|
| Status |
Public on May 24, 2017 |
| Title |
Yap1 Shh-Cre knockout 2 |
| Sample type |
RNA |
| |
|
| Source name |
submandibular gland
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Shh-Cre Yap1-/-
tissue: submandibular gland
developmental stage: E15.5
|
| Treatment protocol |
E15.5 WT and Yap knockout SMGs were dissected and the epithelium was separated from the mesenchyme as previously described (PMID:19247608).
|
| Growth protocol |
SMGs from E15.5 litter mate embryos from three separate timed matings were collected.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SMGs were lysed in RLT buffer and RNA was isolated using a Qiagen RNeasy kit.
|
| Label |
biotin
|
| Label protocol |
Isolated RNA was normalized and then automated sample amplification and biotin labeling were carried out using the NuGEN Ovation RNA Amplification system V2, Ovation WB reagent and Encore Biotin module according to manufacturer’s recommendations using an Arrayplex automated liquid handler (Beckman Coulter).
|
| |
|
| Hybridization protocol |
Two micrograms of biotin labeled sscDNA probe were hybridized to a GPL11180 [HT_MG-430_PM] Affymetrix Array Plate with modifications as previously described (PMID: 23289891)
|
| Scan protocol |
The processed GeneChip plate arrays were scanned using GeneTitan scanner (Affymetrix).
|
| Description |
Gene expression from submandibular gland of Shh-Cre Yap1-/- animal.
|
| Data processing |
Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package in the Bioconductor software suite (version 2.12), using R version 2.15.1 and the Brainarray htmg430pmmmentrezg R package (version 17.0.0) (http://mbni.org/customcdf/17.0.0/entrezg.download/htmg430pm_Mm_ENTREZG_17.0.0.zip).
|
| |
|
| Submission date |
Nov 23, 2016 |
| Last update date |
Jun 25, 2019 |
| Contact name |
Boston University Microarray and Sequencing Resource |
| E-mail(s) |
msrdata@bu.edu
|
| Organization name |
Boston University
|
| Department |
Microarray and Sequencing Resource
|
| Street address |
72 East Concord Street, E631
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL22412 |
| Series (1) |
| GSE90480 |
The Hippo pathway effector YAP is an essential regulator of submandibular gland ductal progenitor patterning |
|
