|
| Status |
Public on Oct 04, 2022 |
| Title |
AG05278_XO9 |
| Sample type |
genomic |
| |
|
| Source name |
hiPSC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hiPSC
chromosome composition: XO
|
| Treatment protocol |
n/a
|
| Growth protocol |
hiPSCs were cultured on mitotically inactive mouse embryonic fibroblasts in standard hiPSC media (80% DMEM/F12, 20% Knockout Serum Replacement, 1% Glutamax, 1% Non-Essential Amino Acids, 0.1% β-Mercaptoethanol, and 8ng/mL bFGF), and passaged weekly by manual disruption of 10-20 representative colonies.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For DNA extraction, cells were pelleted and resuspended in cell lysis buffer (10 mM Tris-HCl, pH 8.0; 100 mM NaCl; 10 mM EDTA, pH 8.0; 1% SDS; 200 μg/ml Proteinase K) and incubated at 55°C overnight. DNA was isolated using Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v), precipitated with isopropanol, washed with 70% ethanol, and resuspended in TE buffer.
|
| Label |
cy3,cy5
|
| Label protocol |
Genomic DNA was labeled and hybridized to an 850K version 1.2 bead chip following the Infinium CytoSNP 850K assay reference guide
|
| |
|
| Hybridization protocol |
see label protocol
|
| Scan protocol |
Bead chips were images on a NextSeq 550 instrument (Illumina) using standard recommended Illumina scanner settings
|
| Data processing |
BlueFuse Multi analysis software
Processed data files include: Median log2 ratio (as calculated by BlueFuse Multi)
|
| |
|
| Submission date |
Jun 28, 2022 |
| Last update date |
Oct 04, 2022 |
| Contact name |
Stefan F Pinter |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Connecticut, UConn Health
|
| Department |
Genetics and Genome Sciences
|
| Lab |
Pinter lab
|
| Street address |
263 Farmington Avenue
|
| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06030-6403 |
| Country |
USA |
| |
|
| Platform ID |
GPL19718 |
| Series (2) |
| GSE207107 |
Monosomy X in isogenic human iPSC-derived trophoblast model impacts expression modules preserved in human placenta [CytoSNP-850k] |
| GSE207114 |
Monosomy X in isogenic human iPSC-derived trophoblast model impacts expression modules preserved in human placenta |
|
