|
| Status |
Public on Sep 03, 2011 |
| Title |
Mutant # 3 |
| Sample type |
RNA |
| |
|
| Source name |
Hoxa1 null
|
| Organism |
Mus musculus |
| Characteristics |
tissue: rhombomere 3-5 region of embryo including neuroectoderm, mesoderm, otic ectoderm
|
| Treatment protocol |
The rhomobere 3-5 from 24 wildtype and 24 Hoxa1Δ/Δ embryos was used. Tissue from each embryo was homogenized and stored at -80° C in RLT buffer and finally pooled into four wildtype and four mutant samples, containing tissue from 1-6 somite embryos (one embryo of each somite stage per pool).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isoltaed using the RNAqueous Micro kit in combination with the Qiagen RLT buffer and on-column DNase treatment. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Agilent One-Color Quick Amp Labeling Protocol
|
| |
|
| Hybridization protocol |
Agilent One-color Heterologous GE Hybridization and Wash Protocol
|
| Scan protocol |
Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.
|
| Description |
Gene expression in Hoxa1 null compared to wildtype embryos
|
| Data processing |
Array images were processed with Agilent Feature Extraction software version 10.5.1.1. Array data files were filtered to remove positive and negative control features and any features flagged as non-uniform outliers or population outliers, as recommended by Agilent. The remaining features for each unique probe were averaged and finally log transformed (log base 2) to yield a single log 2 intensity for each unique probe sequence.
|
| |
|
| Submission date |
Dec 06, 2010 |
| Last update date |
Sep 03, 2011 |
| Contact name |
Nadja Makki |
| Organization name |
University of Utah
|
| Street address |
15 North ,2030 East
|
| City |
Salt Lake city |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL7202 |
| Series (1) |
| GSE25868 |
Identification of Hoxa1 downstream targets |
|
