NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1103820 Query DataSets for GSM1103820
Status Public on Jul 15, 2014
Title U2OS_30iiB-0hr-replicate2
Sample type RNA
 
Source name U2OS_0 hours_ethanol only_30iiB
Organism Homo sapiens
Characteristics cell line: U2OS
time: 0 hours
treatment: ethanol only
expressed allele: 30iiB
Treatment protocol Dexamethasone (Sigma) at a final concentration of 100 nM was added to the medium for 2, 4, or 24 hours (hr); for the “0 hr” time point, cells were treated with vehicle (ethanol) only for 4 hr.
Growth protocol Cells were plated in 6-well plates using DMEM supplemented with 5% v/v fetal bovine serum.
Extracted molecule total RNA
Extraction protocol Cells were lysed and total RNA was isolated using QIAshredder and RNeasy mini columns (Qiagen). The quality of RNA samples was evaluated by A260/A280 ratio which was at least 1.9 and the integrity was analyzed using the Bioanalyzer 2100
(Agilent) with the Experion RNA Stdsens analysis kit (Biorad). For each experimental condition 2 μg of high quality total RNA was submitted to the University of Southern California Epigenome Center.
Label biotin
Label protocol Labeling was done by the University of Southern California Epigenome Center.
 
Hybridization protocol Hybridization was done by the University of Southern California Epigenome Center.
Scan protocol Scanning and image acquisition was done by the University of Southern California Epigenome Center.
Description 4858944020_A
replicate 2
Data processing Bead-level data outputted from Illumina’s BeadScan software were read using the beadarray package from Bioconductor. BASH was used to correct for compact and diffuse spatial artifacts on the arrays. Bead-level data were summarized using
beadarray, filtering out beads that were > 3 MADs from the median (this is the raw data). Probe annotations were retrieved using the illuminaHumanv3.db package from Bioconductor; bad quality probes and probes not corresponding to known
HUGO gene symbols were removed from the data before further processing. Bead summary data were log2 transformed and quantile normalized. We then used the non-parametric empirical Bayes method described by Johnson and Rabinovic to
correct for chip-to-chip batch effects. Detection pvalues were not available after batch correction.
 
Submission date Mar 21, 2013
Last update date Jul 15, 2014
Contact name Benjamin J Schiller
Organization name University of California, San Francisco
Lab Keith Yamamoto
Street address 600 16th St
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
 
Platform ID GPL6883
Series (1)
GSE45407 Gene expression of hormone-treated U2OS cells expressing GR alleles

Data table header descriptions
ID_REF
VALUE log2-transformed, quantile-normalized, and batch-corrected relative expression values

Data table
ID_REF VALUE
ILMN_1802380 9.951258749
ILMN_1792389 8.677702601
ILMN_2375156 7.634251341
ILMN_1697642 10.8286079
ILMN_1681845 10.60010497
ILMN_1690979 7.338554763
ILMN_1811114 7.016869438
ILMN_1660729 7.259406195
ILMN_2129572 8.359915214
ILMN_1705659 7.172321811
ILMN_1797055 9.633074442
ILMN_1670547 7.066809612
ILMN_2342515 8.162848379
ILMN_1800425 10.61995427
ILMN_1783852 7.932851964
ILMN_1721344 9.045259417
ILMN_1679973 7.199354703
ILMN_1701854 11.05899994
ILMN_1678707 11.98893119
ILMN_2276504 7.300705708

Total number of rows: 21241

Table truncated, full table size 516 Kbytes.




Supplementary file Size Download File type/resource
GSM1103820_4858944020_A.tar.gz 20.6 Mb (ftp)(http) TAR
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap