|
| Status |
Public on Dec 06, 2010 |
| Title |
E3-xGem injected st.10.5 |
| Sample type |
RNA |
| |
|
| Source name |
embryonic ectoderm
|
| Organism |
Xenopus laevis |
| Characteristics |
developmental stage: st. 10.5
manipulation: xGem injected
|
| Treatment protocol |
xGemininΔcoil RNA/300 pg was injected into both blastomeres of two-cell stage pigmented Xenopus laevis embryos (animal hemisphere). Injected embryos were raised until stage 8-9 and 80 ectodermal (animal cap) explants/sample were isolated and incubated in 0.7X MMR/25ºC.
|
| Growth protocol |
Xenopus laevis embryos were obtained by in vitro fertilization
|
| Extracted molecule |
total RNA |
| Extraction protocol |
When sibling embryos reached stage 10.5 or 12, total RNA (20 μg/sample) was isolated using Trizol (Invitrogen).
|
| Label |
biotin
|
| Label protocol |
biotin
|
| |
|
| Hybridization protocol |
Performed by the Washington University Genome Technololgy Access Center
|
| Scan protocol |
Affymetrix Genechip 3000 used by the Washington University Genome Technololgy Access Center
|
| Description |
xGem St.10.5-set 3.CEL
|
| Data processing |
To define microarray target genes, raw CEL and DAT files were analyzed with dChip software (http://biosun1.harvard.edu/complab/dchip/)(Li and Hung Wong, 2001) after normalization to exclude probesets that did not meet the following preliminary cutoff values: i) expression, represented by model-based expression indices (MBEI), was changed more than 2-fold in treated versus untreated samples (E/B >2.0) groups, ii) MBEI differences were larger than 70 (E-B > 70), iii) expression was claimed as “present (P)” in at least one sample in each experiment. Probesets were considered putatively Geminin-regulated if they met microarray cutoff values in at least 2 of the 3 experiments. A subset of these genes was then further validated.
|
| |
|
| Submission date |
Nov 05, 2010 |
| Last update date |
Dec 06, 2010 |
| Contact name |
Kristen L Kroll |
| E-mail(s) |
kkroll@wustl.edu
|
| Organization name |
Washington University School of Medicine
|
| Department |
Developmental Biology
|
| Lab |
Kristen Kroll
|
| Street address |
320 McDonnell Sciences/660 S. Euclid Ave.
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL1318 |
| Series (1) |
| GSE25158 |
Geminin-regulated genes in the Xenopus laevis embryonic ectoderm |
|
