|
| Status |
Public on Dec 15, 2015 |
| Title |
B3-Hr0-3 |
| Sample type |
genomic |
| |
|
| Source name |
iCell Neurons 3
|
| Organism |
Homo sapiens |
| Characteristics |
time point: 0 hr
cell type: iCell Neurons
disease state: normal
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
At each timepoint, DNA was extracted by adding 50 ul per well of tissue digestion buffer (100 mM NaCl, 50 mM Tris 8.0, 100 mM EDTA, 1% SDS) along with 2 mg/ml Proteinase K (Denville Scientific; South Plainfield, NJ). The plate was sealed with parafilm and agitated overnight at 55°C using 200 RPM in an Innova orbital shaker (Eppendorf; Enfield, CT). The digested cells from each well was combined and DNA extracted with equal volume of phenol:chloroform (Invitrogen), vortexing for 10 minutes (Lab Vortex-setting of 4) and the samples were centrifuged for 5 minutes at 14000 g. The aqueous phase was collected, extracted with equal volume of chloroform and repeated two times. The DNA was precipitated with equal volume 100% ethanol and centrifuged for 10 minutes as 14000 g. Two washes with 70% ethanol produced a pellet that was air dried for 10 minutes at room temperature and finally dissolved in 50 µl of 10 mM Tris (8.0) for 3 days at 4°C then stored at -70°C.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
B3-Hr0-3
|
| Data processing |
GenomeStudio
Unmethylated and methylated signal intensities
|
| |
|
| Submission date |
Feb 26, 2015 |
| Last update date |
Dec 15, 2015 |
| Contact name |
Wei Zhang |
| E-mail(s) |
wei.zhang1@northwestern.edu
|
| Organization name |
Northwestern University
|
| Street address |
680 N. Lake Shore Drive, Suite 1400
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE66330 |
Evaluation of Inter-Batch Differences in Stem-Cell Derived Neurons |
|
