|
| Status |
Public on Mar 23, 2009 |
| Title |
A/J Air-8day-exposed-2 |
| Sample type |
RNA |
| |
|
| Source name |
A/J Air-8day-2 Lung
|
| Organism |
Mus musculus |
| Characteristics |
strain: A/J mouse strain (Jackson Lab)
gender: male
age: 8 days, n = 1, # of tissue = 1
tissue: Lung
|
| Treatment protocol |
Air exposed
|
| Growth protocol |
no growth protocol
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
ENZO BioArray HighYield RNA Transcript Labeling Kit
|
| Label protocol |
cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 1 200 ul of hybridization cocktail containing 10 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip FluidiAir Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manual- Affymetrix)
|
| Scan protocol |
Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.
|
| Description |
A/J Air Lung gene expression
|
| Data processing |
Data extraction was processed by Affy GeneChip« Operating Software v1.3 (Affymetrix). Global scaling was equal to 500. Normalization factor was equal to 1. Analysis of differentially expressed transcripts was accomplished using a pairwise comparative analysis (Affy Data Mining Tool v3.1; Affymetrix). 3 sets A/J 8 day CS x 3 sets A/J 8 day Air comparison (1.5 fold cutoff (FC), Mann-Whitney test < 0.05, 6 out of 9 comparisons).
|
| |
|
| Submission date |
Aug 15, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
vikas misra |
| E-mail(s) |
vmisra@jhsph.edu
|
| Organization name |
Johns Hopkins University School of public health
|
| Department |
Environmental health sciences
|
| Lab |
Clarke G Tankersley
|
| Street address |
615 N. Wolfe street, E6609
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE8790 |
Comparative analysis of gene expression in A/J CS vs Air lungs. |
|
| Relations |
| Reanalyzed by |
GSE119085 |
