Tag Archives: SOLiD libraries

SOLiD – Retrieved SOLiD Library Samples from CEG from 20101213

Retrieved the following SOLiD libraries from the CEG and stored in -80C in the “NGS Libraries” Box.

CC SOLiD Library (20010408 13.8ng/uL)

Herring 2L HKOD09 SOLiD Library (20091209 76.1ng/uL)

Herring 3L HSITK09 SOLiD Library (20091209 88.5ng/uL)

Herring 4L HTOG09 SOLiD Library (20091209 20.1ng/uL)

Herring 6L HPWS09 SOLiD Library (20091209 51.4ng/uL)

HPWS09 SOLiD Library (20010408 9.29ng/uL)

PQ SOLid Library (20100408 20.77ng/uL)

Sisco SOLiD Library (20100408 42.29ng/uL)

CE SOLiD Library (20100408 23.01ng/uL)

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SOLiD ePCR/Templated Bead Prep – Lake Trout Lean library

ePCR was performed following ABI’s “full scale” protocol, using 1pM of SOLiD cDNA library.

Templated bead preparation was performed according to the “full scale” protocol.

Bead counts are calculated as follows:

Avg bead count x # hemacytometer squares x volume in hemacytometer (uL) x dilution factor = beads/uL x suspension volume (uL) = total beads

Initial Bead count: (1:200 dilution)

Lean: 126, 138, 122, 138 Avg. = 131

Lean: 131 x 25 x 10 x 200 = 6.55×10^6 beads/uL x 200uL = 1.31×10^9 beads

Templated Bead counts (1:10 dilution)

Lean: 165, 171, 186, 160 Avg. = 170.5

170.5 x 25 x 10 x 10 = 426250 beads/uL x 400uL = 1.705×10^8 beads

Percent Recovery Templated Beads

Lean: (1.705×10^8 beads)/(1.31×10^9 beads) x 100 = 13.02% recovery

Results: Yield is significantly higher than the previous preparation performed with this sample. The percent recovery falls into the desired range of 5-15%, so things look good there, too. Will contact Rhonda and get info regarding when this and the other 7 samples can go on a run.

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SOLiD Templated Bead Prep – Yellow perch CT, WB and lake trout Lean libraries (continued from yesterday)

Templated bead preparation was performed according to the “full scale” protocol.

Bead counts are calculated as follows:

Avg bead count x # hemacytometer squares x volume in hemacytometer (uL) x dilution factor = beads/uL x suspension volume (uL) = total beads

Initial Bead counts: (1:200 dilution)

CT: 132, 133, 127, 136 Avg. = 132

WB: 127, 128, 119, 126 Avg. = 125

Lean: 121, 114, 132, 109 Avg. = 119

CT: 132 x 25 x 10 x 200 = 6.6×10^6 beads/uL x 200uL = 1.32×10^9 beads

WB: 125 x 25 x 10 x 200 = 6.25×10^6 beads/uL x 200uL = 1.25×10^9 beads

Lean: 119 x 25 x 10 x 200 = 5.95×10^6 beads/uL x 200uL = 1.19×10^9 beads

Templated Bead counts (1:10 dilution)

CT: 91, 80, 100, 78 Avg. = 87.25

WB: 69, 70, 75, 65 Avg. = 69.75

Lean: 40, 52, 48, 46 Avg. = 46.5

CT: 87.25 x 25 x 10 x 10 = 218125 beads/uL x 400uL = 8.7525×10^7 beads

WB: 39.75 x 25 x 10 x 10 = 174375 beads/uL x 400uL = 6.975×10^7 beads

Lean: 46.5 x 25 x 10 x 10 = 116250 beads/uL x 400uL = 4.65×10^7 beads

Percent Recovery Templated Beads

CT: (8.7252×10^7 beads)/(1.32×10^9 beads) x 100 = 6.61%

WB: (6.975×10^7 beads)/(1.25×10^9 beads) x 100 = 5.58%

Lean: (4.65×10^7 beads)/(1.19×10^9 beads) x 100 = 3.91%

Results: Everything looks pretty darn good. One mild concern, however, is the yield from the the Lean library. An 8-well slide requires 41 million beads for a run. Additionally, I believe 15 million are needed for a WFA (quality check, pre-run). This means that the Lean prep is nearly 10 million beads short of what is necessary for a “complete” run of this sample. Will send the numbers to Rhonda and see what her opinion is and what she suggests to do. But, based on the percent recovery, all the samples should be really high quality (extremely few polyclonal beads).

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SOLiD ePCRs – Yellow perch CT, WB and lake trout Lean libraries

Performed ePCRs on these samples from DATE, following the “full scale” protocol. A work flow analysis (WFA) run on these samples from the initial ePCRs/templated bead prep (DATE) revealed too many polyclonal beads, thus requiring them to be redone. ePCRs will be performed using 1.0pM (120pg/uL) of the SOLiD cDNA fragment libraries, instead of the 1.5pM (180pg/uL) used previously.

CT –

WB –

Lean -

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Templated Bead Prep SOLiD Libraries – Yellow perch WB, lake trout Lean and Sisco, and herring G/O HWS09 libraries

All libraries were prepped according to ABI’s “full-scale” bead prep protocol. Initial bead counts were performed using a hemocytometer in a 1:200 dilution:

Formula for calculating bead counts:

Average hemo count x hemo volume x hemo squares x dilution x bead volume

Initial Bead Counts

WB: 111, 96, 90, 100 Average = 99.25 Count: 99.25 x 10 x 25 x 200 x 200 = 9.925 x 10^8 beads

Lean: 101, 100, 108, 108 Average = 104.25 Count: 104.25 x 10 x 25 x 200 x 200 = 1.0425 x 10^9 beads

Sisco: 142, 144, 120, 112 Average = 129.5 Count: 129.5 x 10 x 25 x 200 x 200 = 1.295 x 10^9 beads

HPWS09: 112, 115, 105, 104 Average = 109 Count: 109 x 10 x 25 x 200 x 200 = 1.09 x 10^9 beads

Templated Bead Counts

Templated bead counts were performed using a hemocytometer with a 1:10 dilution:

WB: 198, 186, 198, 175 Average = 189.25 Count: 189.25 x 10 x 25 x 10 x 400 = 1.8925 x 10^8 beads

Lean: 253, 259, 236, 244 Average = 248 Count: 248 x 10 x 25 x 10 x 400 = 2.48 x 10^8 beads

Sisco: 267, 241, 252, 255 Average = 253.75 Count: 253.75 x 10 x 25 x 10 x 400 = 2.5375 x 10^8 beads

HPWS09: 193, 193, 172, 186 Average = 186 Count: 186 x 10 x 25 x 10 x 400 = 1.86 x 10^8 beads

Templated Bead Recovery: Final bead count divided by initial bead count x 100 = % recovery

WB = 1.8925 x 10^8/9.925 x 10^8 x 100 = 19.07%

Lean = 2.48 x 10^8/1.0425 x 10^9 x 100 = 23.8%

Sisco = 2.5375 x 10^8/1.295 x 10^9 x 100 = 24.34%

HPWS09 = 1.86 x 10^8/1.09 x 10^9 x 100 = 17.06%

Results: Yields of templated beads look fabulous. Recoveries of templated beads are a bit on the high side (desired recoveries are between 5-15%, with 20% being the “cutoff” that Rhonda’s lab uses for runs. The Lean and Sisco samples cross this cutoff value. Will consult with Steven to see what how he wants to proceed (i.e. new ePCRs?). Beads stored @ 4C until ready for running on the SOLiD.

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ePCR SOLiD Libraries – Lake Trout Sisco and Herring G/O HPWS09 libraries (from 20100408)

ePCR was performed for the above three mentioned SOLiD libraries using 1.5pM (180 pg/uL) of cDNA, according to the ABI “full scale” ePCR protocol. ePCRs were stored @ 4C until ready for the emulsion breaking step.

Amounts of cDNA used to make dilutions (in 1x Low TE Buffer) of 180pg/uL:

Sisco (42.29 ng/uL): 2.13uL in 500uL

HPWS09 (9.29 ng/uL): 1.94uL in 100uL

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Templated Bead Prep SOLiD Libraries – Abalone CC, CE pools and yellow perch CT, PQ libraries

All libraries were prepped according to ABI’s “full-scale” bead prep protocol. Initial bead counts were performed using a hemocytometer in a 1:200 dilution:

Formula for calculating bead counts:

Average hemo count x hemo volume x hemo squares x dilution x bead volume

Initial Bead Counts

CC: 127, 120, 126, 113. Average = 96 Count: 96 x 10 x 25 x 200 x 200 = 9.6 x 10^8 beads

CE: 99, 93, 115, 102. Average = 102.25 Count: 102.25 x 10 x 25 x 200 x 200 = 1.0225 x 10^9 beads

CT: 118, 113, 109, 111. Average = 112.75 Count: 112.75 x 10 x 25 x 200 x 200 = 1.1275 x 10^9 beads

PQ: 109, 116, 111, 86. Average = 105.5 Count: 105.5 x 10 x 25 x 200 x 200 = 1.055 x 10^9 beads

Templated Bead Counts

Templated bead counts were performed using a hemocytometer with a 1:10 dilution:

CC: 217, 226, 208, 219 Average = 217.5 Count: 217.5 x 10 x 25 x 10 x 400 = 2.175 x 10^8 beads

CE: 211, 169, 162, 180 Average = 180.5 Count: 180.5 x 10 x 25 x 10 x 400 = 1.805 x 10^8 beads

CT: 223, 219, 254, 214 Average = 227.5 Count: 227.5 x 10 x 25 x 10 x 400 = 2.275 x 10^8 beads

PQ: 176, 177, 161, 163 Average = 169.25 Count: 169.25 x 10 x 25 x 10 x 400 = 1.6925 x 10^8 beads

Templated Bead Recovery: Final bead count divided by initial bead count x 100 = % recovery

CC = 2.17 x 10^8 beads/9.6 x 10^8 beads x 100 = 22.7%

CE = 1.805 x10^8 beads/10.225 x 10^8 beads x 100 = 17.7%

CT = 2.275 x 10^8 beads/11.275 x 10^8 beads x 100 = 20.2%

PQ = 1.6925 x 10^8 beads/10.55 x 10^8 beads x 100 = 16.04%

Results: Yields of templated beads look fabulous. Recoveries of templated beads are a bit on the high side (desired recoveries are between 5-15%, with 20% being the “cutoff” that Rhonda’s lab uses for runs. The CC and CT samples cross this cutoff value. Will consult with Steven to see what how he wants to proceed (i.e. new ePCRs?). Beads stored @ 4C until ready for running on the SOLiD.

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ePCR SOLiD Libraries – Yellow perch PQ, WB and Lake Trout Lean libraries (from 20100408)

ePCR was performed for the above three mentioned SOLiD libraries using 1.5pM (180 pg/uL) of cDNA, according to the ABI “full scale” ePCR protocol. ePCRs were stored @ 4C until ready for the emulsion breaking step.

Amounts of cDNA used to make dilutions (in 1x Low TE Buffer) of 180pg/uL:

PQ (20.77ng/uL): 4.33uL in 500uL

WB (16.81ng/uL): 2.14uL in 200uL

Lean (53.49ng/uL): 1.68uL in 500uL

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ePCR SOLiD Libraries – Abalone CC, CE pools and yellow perch CT SOLiD libraries (from 20100408)

Emulsion PCR (ePCR) was performed for the above three mentioned SOLiD libraries using 1.5pM (180 pg/uL) of cDNA, according to the ABI “full scale” ePCR protocol. ePCRs were stored @ 4C until ready for the emulsion breaking step.

Amounts of cDNA used to make dilutions (in 1x Low TE Buffer) of 180pg/uL:

CC (13.8ng/uL): 1.3uL in 100uL

CE (23.01ng/uL): 1.56uL in 200uL

CT (63.8ng/uL): 1.41 in 500uL

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cDNA clean up & Bioanalyzer for SOLiD Libraries – Abalone, Yellow Perch, Lake Trout, Herring

Amplified cDNA was cleaned up using the Invitrogen PureLink Micro Kit, but was done so according to Ambion’s Whole Transcriptome Analysis Kit protocol and then spec’d.

Results:

0.5uL was removed from each sample and mixed with 0.5uL to run on DNA 1000 chips on the Bioanalyzer 2100. The slideshow below shows the electropherograms from each sample. Each sample (to be considered worthy of moving to the next stage) should have <20% of the sample in the 25-150bp range. All 8 samples exhibit this and their peaks look very good. Will proceed to ePCR/templated bead prep next week.

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