|
| Status |
Public on Sep 10, 2015 |
| Title |
SG_human salisphere transplant_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
salivary gland
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
strain: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ
Sex: Female
age: 14 weeks at sacrifice
|
| Treatment protocol |
NSG mice were locally irradiated in the neck region with 5Gy of X-rays, to induce clinically relevant hyposalivation.
|
| Growth protocol |
Prior to transplantation, human salispheres were maintained in our standard culture medium, as stated in materials and methods section of this paper.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SGs were harvested from mice and homogenized using a tissue processor. Total RNA was extracted using the Qiagen Rneasy Mini Kit, according to manufacturers instructions.
|
| Label |
biotin
|
| Label protocol |
RNA was aplified using the Illumina TotalPrep RNA Amplification Kit
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol.
|
| Scan protocol |
Standard Illumina scanning protocol, using iScan.
|
| Description |
9388211090_B
|
| Data processing |
The data were normalized using data extraction with GenomeStudio Software and normalization in R version 3.0.1 neqc function of the BioConductor version 2.12 library limma 3.16.5 (Smyth, GK 2005)
Differential expression analysis was performed using eBayes function of the BioConductor library limma and an adjustment method BH (Benjamini Hochberg) to exclude false positives, with a p value of 0.05. Assignment of probes upregulated at 1 week post-transplantation to biological pathways was performed using ENrichR online resources
|
| |
|
| Submission date |
Sep 09, 2015 |
| Last update date |
Sep 10, 2015 |
| Contact name |
Sarah Pringle |
| E-mail(s) |
s.a.pringle@umcg.nl
|
| Phone |
0031503638996
|
| Organization name |
University Medical Centrum Groningen
|
| Department |
Cell Biology
|
| Street address |
Antonius Deusinglaan 1
|
| City |
Groningen |
| State/province |
Groningen |
| ZIP/Postal code |
9713 AV |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL6887 |
| Series (2) |
| GSE72869 |
Paracrine stimulation effect of human salispheres on mouse salivary gland |
| GSE72871 |
Paracrine stimulation effect of autologous salispheres and human salispheres on mouse salivary gland |
|
