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*[[Hosuk:Lab_Notes|LabNote]] ===Decode and Analysis of CA12k_Nov2014_V4 and V7 test samples=== ====Information==== *Samples **S1(V7) and S2(V4) done at [[Hosuk:LabNotes/2015-1-25|1/25]] **S5(V4) at [[Hosuk:LabNotes/2015-1-22|1/22]] *Imaging : 4 Positions per sample, 63x, 2k *'''5 cycles''' *Matt's Barcode - Gene map : [[Media:CA12k_Nov2014_Barcode2GeneKEY.xlsx|Barcode2GeneKEY]] *Matlab version : **[[Media:CA12k_Nov2014_BarcodeGene_V4.mat|BarcodeGene_V4]] **[[Media:CA12k_Nov2014_BarcodeGene_V7.mat|BarcodeGene_V7]] ====Notice==== *3 sample dishes - **(1) S1_V7_012215: Padlock probe concentration '''22.86 nM''' in 100uL Ampligase mix **(2) S2_V4_012215: Padlock probe concentration '''18.67 nM''' in 100uL Ampligase mix **(2) S5_V4_012215: Padlock probe concentration '''100 nM''' in 100uL Ampligase mix *Aligning Failed --> S1_V7_Pos1, S1_V7_Pos4, S5_V4_Pos1, S5_V4_Pos2 --> cannot be analyzed, I'll manually align and proceed analysis later *Miss-alignment(about 10 px off) --> S2_V4_Pos1, S2_V4_Pos4 --> cannot trust analyzed result, I'll manually align and proceed analysis later ====Result : Files==== *'''Summary''' : Excel including 3 different analysis result by changing threshold value for '0' signal decision **--> [[Media:Analysis_2015-01-28_Try1-3.xlsx|Summary Table]] *Images : [[Media:CA12k_Nov2014_Decode_Result_AllRolony_Images.zip|AllRolony_Images]], [[Media:CA12k_Nov2014_Decode_Result_Composite_Images.zip|Composite_Images]] [[File:CA12k_Nov2014_Decode_Result_Table_2015-01-28.png|800px]] *'''Images : All Rolonies *'''S1_V7_012215''' [[File:CA12k_Nov2014_Decode_Result_2015-01-28_AllRolony_S1_V7_012215.png|800px]] *'''S2_V4_012215''' [[File:CA12k_Nov2014_Decode_Result_2015-01-28_AllRolony_S2_V4_012215.png|800px]] *'''S5_V4_012715''' [[File:CA12k_Nov2014_Decode_Result_2015-01-28_AllRolony_S5_V4_012715.png|800px]] *'''Images : Position of Mapped Genes *'''S1_V7_012215''' [[File:CA12k_Nov2014_Decode_Result_2015-01-28_Mapping_S1_V7_012215.png|1000px]] *'''S2_V4_012215''' [[File:CA12k_Nov2014_Decode_Result_2015-01-28_Mapping_S2_V4_012215.png|1000px]] *'''S5_V4_012715''' [[File:CA12k_Nov2014_Decode_Result_2015-01-28_Mapping_S5_V4_012715.png|1000px]] ====Matlab code for this analysis==== *Matlab Code for Decoding and Aanalysis : [[Media:Matlab_FISSEQ_Decoding_2015-01-28.zip|Data_2015-01-28]]
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