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 |