|
| Status |
Public on Mar 13, 2010 |
| Title |
SPurpuratus_BoilerBay_Individual37 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Tube foot tissue
|
| Organism |
Strongylocentrotus purpuratus |
| Characteristics |
developmental stage: adult
test: restriction digested DNA
|
| Growth protocol |
Animals were collected from the field, then maintained in common garden conditions in flow-through outdoor aquaria at the Hopkins Marine Station in Monterey, CA.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using Nucleospin extraction protocols (Macherey & Nagel).
|
| Label |
Cy3
|
| Label protocol |
DNA was labeled and purified using the BioPrime labeling kit (Invitrogen) and Cy-dyes (Amersham) following manufacturers instructions.
|
| |
|
| Channel 2 |
| Source name |
Tube foot tissue
|
| Organism |
Strongylocentrotus purpuratus |
| Characteristics |
developmental stage: adult
reference: not restriction digested DNA
|
| Growth protocol |
Animals were collected from the field, then maintained in common garden conditions in flow-through outdoor aquaria at the Hopkins Marine Station in Monterey, CA.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using Nucleospin extraction protocols (Macherey & Nagel).
|
| Label |
Cy5
|
| Label protocol |
DNA was labeled and purified using the BioPrime labeling kit (Invitrogen) and Cy-dyes (Amersham) following manufacturers instructions.
|
| |
|
| |
| Hybridization protocol |
DNA was hybridized to Agilent 244K custom arrays using Agilent's aCGH hybridization buffer kit, hyb chambers, oven, and aCGH Wash Buffers I and II following Agilent aCGH protocols.
|
| Scan protocol |
Arrays were scanned using the Axon GenePix Scanner 4000B.
Images were quantified using Agilent's Feature Extraction software (9.5.3).
|
| Description |
ch1 (Cy3) was restriction digested, ch2 (Cy5) was treated as control.
|
| Data processing |
Data were processed using Feature Extraction default settings: LOWESS normalized and background subtracted resulting in log2 of processed Red signal : processed Green signal.
Data from triplicate features on a single array showed very low variation and were averaged in further analyses. GE, GL, and UP probes centered on cut sites (X) are presented in the Series GSE20857 data table.
|
| |
|
| Submission date |
Mar 12, 2010 |
| Last update date |
Mar 12, 2010 |
| Contact name |
Melissa Pespeni |
| E-mail(s) |
[email protected]
|
| Organization name |
Stanford University
|
| Department |
Biology
|
| Lab |
Palumbi
|
| Street address |
120 Oceanview Blvd.
|
| City |
Pacific Grove |
| State/province |
CA |
| ZIP/Postal code |
93950 |
| Country |
USA |
| |
|
| Platform ID |
GPL10171 |
| Series (1) |
| GSE20857 |
Development of the Restriction Site Tiling Analysis (RSTA) method: Accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays |
|
