Matt:LabNotes/2015-7-11

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Decoding MotorNeurons_DARTFISHsuppv2[edit]

Procedure[edit]

  • Did universal Cy3 adpt + 5 cycle decoding on 8 random positions in the dish (Cy5, Cy3, 488)
  • 63x objective, 1x zoom = 184um x 184um FOV
  • 2048pixels x 2048pixels
  • 0.49um z-step size, ~14um total imaging depth

Results[edit]

  • Saved in: Documents\RolonyImages\7-11-2015\MotorNeurons_DARTFISHsuppv2\Aligned\MotorNeurons_07-11-2015
  • Summary results for 8 positions
    • Dropbox\GradZhangLab\DecodeData

Pos6 Example[edit]

File:Comp MotorNeurons 07-11-2015 Pos6 Try 1.png

Color Gene Count
Red MALAT1 146
Lime NEFL 58
Blue KIF5C 43
Yellow SLIT2 34
Cyan UBE3A 26
Magenta MEIS2 24
Silver MIAT 19
Maroon SLIT3 16
Olive ZFHX3 16
Green TENM3 15
Purple SNAP25 14
Teal SEMA6D 13
Navy SEMA3C 11
Maroon QKI 10
Dark red THSD7A 10

Top 20 Detected Genes[edit]

Gene Count
MALAT1 1167
NEFL 516
KIF5C 383
UBE3A 224
SLIT2 219
MEIS2 184
MIAT 145
SEMA6D 145
ZFHX3 138
THSD7A 109
QKI 100
TENM3 96
SEMA3C 89
SLIT3 84
PHKB 78
SNAP25 76
PPFIBP1 71
PCDH7 69
CTNNA2 66
DACH1 56

Top 25 Normalized Detected Genes[edit]

  • Normalized with CA12kNov14suppv2-gDNA_H1H2_sorted_filtered_Genecounts.txt
Gene Count invitro Normalized
MALAT1 1167 442 2.640
NEFL 516 418 1.234
MEIS2 184 294 0.626
TOM1 13 25 0.520
VAV2 4 11 0.364
NAPA 4 12 0.333
SEMA5B 45 143 0.315
DLGAP4 21 67 0.313
KIF5C 383 1248 0.307
SLIT2 219 812 0.270
SLIT3 84 339 0.248
OLFM1 14 57 0.246
NRG1 14 58 0.241
TIMP2 44 191 0.230
SHISA7 14 62 0.226
GPR56 42 245 0.171
QKI 100 688 0.145
MIAT 145 1048 0.138
FAIM2 13 94 0.138
NPTX1 3 22 0.136
CUX2 26 191 0.136
ZFHX3 138 1073 0.129
LRP1 11 95 0.116
SEMA6D 145 1517 0.096
GRIP2 2 23 0.087