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Sample GSM1515783 Query DataSets for GSM1515783
Status Public on Apr 27, 2015
Title kh2_16hrs_rep1
Sample type RNA
 
Source name KH2 cells, 16 hrs RA
Organism Mus musculus
Characteristics cell type: kh2
timepoint: 16hrs after RA
Treatment protocol ES Cells were differentiated with differentiation media (DMEM + 10% Serum + NAA+ 0.03µM RA) RA supplemented 33nm for requisite length of time. Feeders were separated by plating freshly trypsinized cells on gelatinized plate for 30 min. After half an hour media was aspirated and centrifuged for 5 min at 1000 rpm.
Growth protocol KH2 cells at Passage 12 were cultured on gamma irradiated feeder cells with DMEM containg 15% fetal bovine serum, NAA and β-mercaptoethanol.
Extracted molecule total RNA
Extraction protocol RNA isolation was performed using Trizol and later purified by RNA Easy Kit (Quiagen). Total RNA in the amount of 1ug was amplified according to Ambion’s Message Amp II aRNA Amplification Kit, part number AM1751. Positive control RNA from Agilent’s One Color RNA Spike-In Kit, part number 5188-5282, was used to monitor sample amplification and labeling as well as array hybridization.
Label Cy3
Label protocol Amplified mRNA, referred to as aRNA, was quantified on a NanoDrop ND-1000 and a mass of 2ug was labeled with cy3 dye using Kreatech’s ULS Fluorescent Labeling Kit, part number EA-023.
 
Hybridization protocol Labeled aRNA was quantified on the NanoDrop ND-1000 and a 1.5µg mass of cy3 labeled aRNA was hybridized to custom Agilent 2x105K HOX tiling arrays. Hybridizations were performed at 65 degrees C for 17 hours under standard conditions (1X Agilent blocking agent, and 1X Agilent hybridization buffer) and slides were washed successively with Agilent GE wash buffer 1, at room temperature and with Agilent GE wash buffer 2, at 31oC, prior to scanning.
Scan protocol Microarray images were acquired with an Agilent High-Resolution DNA Microarray Scanner (G2505C). Hybridization, array washing, scanning and probe information extraction with Agilent’s Feature Extraction Software (Version 10.5.1.1) were all performed according to Agilent’s One-Color Microarray-Based Gene Expression Analysis Protocol, Version 6.0, December 2009 (Low Input Quick Amp Labeling).
Data processing Agilent tiling arrays were hybridized in a single-color configuration and data was read into R. Agilent gMeanSignal was used as the measurement (mean green signal for each spot). Data was analyzed using the limma package. Data was normalized between arrays using scale normalization. Replicates were averaged and bedgraph files were created and visualized using IGV and UCSC genome browser.
 
Submission date Sep 29, 2014
Last update date Apr 27, 2015
Contact name Madelaine Gogol
Organization name Stowers Institute
Department Computational Biology Core
Street address 1000 E. 50th Street
City Kansas City
State/province MO
ZIP/Postal code 64110
Country USA
 
Platform ID GPL19214
Series (1)
GSE61585 Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters (tiling)

Data table header descriptions
ID_REF
VALUE scale normalized log2 (timepoint/average wt)

Data table
ID_REF VALUE
4 -0.296188715
5 0.382369474
6 -0.317031882
7 -0.231661139
8 0.695359101
9 -0.132735406
10 0.120036859
11 0.134496987
12 0.240269041
13 0.361501343
14 0.59052449
15 0.205032639
16 -0.155228137
17 0.685753733
18 0.087023424
19 0.117553497
20 0.346306478
21 -0.067767246
22 0.140175459
23 0.105332136

Total number of rows: 103446

Table truncated, full table size 1863 Kbytes.




Supplementary file Size Download File type/resource
GSM1515783_252788710006_201005181443_S01_GE1_105_Dec08_1_2.txt.gz 15.3 Mb (ftp)(http) TXT
GSM1515783_t16a.wt.c.bw 504.3 Kb (ftp)(http) BW
GSM1515783_t16a.wt.w.bw 497.0 Kb (ftp)(http) BW
Processed data included within Sample table

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