Growth protocol Seven-week-old male Sprague-Dawley (Crl:CD[SD]) rats were purchased from Charles River Laboratories Japan (Yokohama, Japan). Rats were housed in metal cages with in a room with 35%– 70% humidity and a controlled temperature of 20°C–26°C and fed a chow diet ad libitum. All procedures and animal handling were approved by the Institutional Animal Care and Use Committee of the National Institute of Advanced Industrial Science (Tsukuba, Japan) and Technology and the BioSafety Research Center Inc. (Iwata, Japan)..
Extracted molecule total RNA
Extraction protocol Blood-perfused rat right lungs (n = 4 per group per time point) were homogenized using QIAzol lysis reagent with a Tissue Ruptor (Qiagen, Tokyo, Japan). Total RNA from the homogenates was extracted using the RNeasy Midi kit (Qiagen) following the manufacturer’s instructions.
Label Cy3
Label protocol Cyanine-3-labeled cRNA was prepared from RNA using a Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer’s instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop 2000 spectrophotometer.
 
Hybridization protocol Each labeled cRNA probe was used separately for hybridization to a 4×44 K Whole Rat Genome Microarray (G4131F; Agilent Technologies) at 65 °C for 17 h.
Scan protocol Hybridized microarray slides were washed according to the manufacturer’s instructions and scanned with a DNA Microarray Scanner (Agilent, G2505C) at 5 μm resolution.
Description Rat lung, Day03, 2.0mg/kg CNF1, replicate 4
Data processing The scanned images were analyzed numerically using Agilent Feature Extraction Software, version 12.0.3.1.
 
Submission date Jul 08, 2020
Last update date Jul 09, 2020
Contact name Katsuhide Fujita
E-mail(s) ka-fujita@aist.go.jp
Organization name National Institute of Advanced Industrial Science and Technology
Department Research Institute of Science for Safety and Sustainability
Street address Onogawa 16-1
City Tsukuba
ZIP/Postal code 3058569
Country Japan
 
Platform ID GPL7294
Series (1)
GSE154013 Gene expression profiles in rat lung following intratracheal instillation with cellulose nanofibrils and multi-walled carbon nanotubes

Data table header descriptions
ID_REF
VALUE log2 average normalized signal intensity

Data table
ID_REF VALUE
A_44_P465448 -0.3196113
A_44_P514796 -0.50189734
A_44_P409518 7.84E-04
A_44_P279262 -0.033684492
A_44_P375042 0.9993427
A_44_P269499 0.49367118
A_44_P204808 -1.0823092
A_44_P438090 0.31589282
A_44_P330643 -0.37762213
A_44_P421941 -0.96182835
A_42_P504653 4.152661
A_44_P260580 0.51480293
A_44_P445440 -0.8672658
A_44_P313825 1.0845549
A_44_P788423 -0.8455787
A_44_P549509 0.09095645
A_43_P12354 0.20096707
A_43_P14989 -0.0658133
A_44_P172767 -0.5579561
A_44_P884555 -0.05442834

Total number of rows: 41103

Table truncated, full table size 968 Kbytes.




Supplementary file Size Download File type/resource
GSM4661761_CF01_08.txt.gz 371.0 Kb (ftp)(http) TXT
Processed data included within Sample table

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