|
| Status |
Public on Nov 05, 2018 |
| Title |
alveolar_macrophage_B1KO_1 |
| Sample type |
RNA |
| |
|
| Source name |
AM, B1KO
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
gender: female
age: 8-9w
cell type: alveolar macrophage
genotype/variation: B1 KO
|
| Treatment protocol |
Bronchoalveolar lavage was collected from mouse and alveolar macropahges were sorted by flow cytometer.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with an RNeasy micro kit (Qiagen) according to the manufacturer's protocol.
|
| Label |
Cy3
|
| Label protocol |
Total RNA was amplified with an Amino Allyl MessageAmpII aRNA Amplification Kit (Ambion) and was labeled with indocarbocyanine through the use of a CyDye post-labeling Reactive Dye Pack (Amersham).
|
| |
|
| Hybridization protocol |
Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (Agilent-028005) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides
|
| Description |
Gene expression alveolar macropahge from Bach1_KO mouse
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_107_Sep9 and Grid: 028005_D_F_20101029) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Normalized signal intensities filtered on expression flags error (CV <50)
|
| |
|
| Submission date |
Mar 09, 2016 |
| Last update date |
Nov 05, 2018 |
| Contact name |
Kazuhiko Igarashi |
| E-mail(s) |
igarashi@med.tohoku.ac.jp
|
| Phone |
+81227177597
|
| Organization name |
Tohoku University
|
| Street address |
Seiryo 2-1
|
| City |
Sendai |
| ZIP/Postal code |
980-8575 |
| Country |
Japan |
| |
|
| Platform ID |
GPL10787 |
| Series (2) |
| GSE79023 |
Bach2 keeps homeostasis in lung by regulating inflammatory response and maintaining function of alveolar macrophage [array] |
| GSE79139 |
Double knockout of Bach1 and Bach2 reveals shared compensatory mechanisms in regulating alveolar macrophage function and lung surfactant homeostasis |
|
