Matt:LabNotes/2015-9-29: Difference between revisions
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===Day 2=== | ===Day 2=== | ||
#Wash with 1X PBS once | #Wash with 1X PBS once | ||
#*FISSEQ Dish has very little solution left... but not bone dry | |||
#Add 200ul BS(PEG)9 (20ul BS(PEG)9 + 980ul 1X PBS) and incubate 1hr at RT | #Add 200ul BS(PEG)9 (20ul BS(PEG)9 + 980ul 1X PBS) and incubate 1hr at RT | ||
#*Opened a new BS(PEG)9, couldn't see any solution in the vial but added 465ul DMSO just in case | |||
#*'''THERE WAS NOTHING IN THE VIAL! AFTER 465ul DMSO ADDED FINAL VOLUME 465 WHEN SHOULD BE 565 AND NOT VISCOUS LIKE NORMAL''' | |||
#Wash with 1X PBS twice | #Wash with 1X PBS twice | ||
#Add Tris pH8.0 and incubate 30min at RT | #Add Tris pH8.0 and incubate 30min at RT | ||
Line 58: | Line 61: | ||
#*Add 200ul RNase Mix (100ul RNase H 10X Buffer + 10ul Riboshredder + 50ul RNase H + 840ul H2O) and incubate 1hr at 37C | #*Add 200ul RNase Mix (100ul RNase H 10X Buffer + 10ul Riboshredder + 50ul RNase H + 840ul H2O) and incubate 1hr at 37C | ||
#Wash with H2O twice | #Wash with H2O twice | ||
#To DARTFISH slide: Add 100nM Padlock Probe Mix with 1000X suppv2 oligos and incubate ~1hr at 60C as oven slowly decreases to 55C and held for another ~20hr | #To DARTFISH slide: Add 100nM Padlock Probe Mix with 1000X suppv2 oligos in one sample and only 100nM Padlock Probe Mix in other and incubate ~1hr at 60C as oven slowly decreases to 55C and held for another ~20hr | ||
#*Put in pipette tip box with bottom filled with water and parafilmed around edges of box | #*Put in pipette tip box with bottom filled with water and parafilmed around edges of box | ||
{| {{table}} | {| {{table}} | ||
Line 64: | Line 67: | ||
| align="center" style="background:#f0f0f0;"|'''Volume''' | | align="center" style="background:#f0f0f0;"|'''Volume''' | ||
|- | |- | ||
| DEPC-H2O|| | | DEPC-H2O||33.43 | ||
|- | |- | ||
| Ampligase Buffer||10 | | Ampligase Buffer||10 | ||
|- | |- | ||
| | | Justin's Batch 4 7/13/2015 Padlock Probes 559nM]]||18 | ||
|- | |- | ||
| 100nM suppv2 Oligos || 28.57 | | 100nM suppv2 Oligos || 28.57 | ||
Line 76: | Line 79: | ||
| Total||100 | | Total||100 | ||
|} | |} | ||
#To FISSEQ slide and dish: Add CircLigaseII mix and incuabate 1hr at 60C | {| {{table}} | ||
| align="center" style="background:#f0f0f0;"|'''Component''' | |||
| align="center" style="background:#f0f0f0;"|'''Volume''' | |||
|- | |||
| DEPC-H2O||62 | |||
|- | |||
| Ampligase Buffer||10 | |||
|- | |||
| Justin's Batch 4 7/13/2015 Padlock Probes 559nM]]||18 | |||
|- | |||
| Ampligase||10 | |||
|- | |||
| Total||100 | |||
|} | |||
#To FISSEQ slide and dish: Add 200ul CircLigaseII mix and incuabate 1hr at 60C | |||
#*Put in pipette tip box with bottom filled with water and parafilmed around edges of box | #*Put in pipette tip box with bottom filled with water and parafilmed around edges of box | ||
{| {{table}} | {| {{table}} | ||
Line 82: | Line 99: | ||
| align="center" style="background:#f0f0f0;"|'''Volume''' | | align="center" style="background:#f0f0f0;"|'''Volume''' | ||
|- | |- | ||
| DEPC-H2O|| | | DEPC-H2O||384 | ||
|- | |- | ||
| CircLigase Buffer 10X|| | | CircLigase Buffer 10X||60 | ||
|- | |- | ||
| MnCl2 50mM|| | | MnCl2 50mM||30 | ||
|- | |- | ||
| Betaine 5M|| | | Betaine 5M|| 120 | ||
|- | |- | ||
| CircLigase II (100U/ul)|| | | CircLigase II (100U/ul)||6 | ||
|- | |- | ||
| Total|| | | Total||600 | ||
|} | |} | ||
#Wash FISSEQ samples with PBS and store in PBS at 4C overnight | #Wash FISSEQ samples with PBS and store in PBS at 4C overnight | ||
Line 98: | Line 115: | ||
===Day 3=== | ===Day 3=== | ||
#Wash with 1X PBS once | #Wash with 1X PBS once | ||
# | #To DARTFISH slide add 1uM FISSEQ_ppRCA (2ul 200uM FISSEQ_ppRCA + 398ul 2X SSC + 30% formamide) and incubate 1hr at 55C | ||
#*'''DARTFISH slide was dried out''' | |||
#*'''Edit: the slide may not have dried out so much as leaked. The slide has been leaking since this step.''' | |||
#**Possible the 3M 200M adhesive is not resistant to long term high temp incubation. | |||
#To FISSEQ slide and dish add 1uM FISSEQ_RCA (6ul 100uM FISSEQ_RCA + 594ul 2X SSC + 30% formamide) and incubate 1hr at 55C (should be 60C but only one oven) | |||
#*Preheated to 70C before adding | #*Preheated to 70C before adding | ||
#Wash with 2X SSC once, 1X SSC once, and 1X PBS once | #Wash with 2X SSC once, 1X SSC once, and 1X PBS once | ||
Line 106: | Line 127: | ||
| align="center" style="background:#f0f0f0;"|'''Volume''' | | align="center" style="background:#f0f0f0;"|'''Volume''' | ||
|- | |- | ||
| H2O|| | | H2O||174 | ||
|- | |- | ||
| 10X Phi29 Buffer||20 | | 10X Phi29 Buffer||20 | ||
Line 112: | Line 133: | ||
| 25mM dNTP||2 | | 25mM dNTP||2 | ||
|- | |- | ||
| | | 4mM aa-dUTP||2 | ||
|- | |- | ||
| Phi 29 (low conc)||2 | | Phi 29 (low conc)||2 | ||
Line 119: | Line 140: | ||
|} | |} | ||
#Wash with | #Wash with 1X PBS once | ||
#Add 300ul BS(PEG)9 (6ul BS(PEG)9 + 294ul 1X PBS) and incubate at RT for 1hr | |||
#Add 300ul BS(PEG)9 (6ul BS(PEG)9 + 294ul | |||
#Wash with 1X PBS twice | #Wash with 1X PBS twice | ||
#Add 1M Tris pH 8.0 and incubate at RT for 30min | #Add 1M Tris pH 8.0 and incubate at RT for 30min | ||
#Wash with 1X PBS twice and store in 1X PBS at 4C | #Wash with 1X PBS twice and store in 1X PBS at 4C | ||
==Imaging== | |||
*FISSEQ rolonies in control dish | |||
**Density is low and spots are irregular shapes and sizes | |||
[[File:20151002_BA8FISSEQforHarvard_ControlDish_Position1.jpg|450px]] | |||
[[File:20151002_BA8FISSEQforHarvard_ControlDish_Position2.jpg|450px]] | |||
==Takeaways== | |||
#BS(PEG)9 vial was empty even though brand new, contact Fisher Sci for free replacement | |||
#Attaching 22mmx22mm coverslip to bottom of 18mm diameter hole with 20mm diameter adhesive ring has too much room for error (leaking) | |||
#*Cut 16mm holes in culture dishes and use 16mm diameter adhesive ring | |||
#*Buy new adhesive ([http://www.adhesivesresearch.com/technologies/chemistries/silicone-based-adhesives/ ARclad 7876]) because when it gets old it becomes hard to peel off liner without messing up adhesive | |||
#**Correction: Adhesives Research IS-8458-19 is the adhesive used | |||
#55-60C 20hr incubation dried out DARTFISH glass slide | |||
#*Need foolproof method to prevent evaporation, maybe must use mineral oil layer on top | |||
#*Edit: Leaking actually the problem in this case. Though [http://multimedia.3m.com/mws/media/104064O/high-performance-adhesive-transfer-tapes-with-3m-adhesive-200mp.pdf 3M 300MP adhesive] should be able to withstand 149C temperature for days |
Latest revision as of 02:09, 21 October 2015
FISSEQ and DARTFISH[edit]
- Prepare FISSEQ and DARTFISH samples from human brain tissue (BA8) for Harvard on glass slides
- Two sections per glass slide
- FISSEQ slide just do duplicates
- DARTFISH slide do one without suppressorv2 (tissue close to frosted edge) and one with supperssorv2 (far from frosted edge)
- Two sections per glass slide
- Do one FISSEQ and one DARTFISH in culture dish as control
- DARTFISH coverslip glass cracked
Protocol[edit]
Day 1[edit]
- Prepare 2 plastic culture dishes with hole, tweezers, large plastic dish, and 50C hot plate
- EtOH sterilize and UV
- Made 40ml 4% PFA at RT
- 10ml 16% PFA from ampule + 4ml 10X PBS + 26ml nuclease-free H2O
- Take out BA8 section (2 glass slides and 2 coverslips) from -80C and incubate on 50C hot plate for 3min
- Submerge coverslips in 5ml 4% PFA in 6 well culture plate for 15min at 37C
- Submerge glass slides in 30ml 4%PFA in 50ml tube for 15min at 37C
- Wash with 2X SSPE by submerging
- Aspirate any liquid and attach glass to bottom of culture dish with double-sided adhesive
- Aspirate any liquid and attach gaskets to glass slides
- Add 0.25% TX-100 in 2XSSPE and incubate 5min at RT
- Wash with nuclease-free H2O three times
- Add 0.01% Pepsin in 0.01N HCl and incubate for 5min at 37C
- 2ul 1%Pepsin + 1ul 2N HCl + 197ul H2O
- Wash with nuclease-free PBS three times
- Let sit in PBS for ~10min while preparing RT Mix
- Prepare 5X Reverse Transcription Mix on ice
Components | Volume |
H2O | 157 |
10X M-MuLV Buffer | 20 |
25mM dNTP | 2 |
4mM aa-dUTP | 2 |
100uM N9 or 100uM FISSEQ_RT | 5 |
RNase Inhibitor | 2 |
M-MuLV RTase | 10 |
Total | 200 |
- Incubate 10min at 4C and then ~18hr at 37C
- Put in pipette tip box with bottom filled with water and parafilmed around edges of box
Day 2[edit]
- Wash with 1X PBS once
- FISSEQ Dish has very little solution left... but not bone dry
- Add 200ul BS(PEG)9 (20ul BS(PEG)9 + 980ul 1X PBS) and incubate 1hr at RT
- Opened a new BS(PEG)9, couldn't see any solution in the vial but added 465ul DMSO just in case
- THERE WAS NOTHING IN THE VIAL! AFTER 465ul DMSO ADDED FINAL VOLUME 465 WHEN SHOULD BE 565 AND NOT VISCOUS LIKE NORMAL
- Wash with 1X PBS twice
- Add Tris pH8.0 and incubate 30min at RT
- Wash with 1X PBS twice
- RNA Removal
- Add 200ul RNase Mix (100ul RNase H 10X Buffer + 10ul Riboshredder + 50ul RNase H + 840ul H2O) and incubate 1hr at 37C
- Wash with H2O twice
- To DARTFISH slide: Add 100nM Padlock Probe Mix with 1000X suppv2 oligos in one sample and only 100nM Padlock Probe Mix in other and incubate ~1hr at 60C as oven slowly decreases to 55C and held for another ~20hr
- Put in pipette tip box with bottom filled with water and parafilmed around edges of box
Component | Volume |
DEPC-H2O | 33.43 |
Ampligase Buffer | 10 |
Justin's Batch 4 7/13/2015 Padlock Probes 559nM]] | 18 |
100nM suppv2 Oligos | 28.57 |
Ampligase | 10 |
Total | 100 |
Component | Volume |
DEPC-H2O | 62 |
Ampligase Buffer | 10 |
Justin's Batch 4 7/13/2015 Padlock Probes 559nM]] | 18 |
Ampligase | 10 |
Total | 100 |
- To FISSEQ slide and dish: Add 200ul CircLigaseII mix and incuabate 1hr at 60C
- Put in pipette tip box with bottom filled with water and parafilmed around edges of box
Component | Volume |
DEPC-H2O | 384 |
CircLigase Buffer 10X | 60 |
MnCl2 50mM | 30 |
Betaine 5M | 120 |
CircLigase II (100U/ul) | 6 |
Total | 600 |
- Wash FISSEQ samples with PBS and store in PBS at 4C overnight
Day 3[edit]
- Wash with 1X PBS once
- To DARTFISH slide add 1uM FISSEQ_ppRCA (2ul 200uM FISSEQ_ppRCA + 398ul 2X SSC + 30% formamide) and incubate 1hr at 55C
- DARTFISH slide was dried out
- Edit: the slide may not have dried out so much as leaked. The slide has been leaking since this step.
- Possible the 3M 200M adhesive is not resistant to long term high temp incubation.
- To FISSEQ slide and dish add 1uM FISSEQ_RCA (6ul 100uM FISSEQ_RCA + 594ul 2X SSC + 30% formamide) and incubate 1hr at 55C (should be 60C but only one oven)
- Preheated to 70C before adding
- Wash with 2X SSC once, 1X SSC once, and 1X PBS once
- Add RCA mix and incubate 6hr at 30C
Component | Volume |
H2O | 174 |
10X Phi29 Buffer | 20 |
25mM dNTP | 2 |
4mM aa-dUTP | 2 |
Phi 29 (low conc) | 2 |
Total | 200 |
- Wash with 1X PBS once
- Add 300ul BS(PEG)9 (6ul BS(PEG)9 + 294ul 1X PBS) and incubate at RT for 1hr
- Wash with 1X PBS twice
- Add 1M Tris pH 8.0 and incubate at RT for 30min
- Wash with 1X PBS twice and store in 1X PBS at 4C
Imaging[edit]
- FISSEQ rolonies in control dish
- Density is low and spots are irregular shapes and sizes
File:20151002 BA8FISSEQforHarvard ControlDish Position1.jpg
File:20151002 BA8FISSEQforHarvard ControlDish Position2.jpg
Takeaways[edit]
- BS(PEG)9 vial was empty even though brand new, contact Fisher Sci for free replacement
- Attaching 22mmx22mm coverslip to bottom of 18mm diameter hole with 20mm diameter adhesive ring has too much room for error (leaking)
- Cut 16mm holes in culture dishes and use 16mm diameter adhesive ring
- Buy new adhesive (ARclad 7876) because when it gets old it becomes hard to peel off liner without messing up adhesive
- Correction: Adhesives Research IS-8458-19 is the adhesive used
- 55-60C 20hr incubation dried out DARTFISH glass slide
- Need foolproof method to prevent evaporation, maybe must use mineral oil layer on top
- Edit: Leaking actually the problem in this case. Though 3M 300MP adhesive should be able to withstand 149C temperature for days