|
| Status |
Public on Oct 10, 2011 |
| Title |
gill 7_day 7_elevated pCO2_rep4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
homogenized whole posterior gill 7, exposed to control (39 Pa) pCO2
|
| Organism |
Carcinus maenas |
| Characteristics |
tissue: whole posterior gill 7
exposure: day 7 control pCO2
gender: female
origin: Baltic Sea / Kiel Fjord
|
| Treatment protocol |
After dissection, gills were immediately stored in RNAlater until RNA was isolated.
|
| Growth protocol |
The experiment took place in April 2009 at the IFM-GEOMAR, Kiel, Germany. C. maenas were acclimated for 24h in a flow-through seawater manipulation systen at IFM-GEOMAR and then exposed to 39 or 400 Pa CO2 for 3 or 7 days using an automatic gas mixing facility (Linde gas, HTK Hamburg, Germany). Temperature was held constant at 13 °C, Salinity was app. 15.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Gills were homogenized with an OMNI international TH/G7-196STW for 50 s in 4 ml buffer RLT (of kit as follows). Total RNA was then extracted using the RNeasy Midi-Kit (Qiagen #75144)
|
| Label |
AlexaFluor555
|
| Label protocol |
following provided protocols of SuperScript™ Plus Direct cDNA Labeling System (Invitrogen #L1015-06)
|
| |
|
| Channel 2 |
| Source name |
homogenized whole posterior gill 7, exposed to elevated (400 Pa) pCO2
|
| Organism |
Carcinus maenas |
| Characteristics |
tissue: whole posterior gill 7
exposure: day 7 elevated pCO2
gender: female
origin: Baltic Sea / Kiel Fjord
|
| Treatment protocol |
After dissection, gills were immediately stored in RNAlater until RNA was isolated.
|
| Growth protocol |
The experiment took place in April 2009 at the IFM-GEOMAR, Kiel, Germany. C. maenas were acclimated for 24h in a flow-through seawater manipulation systen at IFM-GEOMAR and then exposed to 39 or 400 Pa CO2 for 3 or 7 days using an automatic gas mixing facility (Linde gas, HTK Hamburg, Germany). Temperature was held constant at 13 °C, Salinity was app. 15.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Gills were homogenized with an OMNI international TH/G7-196STW for 50 s in 4 ml buffer RLT (of kit as follows). Total RNA was then extracted using the RNeasy Midi-Kit (Qiagen #75144)
|
| Label |
AlexaFluor647
|
| Label protocol |
following provided protocols of SuperScript™ Plus Direct cDNA Labeling System (Invitrogen #L1015-06)
|
| |
|
| |
| Hybridization protocol |
following provided protocols by MAUI hybridization system (MAUI Mixer SC Hybridization Chamber mixers, Biomicro Cat.no. 02A00830) + Protnto!Universal Hybridization Kit
|
| Scan protocol |
Axon GenePix 4000B dual wavelength scanner + GenePix 6.0 software
|
| Description |
Contig IDs (CMX) according to Towle DW, Henry RP, Terwilliger NB: Microarray-detected changes in gene expression in gills of green crabs (Carcinus maenas) upon dilution of environmental salinity. Comp.Biochem. Physiol.D 2010.
|
| Data processing |
lowess-normalization (by Acuity 4.0 software; Input parameter: Smoothing = 0.19, Iterations = 3, Delta = 0.01); further processing in Excel: filtering by excluding low-quality features (according to flags assigned by Acuity software 4.0); exluding of features with fluorescence intensity of one or both channels lower than 30 % of the background fluorescence intensity; excluding of features with a variance of more than 20 % in the 4 technical replicated included on one microarray slide for each transcript.
|
| |
|
| Submission date |
Apr 26, 2011 |
| Last update date |
Oct 11, 2011 |
| Contact name |
Sandra Fehsenfeld |
| E-mail(s) |
umfehsen@cc.umanitoba.ca
|
| Organization name |
University of Manitoba
|
| Department |
Biological Science
|
| Street address |
509 Buller Building, 45 Chancellors Circle
|
| City |
Winnipeg |
| State/province |
MB |
| ZIP/Postal code |
R3L 0M7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13453 |
| Series (1) |
| GSE28870 |
Effects of elevated seawater pCO2 on gene expression patterns in the gills of the green crab, Carcinus maenas |
|
