|
| Status |
Public on Aug 02, 2018 |
| Title |
mRNA_NHLF_IL-13_1hr |
| Sample type |
RNA |
| |
|
| Source name |
NHLF_IL-13_1hr
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Normal Human Lung fibrobasts (NHLF)
time (hours): 1
|
| Treatment protocol |
NHLF were treated with 10 ng/ml of IL-13 on 1, 4, and 24 hr.
|
| Growth protocol |
NHLF (Lonza, and Walkersville, MD) were cultured in DMEM + 10F FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
miRNeasy mini kit (Qiagen) was used for total RNA extraction.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug Total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer’s instruction, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green, and Green PMT is set to 100%).
|
| Description |
Gene expression at 1 hr after stimulation with IL-13 10 ng/ml
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
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| |
|
| Submission date |
Sep 25, 2017 |
| Last update date |
Aug 02, 2018 |
| Contact name |
Masafumi Horie |
| E-mail(s) |
mhorie-tky@umin.ac.jp
|
| Organization name |
University of Southern California
|
| Street address |
2011 Zonal Ave
|
| City |
Los Angeles |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL20844 |
| Series (2) |
| GSE104228 |
Genome-wide analysis of gene expression for NHLF after treatment with 10 ng/ml of IL-13 |
| GSE104230 |
Genome-wide analysis of coding, long noncoding RNA and miRNA expression for NHLF after treatment with 10 ng/ml of IL-13 |
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