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Sample GSM72260 Query DataSets for GSM72260
Status Public on Aug 30, 2005
Title ES cells, sample #3(16011321011189)
Sample type RNA
 
Channel 1
Source name ES cells R1
Organism Mus musculus
Characteristics ES cells 129/Sv male
Biomaterial provider Dr. Tilo Kunath
Growth protocol The cells were derived from F1 hybrid mouse between 129X1/SvJ and 129S1/Sv, cultreed on gelatin with LIF; see Nagy et al. Proc. Natl. Acad. Sci. 1993.
Extracted molecule total RNA
Extraction protocol Using the QIAGEN RNeasy midi kit (QIAGEN Inc., Santa Clarita, CA), total RNA was extracted from the diploid-sorted TS cell lines derived from ICR E3.5 blastcysts and the extraembryonic ectoderm of E6. 5 embryos, cultured in the presence of feeder-conditioned medium with FGF4 (details on Tanaka et al. 1998. Science 282: 2072-2075).
Label Cy3
Label protocol Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).
 
Channel 2
Source name Universal Mouse Reference RNA
Organism Mus musculus
Characteristics Universale Mouse Reference
Biomaterial provider Mark Carter
Growth protocol The UMRR is provided in a solution of 70% ethanol and 0.1 M sodium acetate. Prepare the UMRR for use as follows: 1.Centrifuge the tube at 12,000 x g for 15 minutes at 4C. 2.Carefully remove the supernatant. 3.Wash the pellet in 70% ethanol. 4.Centrifuge the tube at 12,000 x g for 15 minutes at 4C. 5.Carefully remove the supernatant and air-dry the pellet at room temperature for 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts
Label Cy5
Label protocol Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).
 
 
Hybridization protocol Agilent 60-mer oligo microarray processing protocol (SSC Wash/SureHyb Chamber set-up) V4.1, April 2004. Agilent Publication Number: G4140-90030 V4.1 APRIL 2004. The manual can be found at https://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=34961, or through a WEB search on the manual title.
Scan protocol Slides were scanned with an Agilent DNA Microarray Scanner model G2505-64120 at 100% PMT in both channels, with a scan resolution of 10um. A scan window of 61 x 21.6 mm was used, then images were cropped to size and saved in a modified two-color TIFF format. Images were examined visually for evidence of foreign debris or major failures. Agilent Microarray Scanner User Manual (6.3) http://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=33696
Description ES cells R1
Data processing Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
 
Submission date Aug 27, 2005
Last update date Feb 05, 2007
Contact name Minoru S.H. Ko
E-mail(s) kom@mail.nih.gov
Phone 410-558-8359
Organization name NIH
Department National Institute on Aging
Lab Lab of Genetics
Street address 251 Bayview Blvd, Suite 100, 10C
City Baltimore
State/province MD
ZIP/Postal code 21224
Country USA
 
Platform ID GPL870
Series (1)
GSE3214 High-throughput screen for genes predominantly expressed in the ICM of mouse blastocysts by whole mount in situ hybridiz

Data table header descriptions
ID_REF Feature Number (FeatureNum)
VALUE The normalized VALUE among all the arrays in the series. It is caculated with the following method: (1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number. (2) Take average of Xri's for the oligo among 6 arrays in the series: AverXr = average(Xri). (3) For each array estimate Yi = Xgi-Xri+AverXr (4) Round Yi to 4 decimal digits. This is used as the normalized VALUE. More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

Data table
ID_REF VALUE
217 3.0847
218 2.8254
219 3.6620
220 2.3638
221 2.6200
222 2.1953
223 2.8842
224 2.0804
225 3.5332
226 2.3446
227 2.5011
228 3.1562
229 2.7830
230 2.7633
231 2.8472
232 2.6567
233 3.4248
234 2.3065
235 2.6960
236 2.6650

Total number of rows: 21939

Table truncated, full table size 268 Kbytes.




Supplementary file Size Download File type/resource
GSM72260.tif.gz 20.4 Mb (ftp)(http) TIFF
GSM72260.txt.gz 3.8 Mb (ftp)(http) TXT

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