Talk:20.109(S12):Aptamer binding assay (Day7)

Binding Data Files

Group	T/R zip data file	W/F zip data file
Red	Media:S12-M1-TR_Red.csv	Media:S12-M1-WF_Red.csv
Orange	Media:S12-M1-TR_Orange.csv	Media:S12-M1-WF_Orange.csv
Yellow	Media:S12-M1-TR_Yellow.csv	Media:S12-M1-WF_Yellow.csv
Green	Media:S12-M1-TR_Green.csv	Media:S12-M1-WF_Green.csv
Blue	Media:S12-M1-TR_Blue.csv	Media:S12-M1-WF_Blue.csv
Pink	Media:S12-M1-TR_Pink.csv	Media:S12-M1-WF_Pink.csv
Purple	Media:S12-M1-TR_Purple.csv	Media:S12-M1-WF_Purple.csv

Binding Data Results Summary

T/R

* Be sure to post the values you got after baseline correction, not the raw data (if your curves didn't line up)!
* Order: heme, 6-5, 8-12, "pre" mix, post low wash, post high wash
* Recommended syntax for A405 column: "#1 ; #2; #3 <br> #4; #5; #6"

Group	Corrected A405 values*	Pre % 8-12: expected, measured	Post % 8-12: fewer washes, more washes (measured)	Additional comments
Syntax sample	0.1; 0.2; 0.3 0.4; 0.5; 0.6	10%, 12%	40%, 50% (4, 24 washes)	We used Grey group's 6-5 because we didn't have any.
Pink	0.14025053 (heme) 0.1422987 (6-5 pre) 0.21195409 (8-12 pre) 0.13888393 (mix pre) 0.16228816 (4 wash) 0.17831185 (24 wash)	0.5%, -0.049%	28.70% (4 wash), 51.70% (24 wash)	We started with a 0.5% 8-12 mixture and washed with 4 and 24 washes to measure enrichment	Binding Curves - Pink
Orange	0.034495637(heme) 0.03498132(pre6-5) 0.045843026(pre8-12) 0.03623888(pre-mix) 0.041412034 (4 Wash) 0.040929238(24 Wash)	1%, 11.5%	59.2% (4 Washes), 54.7% (24 Washes)	We started with a 1% 8-12 mixture and washed with 4 and 24 washes to measure enrichment. We also generated very little RNA (~.3nmol), and thus had to dilute everything down to this amount.	Error creating thumbnail: File missing Binding Curves - Orange
Yellow	0.155;0.160212;0.2070; 0.1642;0.1768;0.1776	0.25%, 8.6%	35%, 37%(4 and 24 washes)	We started with 0.25% 8-12 mixture and washed with 4 and 24 washes
Red	0.218110 (heme) 0.211707 (6-5 pre) 0.277449 (8-12 pre) 0.215079 (mix pre) 0.237636 (4 wash) 0.256438 (24 wash)	2% (expected) 5.13% (measured)	39.44% (4 washes) 62.91% (24 washes)	Started with 2% 8-12 mixture and washed with 4 and 24 washes.	Error creating thumbnail: File missing Binding Curves - Red
Green	0.182316407(heme) 0.174965575(6-5 pre) 0.257898369(8-12 pre) 0.178721126 (mix pre) 0.185683139 (8 wash) 0.192153301(36 wash)	1% (expected),4.52 %(measured)	12.92, 20.72 % (8 and 36 washes)	Started with 1% 8-12 mixture and washed with 8 and 36 washes.
Purple	0.084126; 0.085602645; 0.13737727; 0.09304013; 0.14838624; 0.12533093	10% (expected), 14.37% (measured)	121.1 % (4 washes), 76.7% (24 washes)	Started with 10% 8-12 mixture and washed with 4 and 24 washes.	Error creating thumbnail: File missing Binding Curves - Purple
Blue	0.0415141 (heme) 0.040754 (6-5 pre) 0.068389 (8-12 pre) 0.05368(mix pre) 0.066094(10 wash) 0.067595 (30 wash)	10% (expected), 46.77% (measured)	91.69% (10 washes), 97.13% (30 washes)	Started with 10% 8-12 mixture and washed with 10 and 30 washes.

W/F

* Be sure to post the values you got after baseline correction, not the raw data (if your curves didn't line up)!
* Order: heme, 6-5, 8-12, "pre" mix, post low wash, post high wash
* Recommended syntax for A405 column: "#1 ; #2; #3 <br> #4; #5; #6"

Group	Corrected A405 values*	Pre % 8-12: expected, measured	Post % 8-12: fewer washes, more washes (measured)	Additional comments
Syntax sample	0.1; 0.2; 0.3 0.4; 0.5; 0.6	10%, 12%	40%, 50% (4, 24 washes)	We used Grey group's 6-5 because we didn't have any.
Purple	0.116802; 0.114059; 0.189595 0.11671; 0.148567 (4degC); 0.161949 (22degC)	2%, 3.51%	45.89% (4degC), 63.39% (22degC)	We varied temperature (4deg, 22degC), keeping 20 washes constant.	Error creating thumbnail: File missing Binding Curves - Purple
Orange	0.172318067; 0.240679354; 0.174157415 0.188253912 (4 washes); 0.18944774(24 washes)	0.5%, 2.69%	23.31% (4 washes), 25.05% (24 washes)	We lowered the pre-selection % of 8-12 keeping average wash conditions of 4 and 24 washes.	Error creating thumbnail: File missing Binding Curves - Orange
Blue	0.139942214; 0.136271253; 0.220732734 0.147463577; 0.179008305 (8 Washes); 0.170598522 (16 Washes)	10.0%, 14.0%	53.4% (8 Washes), 42.9% (16 Washes)
Red	.1380; .1326; .1620 .1320; 1709 (12 washes); .1669 (18 washes); .1678 (24 washes)	10%,negative percentage	more than 100% for all three wash conditions (12, 18, 24)
Green	0.101436131 (heme) 0.116573468 (6-5 pre) 0.175222094 (8-12 pre) 0.143155725 (mix pre) 0.141258046 (24 wash)	50%, 44.26%	41.1% (24 wash)	We lost our other sample (4 washes) due to a problem in either the wash step or the RTPCR step, so we had just one sample.	Error creating thumbnail: File missing Binding Curves - Green
Yellow	0.1091; 0.1751; 0.2597 0.1728; 0.1868; 0.2064	1%, -2.6% (wrong)	14% (4 washes), 37% (24 washes)	Something has definitely gone wrong! We aren't sure what yet, but you may want to exclude our data from your analysis :/	Error creating thumbnail: File missing Binding Curves (Yellow)
Pink	0.16402881 (blank) 0.18001003(heme) 0.17570107 (pre 6-5) 0.22806994 (pre 8-12) 0.18219722 (pre mix) 0.19595873 (2 wash) 0.19819184 (34 wash)	10%, 12.4%	38.7% (2 wash), 42.9% (34 wash)	Error creating thumbnail: File missing Binding Curves (Pink)