|
| Status |
Public on Dec 25, 2011 |
| Title |
CC_BJRiPSMPC.1.1.P..2._8.2010 [HuGene-1_0-st] |
| Sample type |
RNA |
| |
|
| Source name |
BJRiPS_derived_MPCs_+PPAR2_rep2
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: MPC
agent: PPAR2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from human cell lines or human fat was extracted with Trizol (Invitrogen) and purified via the RNeasy mini kit (Qiagen) according to the manufacturers’ instructions. RNA quality was assessed using an Aglient Bioanalyzer
|
| 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
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Description |
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_B02_647004.CEL
CC_BJRiPSMPC#1.1(P)(2)_8-2010
|
| Data processing |
Data were processed using the BioConductor affy package in R. RMA background correction was applied to probe intensities followed by quantile normalization. Probe set intensities were summarized from individual probes (excluding mismatch probes) using median polished. Gene level intensities were generated by mapping probe sets to refseq annotations. Probe sets that did not map to refseq annotations were not considered in further analyses. Probe Sets mapping to the same genes were median collapsed by gene symbol. Final normalized data was generated by median centering each array after the prior processing.
probe group file: [Exon array] probe group file: HuGene-1_0-st-v1.r4.pgf/HG-U133_Plus_2.pgf
meta-probeset file: [Exon array] meta-probeset file: HuGene-1_0-st-v1.r4.mps/HG-U133_Plus_2.mps
|
| |
|
| Submission date |
Jun 16, 2011 |
| Last update date |
Dec 25, 2011 |
| Contact name |
Tim D Ahfeldt |
| E-mail(s) |
tim.ahfeldt@mssm.edu
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Neuroscience
|
| Lab |
Tim D Ahfeldt
|
| Street address |
1425 Madison Ave
|
| City |
NYC |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (2) |
| GSE30038 |
Programming human pluripotent stem cells into adipocytes [Affymetrix] |
| GSE30041 |
Programming human pluripotent stem cells into adipocytes |
|
