|
| Status |
Public on Nov 15, 2009 |
| Title |
Glis3WT pancreas vs Glis3KO pancreas |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Glis3WT pancreas
|
| Organism |
Mus musculus |
| Characteristics |
Total RNAs from Pancreas of Glis3 WT P3 pups
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using RNeasy mini kit (Qiagen) from WT P3 pancreas
|
| Label |
Cy 3
|
| Label protocol |
Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.
|
| |
|
| Channel 2 |
| Source name |
Glis3KO pancreas
|
| Organism |
Mus musculus |
| Characteristics |
Total RNAs from Pancreas of Glis3zf/zf P3 pups, which have a deletion mutation in exon 4.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using RNeasy mini kit (Qiagen) from Glis3zf/zf P3 pancreas
|
| Label |
Cy 5
|
| Label protocol |
Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.
|
| |
|
| |
| Hybridization protocol |
For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.
|
| Scan protocol |
Slides were washed as indicated in the Agilent 60-mer oligo microarray processing protocol and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software, using defaults for all parameters.
|
| Description |
Total RNAs were extracted using RNeasy mini kit (Qiagen, Valencia, CA) from WT P3 pancreas or from Glis3zf/zf P3 pancreas according to the manufacturer's protocols. RNA samples from 2 pups for each WT or Glis3zf/zf pups were pooled, then analyzed. Gene expression analysis was conducted using Agilent Mouse Whole Oligo Microarrays (Agilent Technologies, Palo Alto, CA). Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 500ng of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer’s protocol. For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol. Slides were washed as indicated in this protocol and then scanned with an Agilent Scanner. Two arrays were utilized for each comparison allowing for dye reversals. Data was obtained using the Agilent Feature Extraction software (v7.5), using defaults for all parameters and loaded into the Rosetta Resolver® system (v6.0) (Rosetta Biosoftware, Kirkland, WA).
|
| Data processing |
Data was obtained using the Agilent Feature Extraction software (v7.5), using defaults for all parameters and loaded into the Rosetta Resolver® system (v6.0) (Rosetta Biosoftware, Kirkland, WA).
|
| |
|
| Submission date |
Jan 12, 2009 |
| Last update date |
Jul 06, 2009 |
| Contact name |
NIEHS Microarray Core |
| E-mail(s) |
microarray@niehs.nih.gov, liuliw@niehs.nih.gov
|
| Organization name |
NIEHS
|
| Department |
DIR
|
| Lab |
Microarray Core
|
| Street address |
111 T.W. Alexander Drive
|
| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL7042 |
| Series (1) |
| GSE14430 |
Glis3: a critical player in the regulation of pancreatic beta cell development |
|
