Tag Archives: Opticon2

qPCR – Manila Clam Larvae cDNA (from August 2012 – Dave’s Notebook)

Ran qPCR on manila clam larvae cDNA that Dave made on 8/7/2012, using the sample sets from 7/29/2011 and 8/5/2011 of the OA manila clam experiment he ran.

Primers used:

Rp_Calmodulin_F/R2 (SR IDs: 1449, 1467)

Rp_Crumbs_F/R (SR IDs: 1477, 1476)

Primers were verified to be in good working order by Dave on 4/1/2012 (see Dave’s notebook).

Master mix calcs are here. Cycling params can be found in the qPCR Data File (see Results). Plate layout and PCR Miner analysis can be found in the qPCR Raw Data file (see Results). All samples run in duplicate.


qPCR Data File(Opticon 2) http://eagle.fish.washington.edu/Arabidopsis/qPCR/Opticon/Sam_20121108_161738.tad

qPCR Raw Data and PCR Miner Analysis (Excel) http://eagle.fish.washington.edu/Arabidopsis/qPCR/Opticon/Sam_20121108_161738.xlsx

Reps look pretty good, although the 4C2 8.5.11 sample has consistently bad reps across all of today’s runs. Data will be shared with Steven for comparison to Dave’s Illumina data. All data was normalized to EF1a expression from later today.


qPCR – DNased Manila Clam Larvae RNA (from August 2012 – Dave’s Notebook)

Performed qPCR on Dave’s manila clam larvae DNased RNA from August 2012 using EF1a primers (SR IDs: 1463, 1474).

Master mix calcs are here. https://docs.google.com/spreadsheet/ccc?key=0AmS_90rPaQMzdHc5amwzZzdDa1d0VXQzLVU0WkFTc0E

Plate layout, cycling params, etc can be found in the qPCR Report (see Results).

Positive control was pooled cDNA taken from Dave’s cDNA plate on 8/7/2012.


qPCR Data File(CFX96) http://eagle.fish.washington.edu/Arabidopsis/qPCR/CFX96/Roberts%20Lab_2012-10-26%2010-48-07_CC009827.pcrd

qPCR Report(PDF) http://eagle.fish.washington.edu/Arabidopsis/qPCR/CFX96/Roberts%20Lab_2012-10-26%2010-48-07_CC009827.pdf

Here’s a quick Google Spreadsheet summary highlighting samples that came up positive/negative.


Approximately half of the samples (~27) came up positive for still having gDNA in them.

There are three pCO2 treatments: 1000ppm, 750ppm, and 400ppm. There are six sampling dates: 7/29/2011, 8/2/2011, 8/9/2011, 8/12/2011. Currently, it is unknown when the Day 0 samples were collected. Have emailed Dave for deets.

There are only two dates (7/29/2011 and 8/5/2011) that have a full set of samples (i.e. 1000ppm, 750ppm and 400ppm) that exhibit DNA-free RNA. Will discuss with Steven on how to proceed.

UPDATE 20121031 – Dave emailed and indicated the experimented started on 7/27/2011. Additionally, the two sample sets that are complete are Day 2 and Day 7. Discussing with Steven, we have decided to run a few genes and see how the expression levels compare to the NGS data analysis for these samples. If the qPCR data supports the NGS data, then that information will be relayed to the BMC Genomics reviewers in response to their critiques. A copy of the manuscript is here(may not be publicly viewable). https://docs.google.com/document/d/1Ii1lODz2oThiyxZtHBblUEdzyhIVq92n8jkEjhkuuts/edit


qPCR – COX qPCR Vibrio Exposure Response Check

Used COX primers (SR IDs 1060, 1061) and cDNA from 20080327, which consisted of 7 control gigas gill and 7 vibrio-exposed (24hrs) gigas gill samples, labeled as C# and VE#, respectively. The experiment was a 24hr. exposure live Vibrio vulnificus, parahaemolyticus Cf = 2.055×10^11 (6.85×10^7 Vibrio cells/oyster).
Note: Used a free sample of 2x Brilliant III Ultra Fast SYBR Green QPCR Master Mix (Stratagene) for this qPCR. Mixed components and set up cycling params according to the manufacturer’s recommendation for the BioRad CFX96.

Master mix calcs are here. Plate layout, cycling params, etc. can be see in the qPCR Report (see Results).


qPCR Report (PDF).

PCR Miner analysis is here. There appears to be an increase in COX expression in samples exposed to Vibrio sp. (see graph below), however, I have not determined if the results are significant.


qPCR – Test Plate for Opticon 2

Ran a full plate for testing well-to-well consistency (or, inconsistency!) of the Opticon 2, since it’s been behaving poorly lately. This will provide us with an idea of whether or not the oddities that we’ve been witnessing have any effect on our actual data.

Used C.gigas gDNA (DH15 from 20100519; 0.5128ug/uL) and IL17 Internal Fw/Rv primers (SR ID: 255, 256), which have previously produced an amplicon with gDNA. Master mix calcs/plate layout/cycling parameters/etc are here.

DNA was combined in master mix so that all wells received ~100ng of gDNA.



Opticon Calibration

Distributed 50uL of FAM calibration dye to wells. Ran out of dye!!

Looking back at old purchasing logs, it turns out we need 2 orders of dye packs to have enough for a 96-well plate.

Will cap existing plate with dye, wrap in foil and store @ -20C.

Ordered an additional pack of dye (Cat# 10006046; not available online, must call BioRad to order). Will ship on Monday. Will finish calibration procedure on Tuesday (20100928). Ugh.


Empty Plate:

Plate with dye (presumably calibrated):

After running the calibration protocol with the dye, all the wells should show consistent fluorescence levels. Clearly, they do not. Oddly enough, there appears to be a cyclical pattern across the wells of low -> high -> low fluorescence. The calibration protocol advises that if the wells do not exhibit consistent fluorescence across wells, then the plate should be read again. The graph above is the 2nd reading, which appears to be the same as the 1st. Conclusion is that the Opticon 2 is not working correctly and will contact BioRad for price quotes on repairs.


qPCRs – Mac’s BB/DH cDNA from 20091223

GNRR2 and CALL primer sets used. These are duplicates based on initial differences seen between BB and DH expression. qPCR set up and plate layout is here.


qPCR Data File (Opticon): 20100111_180230.tad

Data workup: PROPS BB_DH Gene Expression Miner Workup


SPI and CP17A primer sets used. These are duplicates based on initial differences seen between BB and DH expression. qPCR set up and plate layout is here.


qPCR Data File (Opticon): 20100111_141711.tad

Data workup: PROPS BB_DH Gene Expression Miner Workup


EF1 primers in duplicate, since I had not done these primers yet. qPCR set up and plate layout is here.


qPCR Data File (Opticon): 20100111_102001.tad

Data workup: PROPS BB_DH Gene Expression Miner Workup



qPCRs – Tim’s Adult Gigas gill cDNA (from 20091009)

Duplicates of earlier qPCRs.

Primers: Cg_P450 and TNFRAF_5’/3′.

qPCR set up and plate layout are here.



Duplicates of earlier qPCRs.

Primers: Cg_IkB_F997, R1213 and Cg_Prx6_F270, R439.

qPCR set up and plate layout can be found here.