Matt:LabNotes/2015-6-17

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Decoding MotorNeurons_DARTFISH1[edit]

Procedure[edit]

  • Did universal Cy3 adpt + 5 cycle decoding on 8 random positions in the dish
  • 63x objective, 1x zoom = 184um x 184um FOV
  • 2048pixels x 2048pixels
  • 0.49um z-step size, ~15um total imaging depth

Results[edit]

Pos1 Example[edit]

File:Plot MotorNeurons 06-17-2015 Pos1 Try 1 F3.png

File:Comp MotorNeurons 06-17-2015 Pos1 Try 1.png

Color Gene Count
Red KCNC2 1011
Lime GNG4 559
Blue PDE1A 148
Yellow ATP1B2 118
Cyan KCNN3 105
Magenta NEFL 75
Silver MALAT1 48
Maroon PTPRK 41
Olive KIF5C 40
Green UBE3A 36
Purple MEIS2 22
Teal SEMA3C 19
Navy ZFHX3 18
Maroon MIAT 15
Dark red SEMA6D 14
Brown SLC1A3 14
Firebrick SLIT2 13
Crimson PLCL1 13
Tomato MAF 12
Coral QKI 11
Indian red SLIT3 10
Light coral CTNNA2 10

Top 20 Detected Genes[edit]

Gene Count
KCNC2 6996
GNG4 3903
PDE1A 1327
ATP1B2 660
KCNN3 593
NEFL 571
KIF5C 363
PTPRK 331
MALAT1 320
UBE3A 193
SLIT2 164
MEIS2 163
ZFHX3 123
SEMA3C 104
CTNNA2 102
PLCL1 98
MIAT 87
SEMA6D 81
SLIT3 70
QKI 70

Top 25 Normalized Detected Genes[edit]

  • Normalized with CA12kNov2014_V4gDNA_R1_H1H2_sorted_filtered_Genecounts.txt
Gene DARTFISH Count invitro Count Normalized Value
NEFL 571 689 0.8287373
ATP1B2 660 822 0.802919708
MALAT1 320 820 0.390243902
VAV2 2 7 0.285714286
DLGAP4 28 100 0.28
MEIS2 163 886 0.183972912
NRG1 20 122 0.163934426
NAPA 4 26 0.153846154
LRP1 18 125 0.144
KIF5C 363 2785 0.130341113
GPR56 39 343 0.113702624
SLIT3 70 643 0.108864697
NPTX1 2 21 0.095238095
TIMP2 29 319 0.090909091
TOM1 3 34 0.088235294
SHISA7 10 115 0.086956522
SEMA5B 17 208 0.081730769
SDK1 4 58 0.068965517
FAIM2 8 122 0.06557377
KCNN3 593 9199 0.064463529
MAF 64 996 0.064257028
SLIT2 164 2594 0.063222822
OLFM1 7 129 0.054263566
THRA 10 192 0.052083333
KCNC2 6996 139037 0.050317541