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| Status |
Public on Nov 19, 2015 |
| Title |
Lung_SWCNT, 1 day |
| Sample type |
RNA |
| |
|
| Source name |
Rat lungs, 1 day, SWCNT, replicate 4
|
| Organism |
Rattus norvegicus |
| Characteristics |
gender: male
post-instillation period: 1 day
tissue: lung
|
| Treatment protocol |
0.32 mg of SWCNT or MWCNT was suspended in 0.4 ml of 10mg/mL BSA. Each material suspension was intratracheally instilled once in rats. The animals were dissected at 1day, 3 days, 7 days, 30 days, and 90 days after instillation.
|
| Growth protocol |
Nine-week-old male Wistar rats purchased from Japan SLC, Inc. (Shizuoka, Japan) were divided into groups (n = 4 per group per time point). SWCNT or MWCNT were intratracheally administered into rats as a single injection, respectively. The vehicle control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The 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 manufacturers instruct
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Tokyo, Japan). Dye incorporation an
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| |
|
| Hybridization protocol |
Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml o
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan resolution 5um).
|
| Description |
Gene expression after 1 day in SWCNT-instilled rat lungs
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014879_D_F_20110906). Background detrend: On (Feat NCRange, LoPass). Multiplicative detrend: True. Features fla
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| |
|
| Submission date |
Nov 18, 2015 |
| Last update date |
Nov 19, 2015 |
| 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) |
| GSE75148 |
Gene expression profiles in rat lung following intratracheal instillation with short size single-wall and multi-wall carbon nanotubes |
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