|
| Status |
Public on May 13, 2020 |
| Title |
naive state H9 [NH9-4] |
| Sample type |
genomic |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
cell type: embryonic stem cells
state: naïve state
passages: 27-31
qc: Passed
|
| Growth protocol |
Naive state H9 and RUES-2 were maintained in naïve state medium(50% glucose-free DMEM/F12(Life Technologies) and 50% glucose-free Neurobasal(Life Technologies), with 5mM glucose, 1mM glutamine, 1% NEAA, 0.1mM β-mercaptoethanol, penicillin–streptomycin, 20 ng/mL recombinant human LIF (Millipore), 5 mg/mL bovine serum albumin (BSA) (Sigma), 18µg/ml human insulin (Sigma), 1 µM PD0325901 (PD, EMD Millipore), and 3 µM CHIR99021 (CH, Stemgent). Cells were passaged every 3 days by using mechanical and (or) enzymatic methods.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted and purified using QIAamp DNA Blood Mini Kit according to standard instructions
|
| Label |
cy3,cy5
|
| Label protocol |
DNA methylation was determined using Illumina MethylationEPIC array with the Infinium HD Assay Methylation Protocol. 500ng of genomic DNA for each samples is bisulfite converted with Zymo Research EZ DNA Methylation-Gold Kit, then 200ng of each converted sample is amplified and fragmented as per the InfiniumHD Assay Methylation Protocol.
|
| |
|
| Hybridization protocol |
Samples are resuspended and loaded into the Methylation EPIC BeadChips and hybridized overnight as per the Infinium HD Assay Methylation Protocol.
|
| Scan protocol |
Following washing, staining, and addition of a protective coating to the BeadChips as per Infinium HD Assay Methylation Protocol, the BeadChips are imaged using the Illumina iScan Reader to measure the fluorescence intensity of each probe for both methylation and unmethylated DNA.
|
| Data processing |
BeadChip data files are analyzed with Illumina's GenomeStudio (v2011.1) methylation module (v1.9.0) to report control normalization with background subtraction methylation data.
|
| |
|
| Submission date |
Jul 28, 2017 |
| Last update date |
May 15, 2020 |
| Contact name |
Jian Feng |
| E-mail(s) |
jianfeng@buffalo.edu
|
| Phone |
716-829-2345
|
| Organization name |
State University of New York at Buffalo
|
| Department |
Department of Physiology and Biophysics
|
| Lab |
Feng Lab
|
| Street address |
955 Main Street, Room 3102
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14203 |
| Country |
USA |
| |
|
| Platform ID |
GPL21145 |
| Series (1) |
| GSE102031 |
Human Naive Pluripotency Attained by Transient Inhibition of mTOR |
|
