|
| Status |
Public on May 23, 2017 |
| Title |
Dp16-E15: TSm10 |
| Sample type |
RNA |
| |
|
| Source name |
TSm10
|
| Organism |
Mus musculus |
| Characteristics |
gender: Male
tissue: Forebrain
developmental stage: day 15 embryo
|
| Treatment protocol |
No treatment protocol was used in this study
|
| Growth protocol |
Mice were housed in standard cages with food and water ad libitum under a controlled environment (temperature = 20°C; humidity = 60%) and a light/dark cycle of 12h. Ts1Cje (Jax Stock 004838) and Dp16 (Jax Stock 013530) males were crossed to C57Bl/6J (Jax Stock 000664) females, and Ts65Dn/F1 (Jax Stock 005252) females were crossed with B6EiC3Sn.BLiAF1 (Stock 003647) males (Jackson Laboratories, Bar Harbor, ME). For embryonic studies, the presence of a vaginal plug was defined as embryonic day 0.5 (E0.5) and 10-15% weight gain at embryonic day 10 was used to confirm pregnancy. Pregnant females were anesthetized with 2.5% isoflurane in a 3/7 02/N2O mixture and euthanized by decapitation at embryonic day E15.5 (E15.5). Embryos were extracted and decapitated in ice-cold phosphate-buffered-saline (PBS1X). Embryonic brains were rapidly removed and brain hemispheres dissected on a cold platform and snap frozen in liquid nitrogen before storage at -80°C. For adult studies, 6-7 month old animals were euthanaized as described above and brains were removed and dissected on a cold platform. Cerebral cortex, hippocampus and cerebellum were snap frozen in liquid nitrogen before storage at -80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the NucleoSpin RNA II kits following the manufacturer’s instructions (Macherey-Nagel, Bethlehem, PA). RNA concentrations were measured as absorbance at 260 nm on the Nanodrop instrument (Thermo Fisher Scientific, Waltham, MA). RNA quality was analyzed with the Bioanalyzer (Agilent Biotechnologies, Santa Clara, CA) using the RNA 6000 Nano kit according to the manufacturer’s instructions. Only samples displaying an A260/A280 ratio of 2.0-2.1 and a RIN (RNA Integrity Number) > 9 were used for hybridization to the arrays.
|
| Label |
biotin
|
| Label protocol |
Samples were labeled with Biotin Allonamide Triphosphate according to the GeneChip Whole Transcriptome Labeling and Hybridization protocol (http://www.affymetrix.com) the Affymetrix GeneChip WT PLUS Reagent Kit (Thermo Fisher Scientific, Waltham, MA).
|
| |
|
| Hybridization protocol |
Arrays were washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Hybridization, Wash and Stain Kit according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
|
| Scan protocol |
Arrays were scanned on a GeneArray Scanner 3000 7G, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).
|
| Description |
matrix table name: Matrix-Dp16-E15
Forebrain gene expression data from day 15 embryo
|
| Data processing |
Quality control and normalization were performed using the pipeline at the www.arrayanalysis.org website (Maastricht University, the Netherlands). Normalization was done using the Robust Multichip Average (RMA) algorithm and the MBNI custom CDF (http://brainarray.mbni.med.umich.edu/) version #14 for the mouse gene 1.0 ST array. Normalization output consisted of data for 21225 probe sets each corresponding to unique Entrez Gene IDs.
|
| |
|
| Submission date |
May 22, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Faycal Guedj |
| E-mail(s) |
[email protected]
|
| Phone |
6179456729
|
| Organization name |
National Institute of Health
|
| Department |
NHGRI
|
| Lab |
Bianchi Lab
|
| Street address |
35A Convent DR
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL13730 |
| Series (1) |
| GSE99135 |
Life Span Analysis of Brain Development, Gene Expression and Behavioral Phenotypes in the Ts1Cje, Ts65Dn and Dp16 Mouse Models of Down Syndrome |
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