|
| Status |
Public on Sep 18, 2015 |
| Title |
A2 iPS cells, 4d, cholesterol deficient, biological replicate 4 |
| Sample type |
RNA |
| |
|
| Source name |
A2 iPS cells_4d_cholesterol deficient
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A2
cell type: SLOS iPS cell line
genotype/vairation: DHCR7 mutant
cultured in: cholesterol deficient condition
time point: 4 days
|
| Treatment protocol |
Cholesterol rich pluripotent culture consisted of human ES cell media (including 20% KOSR, 7.5 ng/mL bFGF) on a MEF feeder layer. Cholesterol deficient culture was performed in mTeSR1 defined pluripotent conditions devoid of feeders.
|
| Growth protocol |
Control (BJ) and SLOS (A2) iPS cell lines cultured in cholesterol rich conditions (0 hr) were transferred to cholesterol deficient conditions. RNA was isolated after 2, 3, 4, 5, and 7 days cholesterol deficient culture.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were collected by scraping and snap frozen in dry ice. All RNA samples were prepared using PicoPure RNA isolation kit. Samples were then treated with the RiobMinus rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).
|
| Label |
biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials. Standard manufacturing protocols were followed for preparation of arrays, washes, and sample loading.
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Description |
A2_4day_4
SLOS iPS cells removed from mTeSR1 media, 4 days culture
|
| Data processing |
Data were processed using Partek software. GCRMA background correction was applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
|
| |
|
| Submission date |
Sep 08, 2014 |
| Last update date |
Sep 18, 2015 |
| Contact name |
Kevin R Francis |
| E-mail(s) |
kevin.francis@nih.gov
|
| Organization name |
National Institutes of Health
|
| Department |
Program on Genomics of Differentiation
|
| Street address |
9000 Rockville Pike Bldg 6B Rm 215
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL5175 |
| Series (1) |
| GSE61203 |
Expression data from control and Smith-Lemli-Opitz syndrome patient-derived iPS cells - comparison of cholesterol deficient and cholesterol rich culture |
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