Matt:LabNotes/2015-7-11: Difference between revisions
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>Mzcai (Created page with "==Decoding MotorNeurons_DARTFISHsuppv2== * DARTFISH rolonies generated here **Sample: [[Matt:LabNotes/2015-6-18 | second batch iPS derived motor n...") |
>Mzcai mNo edit summary |
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===Results=== | ===Results=== | ||
*Saved in: Documents\RolonyImages\7-11-2015\MotorNeurons_DARTFISHsuppv2\Aligned\MotorNeurons_07-11-2015 | *Saved in: Documents\RolonyImages\7-11-2015\MotorNeurons_DARTFISHsuppv2\Aligned\MotorNeurons_07-11-2015 | ||
*[[Media: | *[[Media:Summary_MotorNeurons_07-11-2015_Try_1.xlsx | Summary results for 8 positions]] | ||
**Dropbox\GradZhangLab\DecodeData | |||
==== | ====Pos6 Example==== | ||
[[File: | [[File:Comp_MotorNeurons_07-11-2015_Pos6_Try_1.png | 500px]] | ||
{| {{table}} | {| {{table}} | ||
| align="center" style="background:#f0f0f0;"|'''Color''' | | align="center" style="background:#f0f0f0;"|'''Color''' | ||
Line 23: | Line 22: | ||
| align="center" style="background:#f0f0f0;"|'''Count''' | | align="center" style="background:#f0f0f0;"|'''Count''' | ||
|- | |- | ||
| Red|| | | 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==== | ====Top 20 Detected Genes==== | ||
Line 72: | Line 57: | ||
| align="center" style="background:#f0f0f0;"|'''Count''' | | align="center" style="background:#f0f0f0;"|'''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==== | ====Top 25 Normalized Detected Genes==== | ||
*Normalized with | *Normalized with CA12kNov14suppv2-gDNA_H1H2_sorted_filtered_Genecounts.txt | ||
{| {{table}} | {| {{table}} | ||
| align="center" style="background:#f0f0f0;"|'''Gene''' | | align="center" style="background:#f0f0f0;"|'''Gene''' | ||
| align="center" style="background:#f0f0f0;"|''' | | align="center" style="background:#f0f0f0;"|'''Count''' | ||
| align="center" style="background:#f0f0f0;"|'''invitro | | align="center" style="background:#f0f0f0;"|'''invitro''' | ||
| align="center" style="background:#f0f0f0;"|'''Normalized | | align="center" style="background:#f0f0f0;"|'''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|| | | 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|| | | 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 | ||
|} | |} |
Latest revision as of 22:30, 14 July 2015
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 |