|
| Status |
Public on Jan 31, 2024 |
| Title |
Infinium Array: Prelim iPSC BPS 50uM rep 2 |
| Sample type |
genomic |
| |
|
| Source name |
Mouse iPSC
|
| Organism |
Mus musculus |
| Characteristics |
gender: Male
treatment: Control
|
| Treatment protocol |
For all cell types except PGCLCs, 1 μM BPS was added to media gassed with 5% CO2, 5% O2, and balanced N2 and then injected into sealed T-25 cell culture flasks and left to incubate for 24 hours. The media was gassed to ensure enrichment to 5% CO2, which is normally regulated by the cell incubator, limiting the potential for the pH to change in the media during this exposure period due to the absorption of CO2 by incubating cells. Following 24 hours of exposure, media containing BPS was removed and cells were washed and allowed to recover in fresh untreated media (without BPS or EtOH) for 24 hours prior to harvesting. PGCLCs were not suitable for this exposure paradigm as EpiLCs undergo differentiation to PGCLCs in cell aggregates formed in low-adherence round-bottom 96 well plates and cannot be maintained in T-25 sealed flasks. Therefore, diluted BPS was added to PGCLC media and added to cells in round-bottom 96 well plates to incubate for 24 hours prior to a shortened wash and “chase” period of 8 hours prior to cell sorting.
|
| Growth protocol |
See the publication for a full description of specific growth protocols for each cell types included in the study.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was bisulfite-converted with the EZ DNA Methylation Kit (D5001) and modified according to the manufacturer’s recommendations (Zymo Research, CA USA & Illumina, CA USA).
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Mouse Methylation Beadchip Array using standard Illumina Infinium HD Methylation protocol.
|
| Scan protocol |
Arrays were imaged using iScan reader using standard recommended Illumina scanner setting
|
| Description |
Infinium Array Preliminary iPSC BPS 50uM in EtOH rep 2
|
| Data processing |
SeSAMe software v1.20.0
|
| |
|
| Submission date |
Jan 08, 2024 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Jake Dean Lehle |
| E-mail(s) |
jakelehle@gmail.com
|
| Phone |
5129928144
|
| Organization name |
The University of Texas at San Antonio
|
| Department |
NDRB
|
| Lab |
McCarrey
|
| Street address |
16631 Vance Jackson Rd APT#1220
|
| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78249 |
| Country |
USA |
| |
|
| Platform ID |
GPL32685 |
| Series (2) |
| GSE252722 |
Endocrine disruptor-induced epimutagenesis in vitro: Insight into molecular mechanisms [Infinium] |
| GSE252723 |
Endocrine disruptor-induced epimutagenesis in vitro: Insight into molecular mechanisms |
|
