|
| Status |
Public on Mar 28, 2014 |
| Title |
Vldlr knockout HDM, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
knock out, lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung
genotype: knock out
|
| Treatment protocol |
Vldlr-/- mice and wild type (WT) B6129SF2/J mice received intranasal challenges of house dust mite (25 ucg) or saline, both in a volume of 10 ul, five days a week for 6 weeks.
|
| Growth protocol |
not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Biotin-labeled sense targets were prepared from samples of total lung RNA using the Affymetrix Whole-Transcript (WT) Sense Target Labeling Protocol without rRNA reduction. Double-stranded cDNA templates were synthesized from 50 ng of total RNA using random hexamers coupled with a T7 promoter sequence and amplified by in vitro transcription (IVT) with T7 RNA polymerase to produce multiple copies of cRNAs. Random hexamers were utilized to prepare sense strand cDNA.
|
| Label |
biotin
|
| Label protocol |
10 µg of sense strand cDNA was fragmented, labeled with biotin using terminal deoxynucleotidyl transferase.
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Description |
lung
|
| Data processing |
Gene-level intensity values for each of the chips were collected using Affymetrix Expression Console (EC) Software (Affymetrix, Santa Clara, CA). The RMA-sketch workflow was applied for raw data preprocessing, which included global background correction, quantile normalization and median polish summarization.
|
| |
|
| Submission date |
Feb 21, 2014 |
| Last update date |
Mar 28, 2014 |
| Contact name |
Yanqin Yang |
| E-mail(s) |
[email protected]
|
| Organization name |
NIH
|
| Street address |
10 Center Dr.
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE55247 |
Expression data from lungs of Vldlr-/- mice and wild type (WT) B6129SF2/J mice that had received intranasal house dust mite (HDM) challenges to induce experimental asthma or saline, as a control. |
|
