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BEST_purification_14102020.py
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BEST_purification_14102020.py
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#######################################
### BEST Library build Purification ###
#######################################
## Description of procedure ##
#
#
# Things do before procedure
#
# 1. Ensure samples are room temperature and place libraries in magnetic module
# 2. Ensure SPRI beads are room temperature
# 3. Make freshly made 80% Ethanol for purification
# 4. Distribute:
# SPRI beads to Column 1,
# Ethanol to Column 2 and 3
# Elution Buffer to Column 12
#
# Procedure
#
# Purification
# 1. Distribute 1.5x beads to library and mixes
# 2. Removes supernatant and adds ethanol for washing, washing will be processed twice
# 3. Beads will air dry for 4 minutes and 35µl elution buffer will be added
# 4. Elutes will incubate for 15 minutes at room temperature and be eluted to a new plate in slot 1
#
# Good Luck!
#
######## IMPORT LIBRARIES ########
from opentrons import protocol_api
#### METADATA ####
metadata = {
'protocolName': 'BEST_Purification',
'author': 'Jacob Agerbo Rasmussen <[email protected]>',
'apiLevel': '2.2',
'description': 'Purification procedure of Automated single tube library preparation after Carøe et al. 2017',
}
def run(protocol):
#### LABWARE SETUP ####
mag_deck = protocol.load_module('magdeck', 10)
trough = protocol.load_labware('usascientific_12_reservoir_22ml', 7) # to add proper model of labware from https://labware.opentrons.com/
trash_box = protocol.load_labware('agilent_1_reservoir_290ml', 8) # to add proper model of labware
mag_plate = mag_deck.load_labware('biorad_96_wellplate_200ul_pcr')
elution_plate = protocol.load_labware('biorad_96_wellplate_200ul_pcr', 2)
tipracks_200_1 = protocol.load_labware('opentrons_96_filtertiprack_200ul', 4)
tipracks_200_2 = protocol.load_labware('opentrons_96_filtertiprack_200ul', 1)
tipracks_200_3 = protocol.load_labware('opentrons_96_filtertiprack_200ul', 5)
tipracks_200_4 = protocol.load_labware('opentrons_96_filtertiprack_200ul', 6)
#### PIPETTE SETUP ####
m300 = protocol.load_instrument('p300_multi_gen2', mount='left', tip_racks=(tipracks_200_1, tipracks_200_2, tipracks_200_3, tipracks_200_4))
# From the v1 the mount is right, but all the other protocols switch from right in v1 to left in v2. Why? Also here?
## Purification reagents SETUP
SPRI_beads = trough['A1']
EtOH1 = trough['A2']
EtOH2 = trough['A3']
Elution_buffer = trough['A12']
Liquid_trash = trash_box['A1']
## Plate SETUP
MA1 = mag_plate['A1']
MA2 = mag_plate['A2']
MA3 = mag_plate['A3']
MA4 = mag_plate['A4']
MA5 = mag_plate['A5']
MA6 = mag_plate['A6']
MA7 = mag_plate['A7']
MA8 = mag_plate['A8']
MA9 = mag_plate['A9']
MA10 = mag_plate['A10']
MA11 = mag_plate['A11']
MA12 = mag_plate['A12']
## Sample Setup
sample_number = 96
col_num = sample_number // 8 + (1 if sample_number % 8 > 0 else 0)
samples = [col for col in mag_plate.columns()[:col_num]]
#### VOLUME SETUP
sample_vol = 50
bead_vol = 1.5*sample_vol
EtOH_vol = 160
EtOH_vol2 = 150
Elution_vol = 35
#### PROTOCOL ####
### Beads addition
mag_deck.disengage() # or mag_mod.disengage() ???
#### Transfer beads to MA1
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A1']) # Slow down head speed 0.5X for bead handling
m300.move_to(SPRI_beads.top(-30))
m300.mix(3, bead_vol, SPRI_beads.bottom(2))
# max_speed_per_axis ==> see end of protocol for info (if need to add them)
# robot.head_speed ==> see end of protocol for info
m300.flow_rate.aspirate = 50
m300.flow_rate.dispense = 50
m300.aspirate(bead_vol, SPRI_beads.bottom(2))
m300.move_to(MA1.bottom(1))
m300.dispense(bead_vol, MA1.bottom(4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, bead_vol, MA1.bottom(4))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.move_to(MA1.top(-4))
m300.blow_out()
# max_speed_per_axis
# robot.head_speed
m300.return_tip()
#### Transfer beads to MA2
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A2']) # Slow down head speed 0.5X for bead handling
m300.move_to(SPRI_beads.top(-30))
m300.mix(3, bead_vol, SPRI_beads.bottom(2))
# max_speed_per_axis ==> see end of protocol for info
# robot.head_speed ==> see end of protocol for info
m300.flow_rate.aspirate = 50
m300.flow_rate.dispense = 50
m300.aspirate(bead_vol, SPRI_beads.bottom(2))
m300.move_to(MA2.bottom(1))
m300.dispense(bead_vol, MA2.bottom(4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, bead_vol, MA2.bottom(4))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.move_to(MA2.top(-4))
m300.blow_out()
# max_speed_per_axis
# robot.head_speed
m300.return_tip()
#### Transfer beads to MA3
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A3']) # Slow down head speed 0.5X for bead handling
m300.move_to(SPRI_beads.top(-30))
m300.mix(3, bead_vol, SPRI_beads.bottom(2))
# max_speed_per_axis ==> see end of protocol for info
# robot.head_speed ==> see end of protocol for info
m300.flow_rate.aspirate = 50
m300.flow_rate.dispense = 50
m300.aspirate(bead_vol, SPRI_beads.bottom(2))
m300.move_to(MA3.bottom(1))
m300.dispense(bead_vol, MA3.bottom(4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, bead_vol, MA3.bottom(4))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.move_to(MA3.top(-4))
m300.blow_out()
# max_speed_per_axis
# robot.head_speed
m300.return_tip()
#### Transfer beads to MA4
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A4']) # Slow down head speed 0.5X for bead handling
m300.move_to(SPRI_beads.top(-30))
m300.mix(3, bead_vol, SPRI_beads.bottom(2))
# max_speed_per_axis ==> see end of protocol for info
# robot.head_speed ==> see end of protocol for info
m300.flow_rate.aspirate = 50
m300.flow_rate.dispense = 50
m300.aspirate(bead_vol, SPRI_beads.bottom(2))
m300.move_to(MA4.bottom(1))
m300.dispense(bead_vol, MA4.bottom(4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, bead_vol, MA4.bottom(4))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.move_to(MA4.top(-4))
m300.blow_out()
# max_speed_per_axis
# robot.head_speed
m300.return_tip()
#### Transfer beads to MA5
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A5']) # Slow down head speed 0.5X for bead handling
m300.move_to(SPRI_beads.top(-30))
m300.mix(3, bead_vol, SPRI_beads.bottom(2))
# max_speed_per_axis ==> see end of protocol for info
# robot.head_speed ==> see end of protocol for info
m300.flow_rate.aspirate = 50
m300.flow_rate.dispense = 50
m300.aspirate(bead_vol, SPRI_beads.bottom(2))
m300.move_to(MA5.bottom(1))
m300.dispense(bead_vol, MA5.bottom(4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, bead_vol, MA5.bottom(4))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.move_to(MA5.top(-4))
m300.blow_out()
# max_speed_per_axis
# robot.head_speed
m300.return_tip()
#### Transfer beads to MA6
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A6']) # Slow down head speed 0.5X for bead handling
m300.move_to(SPRI_beads.top(-30))
m300.mix(3, bead_vol, SPRI_beads.bottom(2))
# max_speed_per_axis ==> see end of protocol for info
# robot.head_speed ==> see end of protocol for info
m300.flow_rate.aspirate = 50
m300.flow_rate.dispense = 50
m300.aspirate(bead_vol, SPRI_beads.bottom(2))
m300.move_to(MA6.bottom(1))
m300.dispense(bead_vol, MA6.bottom(4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, bead_vol, MA6.bottom(4))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.move_to(MA6.top(-4))
m300.blow_out()
# max_speed_per_axis
# robot.head_speed
m300.return_tip()
#### Transfer beads to MA7
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A7']) # Slow down head speed 0.5X for bead handling
m300.move_to(SPRI_beads.top(-30))
m300.mix(3, bead_vol, SPRI_beads.bottom(2))
# max_speed_per_axis ==> see end of protocol for info
# robot.head_speed ==> see end of protocol for info
m300.flow_rate.aspirate = 50
m300.flow_rate.dispense = 50
m300.aspirate(bead_vol, SPRI_beads.bottom(2))
m300.move_to(MA7.bottom(1))
m300.dispense(bead_vol, MA7.bottom(4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, bead_vol, MA7.bottom(4))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.move_to(MA7.top(-4))
m300.blow_out()
# max_speed_per_axis
# robot.head_speed
m300.return_tip()
#### Transfer beads to MA8
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A8']) # Slow down head speed 0.5X for bead handling
m300.move_to(SPRI_beads.top(-30))
m300.mix(3, bead_vol, SPRI_beads.bottom(2))
# max_speed_per_axis ==> see end of protocol for info
# robot.head_speed ==> see end of protocol for info
m300.flow_rate.aspirate = 50
m300.flow_rate.dispense = 50
m300.aspirate(bead_vol, SPRI_beads.bottom(2))
m300.move_to(MA8.bottom(1))
m300.dispense(bead_vol, MA8.bottom(4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, bead_vol, MA8.bottom(4))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.move_to(MA8.top(-4))
m300.blow_out()
# max_speed_per_axis
# robot.head_speed
m300.return_tip()
#### Transfer beads to MA9
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A9']) # Slow down head speed 0.5X for bead handling
m300.move_to(SPRI_beads.top(-30))
m300.mix(3, bead_vol, SPRI_beads.bottom(2))
# max_speed_per_axis ==> see end of protocol for info
# robot.head_speed ==> see end of protocol for info
m300.flow_rate.aspirate = 50
m300.flow_rate.dispense = 50
m300.aspirate(bead_vol, SPRI_beads.bottom(2))
m300.move_to(MA9.bottom(1))
m300.dispense(bead_vol, MA9.bottom(4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, bead_vol, MA9.bottom(4))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.move_to(MA9.top(-4))
m300.blow_out()
# max_speed_per_axis
# robot.head_speed
m300.return_tip()
#### Transfer beads to MA10
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A10']) # Slow down head speed 0.5X for bead handling
m300.move_to(SPRI_beads.top(-30))
m300.mix(3, bead_vol, SPRI_beads.bottom(2))
# max_speed_per_axis ==> see end of protocol for info
# robot.head_speed ==> see end of protocol for info
m300.flow_rate.aspirate = 50
m300.flow_rate.dispense = 50
m300.aspirate(bead_vol, SPRI_beads.bottom(2))
m300.move_to(MA10.bottom(1))
m300.dispense(bead_vol, MA10.bottom(4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, bead_vol, MA10.bottom(4))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.move_to(MA10.top(-4))
m300.blow_out()
# max_speed_per_axis
# robot.head_speed
m300.return_tip()
#### Transfer beads to MA11
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A11']) # Slow down head speed 0.5X for bead handling
m300.move_to(SPRI_beads.top(-30))
m300.mix(3, bead_vol, SPRI_beads.bottom(2))
# max_speed_per_axis ==> see end of protocol for info
# robot.head_speed ==> see end of protocol for info
m300.flow_rate.aspirate = 50
m300.flow_rate.dispense = 50
m300.aspirate(bead_vol, SPRI_beads.bottom(2))
m300.move_to(MA11.bottom(1))
m300.dispense(bead_vol, MA11.bottom(4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, bead_vol, MA11.bottom(4))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.move_to(MA11.top(-4))
m300.blow_out()
# max_speed_per_axis
# robot.head_speed
m300.return_tip()
#### Transfer beads to MA12
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A12']) # Slow down head speed 0.5X for bead handling
m300.move_to(SPRI_beads.top(-30))
m300.mix(3, bead_vol, SPRI_beads.bottom(2))
# max_speed_per_axis ==> see end of protocol for info
# robot.head_speed ==> see end of protocol for info
m300.flow_rate.aspirate = 50
m300.flow_rate.dispense = 50
m300.aspirate(bead_vol, SPRI_beads.bottom(2))
m300.move_to(MA12.bottom(1))
m300.dispense(bead_vol, MA12.bottom(4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, bead_vol, MA12.bottom(4))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.move_to(MA12.top(-4))
m300.blow_out()
# max_speed_per_axis
# robot.head_speed
m300.return_tip()
protocol.comment("Incubating the beads and PCR products at room temperature \
for 5 minutes. Protocol will resume automatically.")
protocol.delay(minutes=5)
mag_deck.engage() # or mag_mod.engage()
protocol.delay(minutes=2)
### Remove supernatant, by re-using tiprack 1
### remove supernatant from MA1
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A1']) # Slow down head speed 0.5X for bead handling
m300.aspirate(180, MA1.bottom(1))
m300.dispense(180, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA2
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A2']) # Slow down head speed 0.5X for bead handling
m300.aspirate(180, MA2.bottom(1))
m300.dispense(180, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA3
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A3']) # Slow down head speed 0.5X for bead handling
m300.aspirate(180, MA3.bottom(1))
m300.dispense(180, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA4
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A4']) # Slow down head speed 0.5X for bead handling
m300.aspirate(180, MA4.bottom(1))
m300.dispense(180, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA5
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A5']) # Slow down head speed 0.5X for bead handling
m300.aspirate(180, MA5.bottom(1))
m300.dispense(180, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA6
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A6']) # Slow down head speed 0.5X for bead handling
m300.aspirate(180, MA6.bottom(1))
m300.dispense(180, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA7
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A7']) # Slow down head speed 0.5X for bead handling
m300.aspirate(180, MA7.bottom(1))
m300.dispense(180, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA8
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A8']) # Slow down head speed 0.5X for bead handling
m300.aspirate(180, MA8.bottom(1))
m300.dispense(180, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA9
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A9']) # Slow down head speed 0.5X for bead handling
m300.aspirate(180, MA9.bottom(1))
m300.dispense(180, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA10
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A10']) # Slow down head speed 0.5X for bead handling
m300.aspirate(180, MA10.bottom(1))
m300.dispense(180, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA11
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A11']) # Slow down head speed 0.5X for bead handling
m300.aspirate(180, MA11.bottom(1))
m300.dispense(180, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA12
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_1['A12']) # Slow down head speed 0.5X for bead handling
m300.aspirate(180, MA12.bottom(1))
m300.dispense(180, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### Wash 1 with Ethanol, using tiprack 2
### Transfer Wash 1 to MA1
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A1']) # Slow down head speed 0.5X for bead handling
m300.move_to(EtOH1.top(-16))
m300.aspirate(EtOH_vol, EtOH1.bottom(2))
m300.dispense(EtOH_vol, MA1.top(-4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, EtOH_vol, MA1.bottom(5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.move_to(MA1.top(-4))
m300.blow_out()
m300.return_tip()
### Transfer Wash 1 to MA2
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A2']) # Slow down head speed 0.5X for bead handling
m300.move_to(EtOH1.top(-16))
m300.aspirate(EtOH_vol, EtOH1.bottom(2))
m300.dispense(EtOH_vol, MA2.top(-4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, EtOH_vol, MA2.bottom(5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.move_to(MA2.top(-4))
m300.blow_out()
m300.return_tip()
### Transfer Wash 1 to MA3
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A3']) # Slow down head speed 0.5X for bead handling
m300.move_to(EtOH1.top(-16))
m300.aspirate(EtOH_vol, EtOH1.bottom(2))
m300.dispense(EtOH_vol, MA3.top(-4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, EtOH_vol, MA3.bottom(5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.move_to(MA3.top(-4))
m300.blow_out()
m300.return_tip()
### Transfer Wash 1 to MA4
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A4']) # Slow down head speed 0.5X for bead handling
m300.move_to(EtOH1.top(-16))
m300.aspirate(EtOH_vol, EtOH1.bottom(2))
m300.dispense(EtOH_vol, MA4.top(-4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, EtOH_vol, MA4.bottom(5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.move_to(MA4.top(-4))
m300.blow_out()
m300.return_tip()
### Transfer Wash 1 to MA5
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A5']) # Slow down head speed 0.5X for bead handling
m300.move_to(EtOH1.top(-16))
m300.aspirate(EtOH_vol, EtOH1.bottom(2))
m300.dispense(EtOH_vol, MA5.top(-4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, EtOH_vol, MA5.bottom(5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.move_to(MA5.top(-4))
m300.blow_out()
m300.return_tip()
### Transfer Wash 1 to MA6
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A6']) # Slow down head speed 0.5X for bead handling
m300.move_to(EtOH1.top(-16))
m300.aspirate(EtOH_vol, EtOH1.bottom(2))
m300.dispense(EtOH_vol, MA6.top(-4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, EtOH_vol, MA6.bottom(5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.move_to(MA6.top(-4))
m300.blow_out()
m300.return_tip()
### Transfer Wash 1 to MA7
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A7']) # Slow down head speed 0.5X for bead handling
m300.move_to(EtOH1.top(-16))
m300.aspirate(EtOH_vol, EtOH1.bottom(2))
m300.dispense(EtOH_vol, MA7.top(-4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, EtOH_vol, MA7.bottom(5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.move_to(MA7.top(-4))
m300.blow_out()
m300.return_tip()
### Transfer Wash 1 to MA8
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A8']) # Slow down head speed 0.5X for bead handling
m300.move_to(EtOH1.top(-16))
m300.aspirate(EtOH_vol, EtOH1.bottom(2))
m300.dispense(EtOH_vol, MA8.top(-4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, EtOH_vol, MA8.bottom(5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.move_to(MA8.top(-4))
m300.blow_out()
m300.return_tip()
### Transfer Wash 1 to MA9
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A9']) # Slow down head speed 0.5X for bead handling
m300.move_to(EtOH1.top(-16))
m300.aspirate(EtOH_vol, EtOH1.bottom(2))
m300.dispense(EtOH_vol, MA9.top(-4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, EtOH_vol, MA9.bottom(5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.move_to(MA9.top(-4))
m300.blow_out()
m300.return_tip()
### Transfer Wash 1 to MA10
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A10']) # Slow down head speed 0.5X for bead handling
m300.move_to(EtOH1.top(-16))
m300.aspirate(EtOH_vol, EtOH1.bottom(2))
m300.dispense(EtOH_vol, MA10.top(-4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, EtOH_vol, MA10.bottom(5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.move_to(MA10.top(-4))
m300.blow_out()
m300.return_tip()
### Transfer Wash 1 to MA11
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A11']) # Slow down head speed 0.5X for bead handling
m300.move_to(EtOH1.top(-16))
m300.aspirate(EtOH_vol, EtOH1.bottom(2))
m300.dispense(EtOH_vol, MA11.top(-4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, EtOH_vol, MA11.bottom(5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.move_to(MA11.top(-4))
m300.blow_out()
m300.return_tip()
### Transfer Wash 1 to MA12
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A12']) # Slow down head speed 0.5X for bead handling
m300.move_to(EtOH1.top(-16))
m300.aspirate(EtOH_vol, EtOH1.bottom(2))
m300.dispense(EtOH_vol, MA12.top(-4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, EtOH_vol, MA12.bottom(5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.move_to(MA12.top(-4))
m300.blow_out()
m300.return_tip()
mag_deck.engage(height=16) # or mag_mod ?
protocol.delay(minutes=2)
### Remove supernatant, by re-using tiprack 2
### remove supernatant from MA1
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A1']) # Slow down head speed 0.5X for bead handling
m300.aspirate(EtOH_vol, MA1.bottom(1))
m300.dispense(EtOH_vol, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA2
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A2']) # Slow down head speed 0.5X for bead handling
m300.aspirate(EtOH_vol, MA2.bottom(1))
m300.dispense(EtOH_vol, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA3
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A3']) # Slow down head speed 0.5X for bead handling
m300.aspirate(EtOH_vol, MA3.bottom(1))
m300.dispense(EtOH_vol, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA4
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A4']) # Slow down head speed 0.5X for bead handling
m300.aspirate(EtOH_vol, MA4.bottom(1))
m300.dispense(EtOH_vol, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA5
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A5']) # Slow down head speed 0.5X for bead handling
m300.aspirate(EtOH_vol, MA5.bottom(1))
m300.dispense(EtOH_vol, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA6
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A6']) # Slow down head speed 0.5X for bead handling
m300.aspirate(EtOH_vol, MA6.bottom(1))
m300.dispense(EtOH_vol, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA7
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A7']) # Slow down head speed 0.5X for bead handling
m300.aspirate(EtOH_vol, MA7.bottom(1))
m300.dispense(EtOH_vol, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA8
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A8']) # Slow down head speed 0.5X for bead handling
m300.aspirate(EtOH_vol, MA8.bottom(1))
m300.dispense(EtOH_vol, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA9
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A9']) # Slow down head speed 0.5X for bead handling
m300.aspirate(EtOH_vol, MA9.bottom(1))
m300.dispense(EtOH_vol, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA10
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A10']) # Slow down head speed 0.5X for bead handling
m300.aspirate(EtOH_vol, MA10.bottom(1))
m300.dispense(EtOH_vol, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA11
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A11']) # Slow down head speed 0.5X for bead handling
m300.aspirate(EtOH_vol, MA11.bottom(1))
m300.dispense(EtOH_vol, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### remove supernatant from MA12
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_2['A12']) # Slow down head speed 0.5X for bead handling
m300.aspirate(EtOH_vol, MA12.bottom(1))
m300.dispense(EtOH_vol, trash_box['A1'].top(-5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.blow_out(trash_box['A1'].top(-5))
m300.air_gap(height = 2)
m300.return_tip()
### Wash 2 with Ethanol, using tiprack 3
### Transfer Wash 2 to MA1
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_3['A1']) # Slow down head speed 0.5X for bead handling
m300.move_to(EtOH2.top(-16))
m300.aspirate(EtOH_vol2, EtOH2.top(-12))
m300.dispense(EtOH_vol2, MA1.top(-4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, EtOH_vol2, MA1.bottom(5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.move_to(MA1.top(-10))
m300.blow_out()
m300.return_tip()
### Transfer Wash 2 to MA2
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_3['A2']) # Slow down head speed 0.5X for bead handling
m300.move_to(EtOH2.top(-16))
m300.aspirate(EtOH_vol2, EtOH2.top(-12))
m300.dispense(EtOH_vol2, MA2.top(-4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, EtOH_vol2, MA2.bottom(5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.move_to(MA2.top(-10))
m300.blow_out()
m300.return_tip()
### Transfer Wash 2 to MA3
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_3['A3']) # Slow down head speed 0.5X for bead handling
m300.move_to(EtOH2.top(-16))
m300.aspirate(EtOH_vol2, EtOH2.top(-12))
m300.dispense(EtOH_vol2, MA3.top(-4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, EtOH_vol2, MA3.bottom(5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.move_to(MA3.top(-10))
m300.blow_out()
m300.return_tip()
### Transfer Wash 2 to MA4
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_3['A4']) # Slow down head speed 0.5X for bead handling
m300.move_to(EtOH2.top(-16))
m300.aspirate(EtOH_vol2, EtOH2.top(-12))
m300.dispense(EtOH_vol2, MA4.top(-4))
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.mix(5, EtOH_vol2, MA4.bottom(5))
protocol.delay(seconds=5)
m300.flow_rate.aspirate = 130
m300.flow_rate.dispense = 130
m300.move_to(MA4.top(-10))
m300.blow_out()
m300.return_tip()
### Transfer Wash 2 to MA5
m300.flow_rate.aspirate = 100
m300.flow_rate.dispense = 100
m300.pick_up_tip(tipracks_200_3['A5']) # Slow down head speed 0.5X for bead handling