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Sample GSM580740 Query DataSets for GSM580740
Status Public on Feb 08, 2011
Title ZF4 Repl 3
Sample type RNA
Source name ZF4 cell line
Organism Danio rerio
Characteristics cell line: ZF4
Growth protocol The ZF4 zebrafish embryo-derived cell line (Amerian Type Culture Collection) was cultured in vitro as described earlier (Driever W and Rangini Z (1993) In Vitro Cell Dev Biol Anim 0029A: 749-754).
Extracted molecule total RNA
Extraction protocol Cells (10e6) were suspended in 2 ml Trizol, incubated for 5 min, RNA extracted with chloroform, cells were sedimented (10,000 g). The upper phase was collected, glycogen was added and RNA precipitated with isopropanol for 10 min before centrifugation. The RNA pellet was washed with 75% ethanol and dissolved prior to DNase I treatment and clean-up using the RNeasy Kit (Qiagen). RNA samples were stored at -80oC until processed for microarray.
Label Cy3
Label protocol Total RNA (200 ng) and spike-in control RNA was converted to cDNA, followed by cRNA synthesis and amplification, and then purification of cRNA. We followed the protocol from Agilent: One-Color Microarray-Based Gene Expression Analysis (Low input Quick Amp Labeling). This method uses T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- labeled CTP which generates cy3 labeled fluorescent cRNA.
Hybridization protocol Arrays were hybridized for 17 hours (65 °C) and washed before scanning as per the protocol recommended by Agilent (One-Color Microarray-Based Gene Expression Analysis (Low input Quick Amp Labeling)).
Scan protocol The arrays were scanned with GenePix 4000b (Molecular Devices, Sunnyvale, CA, USA).
Description Gene expression in ZF4 cells
Data processing Data processed with Bioconductor package Limma (3.4.4); backgroundCorrect('normexp', offset=50); normalizeBetweenArrays(method='quantile')
Submission date Aug 17, 2010
Last update date Feb 09, 2011
Contact name Philippe Collas
Organization name University of Oslo
Department Institute of Basic Medical Sciences
Street address PO Box 1112 Blindern
City Oslo
ZIP/Postal code 0317
Country Norway
Platform ID GPL10816
Series (2)
GSE23679 Mapping of H3K4 and H3K27 trimethylation in zebrafish cells (Gene expression)
GSE23872 Mapping of H3K4 and H3K27 trimethylation in zebrafish cells

Data table header descriptions
VALUE Background-subtracted, quantile normalized signal intensity

Data table
1 1471.602
2 51.105
3 53.102
4 53.102
5 52.102
6 53.102
7 52.102
8 52.102
9 55.102
10 51.105
11 52.102
12 129.102
13 122.102
14 53.102
15 51.105
16 74.436
17 53.102
18 72.102
19 51.105
20 82.769

Total number of rows: 45220

Table truncated, full table size 579 Kbytes.

Supplementary file Size Download File type/resource
GSM580740.gpr.gz 3.6 Mb (ftp)(http) GPR
Processed data included within Sample table

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