Hosuk:LabNotes/2013-9-30: Difference between revisions

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>Hosuki78
(Created page with "*LabNote ===1st Rolonies and ACTB Gene detection in 1st Rolonies together=== ====Goal==== *Count ACTB Gene out of 1st rolonies *Analyze how many ACTBs in...")
 
>Hosuki78
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*strip previous proves,
*strip previous proves,
*rehybridize Cy5 labeled probe for 1st rolonies, and ATTO 488 labeled probe for ACTB target
*rehybridize Cy5 labeled probe for 1st rolonies, and ATTO 488 labeled probe for ACTB target
*
*1uL of 200uM ATTO488-ACTBTargetOn1stRolony + 2uL of 100uM Cy5-1stRolony in 197uL 2x SSC
*Pre-heat probe mix at 60C for 5min, and add the probe mix to two dishes - 0623 3uL Phi29(used ACTB, RAB7A Padlock probing and created 2nd Rolony), and 0623 10uL Phi29 (only 1st Rolonies)
*incubate at RT for 10min, and wash with 2x SSC twice, store in PBS, and image with Confocal
 
 
====Result====
*Confocal setting : 20x oil lens --> 580um x 580um view area (1x zoom)
*512 x 512 pixel seemed not enough, 1024 x 1024 or 2048 x 2048 would be good for recognizing rolonies
**1 pixel size of 512 resolution was 1.14um which is slightly bigger than normal size of rolony (~700nm)
**1024 res. --> 1 px = 580um, 2048 res. --> 290um for 1 pixel
 
 
*I've taken tile scan images --> 8 x 6 tiles, with 19 stacks along z axis. --> Total scan are = 4.64mm x 3.48mm
*For tile scan, we used 512x512 resolution, and the total scan took about 35 min.
**However, we're going to use 2048 resolution for the next time.
*Convert max. projection for image analysis
 
 
*'''Analyzing images is on going.'''
*About 30 cells in one field of view (580um x 580um, 512x512 pixel resolution with 20x obj.) --> Total number of cells = ~ 1440
*But by the temporary analysis,
**'''Roughly''', the ratio (total rolonies)/(ACTB target rolonies) in 8x6 tiles = ~ 4900/140000 = ~ 3.5%
 
 
===PGP1F in 96well plate===
*For testing multiple sets, cells are split in glass bottom 96 well plate.
*2 well plates are used, and 8 wells in one plate have cells.
 
====Split condition====
*About 90% confluenced cells in T25 flask
*After spin dow cells, add 2mL media,
*transfer 60uL cells in a well, and add 100uL media
*Let's see how long it takes time for 100% cells in a well.

Latest revision as of 16:46, 1 October 2013

1st Rolonies and ACTB Gene detection in 1st Rolonies together[edit]

Goal[edit]

  • Count ACTB Gene out of 1st rolonies
  • Analyze how many ACTBs in all cDNA Rolonies quantitatively


Procedure[edit]

  • strip previous proves,
  • rehybridize Cy5 labeled probe for 1st rolonies, and ATTO 488 labeled probe for ACTB target
  • 1uL of 200uM ATTO488-ACTBTargetOn1stRolony + 2uL of 100uM Cy5-1stRolony in 197uL 2x SSC
  • Pre-heat probe mix at 60C for 5min, and add the probe mix to two dishes - 0623 3uL Phi29(used ACTB, RAB7A Padlock probing and created 2nd Rolony), and 0623 10uL Phi29 (only 1st Rolonies)
  • incubate at RT for 10min, and wash with 2x SSC twice, store in PBS, and image with Confocal


Result[edit]

  • Confocal setting : 20x oil lens --> 580um x 580um view area (1x zoom)
  • 512 x 512 pixel seemed not enough, 1024 x 1024 or 2048 x 2048 would be good for recognizing rolonies
    • 1 pixel size of 512 resolution was 1.14um which is slightly bigger than normal size of rolony (~700nm)
    • 1024 res. --> 1 px = 580um, 2048 res. --> 290um for 1 pixel


  • I've taken tile scan images --> 8 x 6 tiles, with 19 stacks along z axis. --> Total scan are = 4.64mm x 3.48mm
  • For tile scan, we used 512x512 resolution, and the total scan took about 35 min.
    • However, we're going to use 2048 resolution for the next time.
  • Convert max. projection for image analysis


  • Analyzing images is on going.
  • About 30 cells in one field of view (580um x 580um, 512x512 pixel resolution with 20x obj.) --> Total number of cells = ~ 1440
  • But by the temporary analysis,
    • Roughly, the ratio (total rolonies)/(ACTB target rolonies) in 8x6 tiles = ~ 4900/140000 = ~ 3.5%


PGP1F in 96well plate[edit]

  • For testing multiple sets, cells are split in glass bottom 96 well plate.
  • 2 well plates are used, and 8 wells in one plate have cells.

Split condition[edit]

  • About 90% confluenced cells in T25 flask
  • After spin dow cells, add 2mL media,
  • transfer 60uL cells in a well, and add 100uL media
  • Let's see how long it takes time for 100% cells in a well.