Matt:LabNotes/2015-6-17
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Decoding MotorNeurons_DARTFISH1[edit]
- Motor Neurons from Gene Yeo lab (Sebastian)
- Only decoded DARTFISH1 sample (fixed at RT for 15min) because universal rolony check showed no difference
- Repeat with suppressor oligos
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]
- Saved in: Documents\RolonyImages\6-17-2015\MotorNeurons_DARTFISH1\Aligned\MotorNeurons_06-17-2015
- Summary results for 8 positions
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 |