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Sample GSM743689 Query DataSets for GSM743689
Status Public on Dec 25, 2011
Title CC_BJRiPSMPC.1.1.P..3._8.2010 [HuGene-1_0-st]
Sample type RNA
 
Source name BJRiPS_derived_MPCs_+PPAR2_rep3
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_B03_646980.CEL
CC_BJRiPSMPC#1.1(P)(3)_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

Data table header descriptions
ID_REF
VALUE Quantile normalized, median centered(array) gene level expression values from Bioconductor affy package

Data table
ID_REF VALUE
7892501 17.5763998
7892502 40.16449662
7892503 27.163678
7892504 632.759929
7892505 24.81916002
7892506 20.51199638
7892507 48.24800957
7892508 19.58323682
7892509 799.3966644
7892510 11.41241554
7892511 18.94177687
7892512 102.0325131
7892513 20.72041416
7892514 1018.848664
7892515 1479.440544
7892516 27.22790213
7892517 54.82616987
7892518 7.368364153
7892519 38.46941387
7892520 1097.093996

Total number of rows: 32321

Table truncated, full table size 627 Kbytes.




Supplementary file Size Download File type/resource
GSM743689.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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