|
| Status |
Public on Mar 17, 2017 |
| Title |
HB9EBs_NCAR125_9wk_24h |
| Sample type |
RNA |
| |
|
| Source name |
Embryoid bodies containing motor neurons
|
| Organism |
Mus musculus |
| Characteristics |
strain: F1 progeny of two different strains (C57BL/6 and SJL)
time point: 9 weeks cultures
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embryoid bodies were harvested by centrifugation and RNA was isolated using Trizol® according to the manufacturer’s recommendations.
|
| Label |
biotin
|
| Label protocol |
The GeneChip® WT Terminal Labeling and Hybridization Kit (Affymetrix) was used according to the manufactures recommendations.
|
| |
|
| Hybridization protocol |
Total RNA samples were checked for quality (Agilent Bioanalyzer 2100) and quantity/concentration levels (NanoDrop ND-1000 spectrophotometer) and 0.1 μg of high quality RNA samples were processed for hybridization on GeneChip® Mouse Exon ST microarrays (Affymetrix) following manufacturers recommendations to generate amplified and biotinylated sense-strand (ss) DNA targets from the expressed genome using the Ambion® Whole Transcript (WT) Expression Kit. Samples were then labeled using the GeneChip® WT Terminal Labeling and Hybridization Kit (Affymetrix).
|
| Scan protocol |
Affymetrix 7G GeneChip Scanner
|
| Description |
Treated with serum from WT littermate of the mutant mice
|
| Data processing |
Microarray data from each batch of neurons were analyzed together using Affymetrix Expression Console™ software, and gene-level expression values were used to generate Pearson’s r scores for each array. Average Pearson’s r scores were evaluated using a Grubbs’ test (two-sided, alpha = 0.05) to identify outliers, which were removed from the data set. Gene expression data was derived from exon array data using the Robust Multi-array Averaging (RMA) [11] algorithm as implemented in the [R] Aroma Affymetrix package [12]. Gene expression was then estimated as the mean expression of all exons in each gene as annotated by release 33 of the Affymetrix MoEx-1_0-st-v1 annotation files.
|
| |
|
| Submission date |
Mar 03, 2017 |
| Last update date |
Mar 17, 2017 |
| Contact name |
G. Adam Whitney |
| Organization name |
PreCyte
|
| Department |
Bioinformatics
|
| Street address |
401 Terry Ave.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98103 |
| Country |
USA |
| |
|
| Platform ID |
GPL23148 |
| Series (2) |
| GSE95659 |
Gene expression from embryoid bodies derived from HBG3 HB9 ES cells exposed to serum from mice carrying an ALS causing mutation, or non-carrier littermates. |
| GSE95843 |
Gene expression from embryoid bodies derived from HBG3 HB9 ES cells |
|
