|
| Status |
Public on Mar 31, 2024 |
| Title |
Rat alveolar macrophages, 24hr, CNF3, 4 replicates |
| Sample type |
RNA |
| |
|
| Source name |
NR8383_CNF3
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell: Rat alveolar macrophages (NR8384)
treatment: CNF3
time: 24h
|
| Treatment protocol |
F-12K + FBS medium was removed by centrifugation. Cell cultures were replaced with six kinds of the CNFs working solutions (CNF1, CNF2, CNF3, CNF4, CNF5, or CNF6), respectively. The cultures were seeded into each well of a 6-well plate and grown for 24 hours at 37 ?C in a humidified incubator with 5% CO2. Cell concentrations at this point were approximately 3.0 x 10^5 cells/mL.
|
| Growth protocol |
Rat alveolar macrophage cells (NR8383) obtained the American Type Culture Collection were cultured at 37 ‹C in 75-cm2 cell culture flasks in F-12K with 10 % (v/v) heat-inactivated fetal bovine serum (FBS) in a humidified atmosphere of 95% air and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a RNeasy Mini Kit (Qiagen, Japan) following the manufacturerfs instructions. RNA was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., US), and sample qualities were monitored with an Agilent 2100 Bioanalyzer (Agilent Technologies, US).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3-labeled cRNA was prepared from RNA using a Low Input Quick Amp Labeling kit (Agilent) according to the manufacturerfs 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 (G2519F#14879; Agilent Technologies) at 65 ‹C for 17 h.
|
| Scan protocol |
Hybridized microarray slides were washed according to the manufacturerfs instructions and scanned with a DNA Microarray Scanner (Agilent) at 5 ƒÊm resolution.
|
| Description |
Gene expression after 24hr in CNF3-exposed rat alveolar macrophages
CF030_03
|
| Data processing |
The scanned images were analyzed numerically using Agilent Feature Extraction Software, version 12.0.3.1.
|
| |
|
| Submission date |
Aug 28, 2023 |
| Last update date |
Mar 31, 2024 |
| 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) |
| GSE241791 |
Gene expression profiles in rat alveolar macrophages exposure to cellulose nanofibrils, microcrystalline cellulose, and lipopolysaccharide. |
|
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7743710_CF030_03_1_NOM.txt.gz |
342.2 Kb |
(ftp)(http) |
TXT |
| GSM7743710_CF030_03_1_RawData.txt.gz |
8.6 Mb |
(ftp)(http) |
TXT |
| GSM7743710_CF030_03_2_NOM.txt.gz |
344.5 Kb |
(ftp)(http) |
TXT |
| GSM7743710_CF030_03_2_RawData.txt.gz |
8.6 Mb |
(ftp)(http) |
TXT |
| GSM7743710_CF030_03_3_NOM.txt.gz |
342.5 Kb |
(ftp)(http) |
TXT |
| GSM7743710_CF030_03_3_RawData.txt.gz |
8.7 Mb |
(ftp)(http) |
TXT |
| GSM7743710_CF030_03_4_RawData.txt.gz |
8.6 Mb |
(ftp)(http) |
TXT |
| GSM7743710_CF030_03_NOM.txt.gz |
359.5 Kb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
