|
| Status |
Public on Sep 30, 2010 |
| Title |
Pax5ko-2 |
| Sample type |
RNA |
| |
|
| Source name |
Pax5ko
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Pax5 deficient
|
| Treatment protocol |
no treatments performed
|
| Growth protocol |
EBFko and Pax5 ko cell grown in standard culture medium's supplemented with 10ng/ml of recombinant human Flt3-ligand and 10ng/ml recombinant mouse IL-7. RAG2ko cells grown in 10ng/ml recombinant mouse IL-7.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extract using Qiagen kit per manufacturer's instructions. Integrity of the RNA was evaluated using the Agilent 2100 bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
Total RNA converted to cDNA using Superscript cDNA synthesis kit. Double stranded cDNA purified by phase lock gel with phenol chloroform extraction. Purified cDNA in vitro transcribed into biotin cRNA using Affymetric labeling reagent.
|
| |
|
| Hybridization protocol |
Bio cRNA hybridized to Affymetrix 430 2.0 arrays per manufacturer's instructions.
|
| Scan protocol |
Arrays scanned using Affymetrix GeneChip Scanner 3000.
|
| Description |
B lineage specified
|
| Data processing |
GCRMA normalization followed by ANOVA analysis of variance performed to identify statistically significant differentially expressed genes (parametric test, variances not assumed equal by Welch t-test, p-value cutoff 0.05). Data from the three individual EBFko, Pax5ko, or RAG2ko samples was merged during the GC-RMA normalization to generate only a single GC-RMA normalized file for each cell type. GC-RMA data available on Series record.
|
| |
|
| Submission date |
May 06, 2009 |
| Last update date |
Apr 26, 2010 |
| Contact name |
Kay L Medina |
| E-mail(s) |
medina.kay@mayo.edu
|
| Phone |
507-266-4283
|
| Organization name |
Mayo Clinic
|
| Department |
Immunology
|
| Street address |
200 1st Street SW
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE16002 |
Molecular Events Initiating B Cell Fate Specification |
|
