|
| Status |
Public on May 18, 2007 |
| Title |
MNR 5-2 KO 2 |
| Sample type |
RNA |
| |
|
| Source name |
Type II cells from Nrf2-/- mouse.
|
| Organism |
Mus musculus |
| Characteristics |
ICR10 mouse strain (Nrf2-/-) gender- female, age- 2 months, n = 1, # of tissue = 1, tissue: Lung, Cell:Type II.
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Type II cells were isolated by instilling and incubating lung with Dispase II for 45 munutes.lungs were teased and cells were incubated on IgG coated plates for an hour to remove lung macrophases. The non adherent cells were further incubated on petridishes for two hours for fibroblast adherence. The non adherent cells were cultured on fibronectin/collagen coated plates in the presense of keratinocyte growth factor for five days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed followed by RNA clean up using Qiagen Rneasy kit according to the manufacturers' 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 5 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 Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)
|
| Scan protocol |
Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.
|
| Description |
Mouse Lung Type II cell 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 B6 18/26 months x 3 sets B6 2 months comparison (1.5 fold cutoff (FC), Mann-Whitney test < 0.05, 6 out of 9 comparisons). Also, ABS |FC - FC SEM| >= 1.5
|
| |
|
| Submission date |
May 15, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Narsa Reddy Machireddy |
| E-mail(s) |
[email protected]
|
| Phone |
1-410-955-4711
|
| Fax |
1-410-955-0299
|
| Organization name |
Bloomberg School of Public Health
|
| Department |
Environmental Health Sciences
|
| Lab |
Sekhar Reddy Lab
|
| Street address |
615, N Wolfe St
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE7810 |
Comparative analysis of gene expression WT and Nrf2-/- mice Type II cells |
|
| Relations |
| Reanalyzed by |
GSE119085 |
