|
| Status |
Public on Apr 07, 2010 |
| Title |
Es10, Ectocarpus siliculosus tiling array Chip5 |
| 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 |
GPL9935 |
| Series (1) |
| GSE19912 |
A high-resolution transcriptome map of Ectocarpus siliculosus |
|
