Performed qPCR using cDNA from 20110311. This was performed for 2 reps with TIMP3(BB) (SR IDs: 1067 & 1106). Master mix calcs are here. Plate layout, cycling params, etc. can be found in the qPCR Report (see Results).

Results:

qPCR Report (PDF)

qPCR Data File (CFX96)

Performed qPCR using cDNA from 20110311. This was performed for 2 reps with HMGP (SR IDs:359 & 360). Master mix calcs are here. Plate layout, cycling params, etc can be found in the qPCR Report (see Results).

Results:

qPCR Report (PDF)

qPCR Data File (CFX96)

Performed qPCR using cDNA from 20110311. This was performed for additional reps for TIMP3(BB) (SR IDs:1067 & 1106) and HMGP (SR IDs:359 & 360). Master mix calcs are here. Plate layout, cycling params, etc can be found in the qPCR Report (see Results).

Results:

qPCR Report (PDF)

qPCR Data File (CFX96)

Will analyze with PCR Miner and incorporate with previous PCR rep done for PROPS with these two genes. Oddly, samples in wells B09 and H09 have weird melt curves. As such, these samples will be excluded from analysis.

Performed RT on DNased RNA using Promega MMLV RT and Oligo dT according to manufacturer’s protocol, using 1ug of DNased RNA, but in a 50uL reaction. Due to large number of samples, cDNA was made in PCR plate. Plate layout and calcs are here.

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

Results:

qPCR Data File (Opticon): 20100115_113154.tad

Data workup is here: PROPS BB_DH Gene Expression Miner Workup

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.

Results:

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.

Results:

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.

Results:

qPCR Data File (Opticon): 20100111_102001.tad

Data workup: PROPS BB_DH Gene Expression Miner Workup

qPCR was set up on these cDNAs using the following primers:

FP008495.p.cg.6 (“GSTO1″, “Glutathione S-transferase omega-1″) – This was upregulated in BB SOLiD data.

These were run in duplicate to take up a full PCR plate. qPCR set up and plate layout can be found here.

Results:

qPCR Data File (Opticon): 20091231_152520.tad

Data workup: PROPS BB_DH Gene Expression Miner Workup

qPCR was set up on these cDNAs using the following primers:

AJ582629.p.cg.6 (“DEF1″, “Defensin 1″) – This was upregulated in BB SOLiD data.

CB617519.p.cg.6 (“RETST”, “All-trans retinol”) – This was upregulated in BB SOLiD data.

qPCR set up and plate layout can be found here.

Results:

qPCR Data File (Opticon): 20091230_173747.tad

Data workup: PROPS BB_DH Gene Expression Miner Workup

qPCR was set up on these cDNAs using the following primers:

CU684779.p.cg.6 (“SEMSA”, “Semaphorin-SA”) – This was upregulated in BB SOLiD data.

FP004879.p.cg.6 (“TIMP3″, “Metalloproteinase inhibitor 3″) – This was upregulated in BB SOLiD data.

qPCR set up and plate layout can be found here.

Results:

qPCR Data File (Opticon): 20091230_143643.tad

Data workup: PROPS BB_DH Gene Expression Miner Workup

qPCR was set up on these cDNAs using the following primers:

FP010108.p.cg.6 (“DJB12″, “DnaJ homolog subfamily B member 12″) – This was upregulated in DH SOLiD data.

AJ565670.p.cg.6 (“TOP1″, “DNA topoisomerase 1″) – This was upregulated in BB SOLiD data.

qPCR set up and plate layout can be found here.

Results:

qPCR Data File (Opticon): 20091229_164912.tad

Data workup: PROPS BB_DH Gene Expression Miner Workup

qPCR was set up on these cDNAs using the following primers:

EW778389.p.cg.6 (“DPGN”, “Serine protease inhibitor dipetalogastin”) – This was upregulated in DH SOLiD data.

FP001672.p.cg.6 (“PGSC1″, “Peptidoglycan-recognition protein SC1a/b”) – This was upregulated in DH SOLiD data.

Included three primer sets of Emma’s (matrillin, beta tub and chaperonin). These were set up with no template and done in duplicate.

qPCR set up and plate layout can be found here.

Results:

qPCR Data File (Opticon): 20091229_133148.tad

Data workup: PROPS BB_DH Gene Expression Miner Workup

Emma’s “beta tub” primers show some weird fluorescence, however none of the primer sets show any thing in the melting curve analysis.