|
| Status |
Public on Mar 13, 2014 |
| Title |
Airway smooth muscle, control animal 3 |
| Sample type |
RNA |
| |
|
| Source name |
Microdissected airway smooth muscle
|
| Organism |
Mus musculus |
| Characteristics |
group: Control
strain: C57BL/6J
|
| Treatment protocol |
Mice were sensitized by two IP injections of 50 ug OVA at day 0 and day 7 followed by 5 days of OVA nebulization between day 14-day 18. Mice were sacrificed on day 19 followed by cell isolation.
|
| Growth protocol |
SMA-GFP mice were crossed with NG2-DsRed mice. Double fluorescent mice were used. In these mice, bronchial smooth muscle is singly GFP+, while vascular smooth muscle is GFP+;DsRed+/
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using QIAGEN’s RNeasy kit (Qiagen, Valencia, CA) and sample integrity was verified using RNA 6000 Pico Assay RNA chips run in Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
|
| Label |
biotin
|
| Label protocol |
Total RNA (5 ng) was reverse transcribed using Ovation Pico WTA System V2 (Nugen, San Carlos, California). The obtained SPIA-amplified cDNA was purified using Agencourt RNA clean XP Purification Beads and fragmented (5 ng) and labeled with biotin using the Encore Biotin Module (NuGEN, San Carlos, California). SPIA-amplified cDNA and fragmented cDNA quality controls were carried out by running an mRNA Pico assay in the Agilent 2100 Bioanalyzer.
|
| |
|
| Hybridization protocol |
The labeled, fragmented DNA was hybridized to the Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.
|
| Scan protocol |
After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).
|
| Description |
Gene expression data from microdissected airway smooth muscle from control animal
|
| Data processing |
Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package in the Bioconductor software suite (version 2.10.0) and the Brainarray mogene10stv1mmentrezg R package (version 14.0.0) (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.0.0/entrezg.download/MoGene10stv1_Mm_ENTREZG_14.0.0.zip).
|
| |
|
| Submission date |
Apr 03, 2013 |
| Last update date |
Jun 25, 2019 |
| Contact name |
Boston University Microarray and Sequencing Resource |
| E-mail(s) |
[email protected]
|
| Organization name |
Boston University
|
| Department |
Microarray and Sequencing Resource
|
| Street address |
72 East Concord Street, E631
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL13730 |
| Series (1) |
| GSE45723 |
A new approach for the study of lung smooth muscle phenotypes and its application in asthma |
|
