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Sample GSM497638 Query DataSets for GSM497638
Status Public on Apr 07, 2010
Title Es14, Ectocarpus siliculosus tiling array Chip7
Sample type genomic
 
Source name genomic DNA from ectocarpus
Organism Ectocarpus siliculosus
Characteristics control: Genomic DNA from Ectocarpus siliculosus genome
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from cells of ectocarpus. The DNA extraction protocol described by Apt et al.^2 was optimised for the Ec 32 strain. About one gram of tissue was ground to a powder under liquid nitrogen in a mortar and pestle using sand. After addition of 2 ml of extraction buffer (100 mM Tris-HCl pH 7.5, 1.5 M NaCl, 2% CTAB, 50 mM EDTA pH 4.5, 50 mM DTT) the tissue was extracted further in a Wheaton glass grinding tube. Extraction buffer was then added to 15 ml final volume, the sample shaken vigorously for 10 min and then incubated at 55°C for 2 hours in the presence of 25 units of proteinase K. After extraction with 1 volume of chloroform:isoamyl alcohol (24:1), polysaccharides were precipitated with 0.3 volumes of 100% ethanol and the chloroform-isoamyl alcohol extraction repeated. RNA was then removed by incubation overnight at 20°C in 4M LiCl and 1% beta-mercaptoethanol and centrifugation at 13,000 rpm for 30 min. The DNA was then precipitated from the supernatant by addition of 0.8 volumes of isopropanol, redissolved in 500 µl of Tris EDTA buffer, extracted with phenol:chloroform:isoamyl alcohol (25:24:1) and then with chloroform:isoamyl alcohol (24:1) and precipitated in 0.3 M sodium acetate and 71% ethanol. The DNA was then purified on a CsCl gradient.
Label Cy3
Label protocol Standard Nimblegen protocol was used to generate labeled DNA from genomic DNA.
 
Hybridization protocol Hybridization was performed by Nimblegen at their Iceland core facility using Nimblegen protocol.
Scan protocol Features were scanned using Nimblescan software.
Description A High-Resolution Transcriptome Map of the Ectocarpus siliculosus
Data processing Custom software tools were used for data processing. Quantile normalization was performed with data on all arrays.
 
Submission date Jan 15, 2010
Last update date Apr 07, 2010
Contact name Manoj Samanta
E-mail(s) [email protected]
Phone 408-472-7927
Organization name Systemix Institute
Street address 2240 Homestead Court #309
City Los Altos
State/province CA
ZIP/Postal code 94024
Country USA
 
Platform ID GPL9937
Series (1)
GSE19912 A high-resolution transcriptome map of Ectocarpus siliculosus

Data table header descriptions
ID_REF
VALUE normalized data

Data table
ID_REF VALUE
65733847.279.711 1.15713512465145
65733848.67.119 0.68166963506984
65733849.619.841 0.797977068082611
65733850.285.955 0.548002011529808
65733851.748.726 0.378730315230229
65733852.178.90 0.21724085582809
65733853.484.50 0.290196793055794
65733854.8.212 0.65165299856337
65733855.246.736 0.229710564989438
65733856.4.678 0.726549516175282
65733857.18.714 0.68989924827322
65733858.586.390 1.95379974733274
65733859.255.299 0.927590361419646
65733860.31.111 4.36739976072729
65733861.101.189 0.825428326468435
65733862.72.878 1.28407680962751
65733863.23.169 0.558439343897996
65733864.317.801 0.892345767164883
65733865.647.429 0.415355765572775
65733866.296.894 0.490330731435179

Total number of rows: 386131

Table truncated, full table size 12884 Kbytes.




Supplementary file Size Download File type/resource
GSM497638_8154402_532.pair.gz 5.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

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