|
| Status |
Public on Apr 07, 2024 |
| Title |
DD037G_distal_RNA |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Normal lung
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Normal lung
airway size: small
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy kit from Qiagen following manufacturer's instructions. These total RNA samples were run on an Agilent Bioanalyzer 2100 (Agilent Technologies, Inc) to ensure RNA quality.
|
| Label |
Cy5
|
| Label protocol |
The total RNA labeling and hybridization protocol used is described in the Agilent low RNA input linear amplification kit (http://www.chem.agilent.com/Scripts/PDS.asp?lPage=10003), with the following two changes: 1) a Qiagen PCR purification kit was used to clean up the cRNA instead of the LiCl precipitation, and 2) all reagents volumes were reduced by one half.
|
| |
|
| Channel 2 |
| Source name |
Stratagene Human Universal Reference
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy kit from Qiagen following manufacturer's instructions. These total RNA samples were run on an Agilent Bioanalyzer 2100 (Agilent Technologies, Inc) to ensure RNA quality.
|
| Label |
Cy3
|
| Label protocol |
The total RNA labeling and hybridization protocol used is described in the Agilent low RNA input linear amplification kit (http://www.chem.agilent.com/Scripts/PDS.asp?lPage=10003), with the following two changes: 1) a Qiagen PCR purification kit was used to clean up the cRNA instead of the LiCl precipitation, and 2) all reagents volumes were reduced by one half.
|
| |
|
| |
| Hybridization protocol |
Microarrays were hybridized in an Robbins Scientific hybridization oven with 850ng of labeled Cy3 Reference and 850ng of Cy5 experimental samples using the Agilent hybridization kit as described by the manufacturer. The arrays were incubated overnight and then washed once for 10 minutes in 2X SSC and 0.0005% Triton X-102, twice for 5 minutes in 0.1XSSC, and then immersed into Agilent Stabilization and Drying solution for 20 seconds.
|
| Scan protocol |
Microarrays were scanned with Agilent Scanner and intensity was recorded using Agilent Feature Extraction Software.
|
| Data processing |
Agilent feature extraction output was processed by normexp background correction and loess normalization using Bioconductor library limma.
Normalized_normalLung.txt file includes normalized log2 ratios (normal/reference).
|
| |
|
| Submission date |
Apr 30, 2022 |
| Last update date |
Apr 07, 2024 |
| Contact name |
Scott H. Randell |
| E-mail(s) |
[email protected]
|
| Phone |
9192102280
|
| Organization name |
UNC Chapel Hill
|
| Street address |
CB 7248, Room 1117 Marsico Hall, 125 Mason Farm Rd.
|
| City |
Chapel Hill |
| State/province |
North Carolina |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL9053 |
| Series (1) |
|
