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Status |
Public on Feb 08, 2011 |
Title |
ZF4 Repl 3 |
Sample type |
RNA |
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|
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.
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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).
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Description |
Gene expression in ZF4 cells
|
Data processing |
Data processed with Bioconductor package Limma (3.4.4); backgroundCorrect('normexp', offset=50); normalizeBetweenArrays(method='quantile')
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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 |
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