def run(protocol: protocol_api.ProtocolContext(api_version=api_version)):
# define deck positions and labware
# tips
tiprack_300 = protocol.load_labware('opentrons_96_tiprack_300ul', 6)
tipracks_10f = [
protocol.load_labware('opentrons_96_filtertiprack_10ul', x)
for x in [1, 4, 7, 10]
]
# plates
reagents = protocol.load_labware('usascientific_12_reservoir_22ml', 3,
'reagents')
assay = protocol.load_labware('corning_384_wellplate_112ul_flat', 9,
'assay')
samples = [
protocol.load_labware('biorad_96_wellplate_200ul_pcr', x, 'samples')
for x in [2, 5, 8, 11]
]
# initialize pipettes
pipette_left = protocol.load_instrument('p300_multi',
'left',
tip_racks=[tiprack_300])
pipette_right = protocol.load_instrument('p10_multi',
'right',
tip_racks=tipracks_10f)
# distribute 38 µL of quantification reagent into each well of the assay
# plate. Use the same tip for the entirety of these transfers, then
# replace it in the rack.
add_buffer(pipette_left, [reagents[x] for x in ['A1', 'A2']],
assay,
cols,
38,
13000 / 8,
tip=None,
tip_vol=300,
remaining=None,
drop_tip=False)
# add 2 µL of each sample to each of the wells. Mix after dispensing.
# Dispose of these tips.
for i, plate in enumerate(samples):
start = i + 1
assay_wells = get_96_from_384_wells(method='interleaved', start=start)
pipette_right.transfer(2,
plate.wells(), [assay[x] for x in assay_wells],
mix_after=(1, 10),
touch_tip=True,
trash=True,
new_tip='always')
def run(protocol: protocol_api.ProtocolContext):
# define deck positions and labware
# tips
tiprack_300 = protocol.load_labware('opentrons_96_tiprack_300ul', 1)
tiprack_10f = protocol.load_labware('opentrons_96_filtertiprack_10ul', 2)
# plates
reagents = protocol.load_labware('usascientific_12_reservoir_22ml',
6, 'reagents')
assay = protocol.load_labware('corning_96_wellplate_360ul_flat',
5, 'assay')
samples = protocol.load_labware('biorad_96_wellplate_200ul_pcr',
4, 'samples')
# initialize pipettes
pipette_left = protocol.load_instrument('p300_multi',
'left',
tip_racks=[tiprack_300])
pipette_right = protocol.load_instrument('p10_multi',
'right',
tip_racks=[tiprack_10f])
# # home instrument
# protocol.home()
# distribute 198 µL of quantification reagent into each well of the assay
# plate. Use the same tip for the entirety of these transfers, then
# replace it in the rack.
add_buffer(pipette_left,
[reagents[x] for x in ['A1', 'A2']],
assay,
cols,
198,
13000/8,
tip=None,
tip_vol=300,
remaining=None,
drop_tip=False)
# add 2 µL of each sample to each of the wells. Mix after dispensing.
# Dispose of these tips.
pipette_right.transfer(2,
[samples[x] for x in cols],
[assay[x] for x in cols],
mix_after=(5, 10),
touch_tip=True,
trash=False,
new_tip='always')
def test_add_buffer_fullplate():
protocol = get_protocol_api(apilevel)
tips = protocol.load_labware('opentrons_96_tiprack_300ul', 8)
plate = protocol.load_labware('biorad_96_wellplate_200ul_pcr',
3, 'plate')
reagents = protocol.load_labware('usascientific_12_reservoir_22ml',
9, 'reagents')
pipette = protocol.load_instrument('p300_multi',
'left',
tip_racks=[tips])
remaining, source_wells = add_buffer(pipette,
[reagents['A1'],
reagents['A2']],
plate,
['A1', 'A2', 'A3', 'A4',
'A5', 'A6', 'A7', 'A8',
'A9', 'A10', 'A11', 'A12'],
300,
20000 / 8,
dead_vol=800 / 8)
assert remaining == 1300
assert source_wells == [reagents['A2']]
def test_add_buffer():
protocol = get_protocol_api(apilevel)
scraper = CommandScraper(logging.getLogger('opentrons'),
'1',
protocol.broker)
tips = protocol.load_labware('opentrons_96_tiprack_300ul', 8)
plate = protocol.load_labware('biorad_96_wellplate_200ul_pcr',
3, 'plate')
reagents = protocol.load_labware('nest_12_reservoir_15ml',
9, 'reagents')
pipette = protocol.load_instrument('p300_multi',
'left',
tip_racks=[tips])
remaining, source_wells = add_buffer(pipette,
[reagents['A1']],
plate,
['A1', 'A2'],
300,
1000)
assert remaining == 400
assert source_wells == [reagents['A1']]
exp = ['Picking up tip from A1 of Opentrons 96 Tip Rack 300 µL on 8',
'Aspirating 150.0 uL from A1 of reagents on 9 at 1.0 speed',
'Air gap',
'Aspirating 10.0 uL from A1 of reagents on 9 at 1.0 speed',
'Dispensing 160.0 uL into A1 of plate on 3 at 1.0 speed',
'Aspirating 150.0 uL from A1 of reagents on 9 at 1.0 speed',
'Air gap',
'Aspirating 10.0 uL from A1 of reagents on 9 at 1.0 speed',
'Dispensing 160.0 uL into A1 of plate on 3 at 1.0 speed',
'Blowing out',
'Aspirating 150.0 uL from A1 of reagents on 9 at 1.0 speed',
'Air gap',
'Aspirating 10.0 uL from A1 of reagents on 9 at 1.0 speed',
'Dispensing 160.0 uL into A2 of plate on 3 at 1.0 speed',
'Aspirating 150.0 uL from A1 of reagents on 9 at 1.0 speed',
'Air gap',
'Aspirating 10.0 uL from A1 of reagents on 9 at 1.0 speed',
'Dispensing 160.0 uL into A2 of plate on 3 at 1.0 speed',
'Blowing out',
'Dropping tip into A1 of Opentrons Fixed Trash on 12']
obs = [x['payload']['text'] for x in scraper.commands]
assert exp == obs
def test_add_buffer_runout():
protocol = get_protocol_api(apilevel)
tips = protocol.load_labware('opentrons_96_tiprack_300ul', 8)
plate = protocol.load_labware('biorad_96_wellplate_200ul_pcr',
3, 'plate')
reagents = protocol.load_labware('nest_12_reservoir_15ml',
9, 'reagents')
pipette = protocol.load_instrument('p300_multi',
'left',
tip_racks=[tips])
with pytest.raises(IndexError):
remaining, source_wells = add_buffer(pipette,
[reagents['A1']],
plate,
['A1', 'A2'],
300,
600)
def run(protocol: protocol_api.ProtocolContext):
# ### Setup
# define deck positions and labware
# define hardware modules
magblock = protocol.load_module('Magnetic Module', 10)
magblock.disengage()
# tips
tiprack_buffers = protocol.load_labware('opentrons_96_tiprack_300ul', 8)
tiprack_elution_1 = protocol.load_labware(
'opentrons_96_filtertiprack_200ul', 5)
tiprack_elution_2 = protocol.load_labware(
'opentrons_96_filtertiprack_200ul', 6)
tiprack_wash = protocol.load_labware('opentrons_96_tiprack_300ul', 4)
# plates
wash_buffers = protocol.load_labware('usascientific_12_reservoir_22ml', 11,
'wash buffers')
eluate = protocol.load_labware('biorad_96_wellplate_200ul_pcr', 3,
'eluate')
waste = protocol.load_labware('nest_1_reservoir_195ml', 7, 'liquid waste')
reagents = protocol.load_labware('usascientific_12_reservoir_22ml', 9,
'reagents')
# load plate on magdeck
# mag_plate = magblock.load_labware('vwr_96_wellplate_1000ul')
mag_plate = magblock.load_labware('vwr_96_wellplate_1000ul')
# initialize pipettes
pipette_left = protocol.load_instrument('p300_multi',
'left',
tip_racks=[tiprack_buffers])
# MagBindingBuffer + beads wells
mbb_wells = [reagents[x] for x in mbb_cols]
# MagBindingBuffer wells
mbw_wells = [reagents[x] for x in mbw_cols]
# Wash 1 columns
w1_wells = [wash_buffers[x] for x in w1_cols]
# Wash 2 columns
w2_wells = [wash_buffers[x] for x in w2_cols]
# ### Prompt user to place plate on mag block
protocol.pause('Add plate containing 200 µL per well of lysis supernatant'
' onto the magdeck in position 10.')
# ### Add MagBinding buffer and beads to plate
protocol.comment('Adding beads to plate.')
# add beads
mbb_remaining, mbb_wells = add_buffer(pipette_left,
mbb_wells,
mag_plate,
cols,
625,
18000 / 8,
pre_mix=10)
# mix beads and samples
for col in cols:
pipette_left.pick_up_tip(tiprack_wash.wells_by_name()[col])
pipette_left.mix(10, 250, mag_plate[col].bottom(z=1))
pipette_left.blow_out(mag_plate[col].top(z=-2))
pipette_left.touch_tip()
pipette_left.return_tip()
# bind to beads
protocol.comment('Binding DNA to beads.')
protocol.delay(seconds=pause_bind)
# mix again
for col in cols:
pipette_left.pick_up_tip(tiprack_wash.wells_by_name()[col])
pipette_left.mix(10, 250, mag_plate[col].bottom(z=1))
pipette_left.blow_out(mag_plate[col].top(z=-2))
pipette_left.touch_tip()
pipette_left.return_tip()
# bind to magnet
protocol.comment('Binding beads to magnet.')
magblock.engage(height_from_base=mag_engage_height)
protocol.delay(seconds=pause_mag)
# ### Do first wash: Wash 500 µL MagBinding buffer
protocol.comment('Doing wash #1.')
mbw_remaining, mbw_wells = bead_wash(
# global arguments
protocol,
magblock,
pipette_left,
mag_plate,
cols,
# super arguments
waste['A1'],
tiprack_wash,
# wash buffer arguments,
mbw_wells,
19000 / 8,
# mix arguments
tiprack_wash,
# optional arguments
wash_vol=500,
super_vol=800,
drop_super_tip=False,
mix_n=wash_mix,
mag_engage_height=mag_engage_height)
# ### Do second wash: Wash 500 µL MagWash 1
protocol.comment('Doing wash #2.')
w1_remaining, w1_wells = bead_wash(
# global arguments
protocol,
magblock,
pipette_left,
mag_plate,
cols,
# super arguments
waste['A1'],
tiprack_wash,
# wash buffer arguments
w1_wells,
19000 / 8,
# mix arguments
tiprack_wash,
# optional arguments,
wash_vol=500,
super_vol=500,
drop_super_tip=False,
mix_n=wash_mix,
remaining=None,
mag_engage_height=mag_engage_height)
# ### Do third wash: Wash 900 µL MagWash 2
protocol.comment('Doing wash #3.')
w2_remaining, w2_wells = bead_wash(
# global arguments
protocol,
magblock,
pipette_left,
mag_plate,
cols,
# super arguments
waste['A1'],
tiprack_wash,
# wash buffer arguments
w2_wells,
21000 / 8,
# mix arguments
tiprack_wash,
# optional arguments,
wash_vol=900,
super_vol=500,
drop_super_tip=False,
mix_n=wash_mix,
remaining=None,
mag_engage_height=mag_engage_height)
# ### Do fourth wash: Wash 900 µL MagWash 2
protocol.comment('Doing wash #4.')
w2_remaining, w2_wells = bead_wash(
# global arguments
protocol,
magblock,
pipette_left,
mag_plate,
cols,
# super arguments
waste['A1'],
tiprack_wash,
# wash buffer arguments
w2_wells,
21000 / 8,
# mix arguments
tiprack_wash,
# optional arguments,
wash_vol=900,
super_vol=900,
drop_super_tip=False,
mix_n=wash_mix,
remaining=w2_remaining,
mag_engage_height=mag_engage_height)
# ### Dry
protocol.comment('Removing wash and drying beads.')
# This should:
# - pick up tip in position 8
# - pick up supernatant from magplate
# - dispense in waste, position 11
# - repeat
# - trash tip
# - leave magnet engaged
# remove supernatant
remove_supernatant(pipette_left,
mag_plate,
cols,
tiprack_wash,
waste['A1'],
super_vol=1000,
rate=bead_flow,
bottom_offset=.5,
drop_tip=True)
# dry
protocol.delay(seconds=pause_dry)
# ### Elute
protocol.comment('Eluting DNA from beads.')
# This should:
# - disengage magnet
# - pick up tip from position 6
# - pick up reagents from column 2 of position 9
# - dispense into magplate
# - mix 10 times
# - blow out, touch tip
# - return tip to position 6
# - wait (5 seconds)
# - engage magnet
# - wait (5 seconds)
# - pick up tip from position 6
# - aspirate from magplate
# - dispense to position 3
# - trash tip
# transfer elution buffer to mag plate
magblock.disengage()
# add elution buffer and mix
for col in cols:
pipette_left.pick_up_tip(tiprack_elution_1.wells_by_name()[col])
pipette_left.aspirate(50, reagents['A8'], rate=1)
pipette_left.dispense(50, mag_plate[col].bottom(z=1))
pipette_left.mix(10, 40, mag_plate[col].bottom(z=1))
pipette_left.blow_out(mag_plate[col].top())
pipette_left.touch_tip()
# we'll use these same tips for final transfer
pipette_left.return_tip()
protocol.delay(seconds=pause_elute)
# # start timer
# t0 = clock()
# # mix again
# t_mix = 0
# while t_mix < pause_elute():
for col in cols:
pipette_left.pick_up_tip(tiprack_elution_1.wells_by_name()[col])
pipette_left.mix(10, 40, mag_plate[col].bottom(z=1))
pipette_left.blow_out(mag_plate[col].top())
pipette_left.touch_tip()
# we'll use these same tips for final transfer
pipette_left.return_tip()
# t_mix = clock() - t0
# bind to magnet
protocol.comment('Binding beads to magnet.')
magblock.engage(height_from_base=mag_engage_height)
protocol.delay(seconds=pause_mag)
protocol.comment('Transferring eluted DNA to final plate.')
for col in cols:
pipette_left.pick_up_tip(tiprack_elution_2.wells_by_name()[col])
pipette_left.aspirate(50, mag_plate[col].bottom(z=2), rate=bead_flow)
pipette_left.dispense(50, eluate[col])
pipette_left.blow_out(eluate[col].top())
pipette_left.touch_tip()
# we're done with these tips now
pipette_left.drop_tip()
magblock.disengage()
def bead_wash( # global arguments
protocol,
magblock,
pipette,
plate,
cols,
# super arguments
super_waste,
super_tiprack,
# wash buffer arguments
source_wells,
source_vol,
# mix arguments
mix_tiprack,
# optional arguments
super_vol=600,
rate=0.25,
super_bottom_offset=2,
super_tip_vol=200,
drop_super_tip=True,
wash_vol=300,
remaining=None,
wash_tip=None,
wash_tip_vol=300,
drop_wash_tip=True,
mix_vol=200,
mix_n=10,
drop_mix_tip=False,
mag_engage_height=None,
pause_s=300):
# Wash
# This should:
# - pick up tip from position 7
# - pick up 190 µL from the mag plate
# - air gap
# - dispense into position 11
# - repeat x
# - trash tip
# - move to next column
# - disengage magnet
# remove supernatant
remove_supernatant(pipette,
plate,
cols,
super_tiprack,
super_waste,
tip_vol=super_tip_vol,
super_vol=super_vol,
rate=rate,
bottom_offset=super_bottom_offset,
drop_tip=drop_super_tip)
# disengage magnet
magblock.disengage()
# This should:
# - Pick up tips from column 3 of location 2
# - pick up isopropanol from position 5 column 3
# - dispense to `cols` in mag plate
# - pick up isopropanol from position 5 column 4
# - dispense to `cols` in mag plate
# - drop tips at end
# add isopropanol
wash_wells, wash_remaining = add_buffer(pipette,
source_wells,
plate,
cols,
wash_vol,
source_vol,
tip=wash_tip,
tip_vol=wash_tip_vol,
remaining=remaining,
drop_tip=drop_wash_tip)
# This should:
# - grab a tip from position 8
# - mix 5 times the corresponding well on mag plate
# - blow out
# - return tip
# - do next col
# - engage magnet
# mix
bead_mix(pipette,
plate,
cols,
mix_tiprack,
n=mix_n,
mix_vol=mix_vol,
drop_tip=drop_mix_tip)
# engage magnet
if mag_engage_height is not None:
magblock.engage(height_from_base=mag_engage_height)
else:
magblock.engage()
protocol.delay(seconds=pause_s)
return(wash_wells, wash_remaining)
def run(protocol: protocol_api.ProtocolContext):
# # Magnetic DNA extraction protocol
# #### This follows the Bio-On-Magnetic_Beads protocol 7.1 for
# genomic DNA extraction.
#
# Isolates should have been bead-beat in our strip tubes and spun down in
# the plate centrifuge.
#
# Reagents needed:
# - reservoir plate with 15 mL lysis buffer in columns 1-4
# - reservoir plate with 15 mL Isopropanol in columns 5-8
# - reservoir plate with 15 mL 80% EtOH in columns 9-12
# - deep well plate with ≥300 µL beads in each well of column 1
# - deep well plate with 1 mL elution buffer in each well of column 2
# ### Deck
# 1. deep well plate (empty)
# 2. 300 µL tips - buffer transfer
# 3. PCR plate (final samples)
# 4. Lysate
# 5. reservoir plate (wash buffers)
# 6. 200 µL filter tips - final transfer
# 7. 200 µL filter tips - lysate transfer
# 8. 300 µL tips - bead washes
# 9. empty
# 10. deep well plate (reagents)
# 11. mag module
# 12. trash
# ### Setup
# define deck positions and labware
# define hardware modules
magblock = protocol.load_module('Magnetic Module', 10)
magblock.disengage()
# tips
tiprack_buffers = protocol.load_labware('opentrons_96_tiprack_300ul', 8)
tiprack_elution_1 = protocol.load_labware(
'opentrons_96_filtertiprack_200ul', 5)
tiprack_elution_2 = protocol.load_labware(
'opentrons_96_filtertiprack_200ul', 6)
tiprack_wash = protocol.load_labware('opentrons_96_tiprack_300ul', 4)
# plates
wash_buffers = protocol.load_labware('usascientific_12_reservoir_22ml', 11,
'wash buffers')
eluate = protocol.load_labware('biorad_96_wellplate_200ul_pcr', 3,
'eluate')
waste = protocol.load_labware('nest_1_reservoir_195ml', 7, 'liquid waste')
reagents = protocol.load_labware('nest_12_reservoir_15ml', 9, 'reagents')
lysate = protocol.load_labware('axygen_96_wellplate_1100ul', 1, 'lysate')
# load plate on magdeck
mag_plate = magblock.load_labware('vwr_96_wellplate_1000ul')
# initialize pipettes
pipette_left = protocol.load_instrument('p300_multi',
'left',
tip_racks=[tiprack_buffers])
# Lysis buffer wells
lys_wells = [wash_buffers[x] for x in lys_cols]
# Isopropanol wells
ipa_wells = [wash_buffers[x] for x in ipa_cols]
# Ethanol columns
eth_wells = [wash_buffers[x] for x in eth_cols]
# ### Prompt user to place cells with beads loaded on position 4
protocol.pause('Add lysis beads to strip tubes containing dry cell pellet'
' and place on position 4 for addition of lysis buffer.')
# ### Add lysis buffer
add_buffer(pipette_left, lys_wells, lysate, cols, 580, 18000 / 8)
# ### Prompt user to remove plate
protocol.pause('Remove plate from position 4. \n\n'
'Cap tubes in tube plate and beadbeat for required time. '
'Then spin down, uncap, and return to position 4. \n\n'
'Press continue to start filling plate on mag deck during '
'this time. There will be another pause after plate is '
'filled to allow you to return strip tube plate to '
'position 4 before continuing.')
# ### Add beads to new plate
protocol.comment('Adding beads to wash plate.')
# This should:
# - pick up a tip from location 2
# - pick up reagents from column 1 of location 9
# - distribute 20 µL to each column from `cols` in location 1.
# - trash tip
pipette_left.pick_up_tip()
# mix beads
pipette_left.mix(10, 150, reagents.wells_by_name()['A1'].bottom(z=2))
pipette_left.distribute(20,
reagents.wells_by_name()['A1'],
[mag_plate[x] for x in cols],
mix_before=(2, 20),
touch_tip=False,
disposal_volume=10,
trash=True,
new_tip='never')
pipette_left.drop_tip()
# ### Add isopropanol
protocol.comment('Adding isopropanol to wash plate.')
# This should:
# - Pick up tips from column 2 of location 2
# - pick up isopropanol from position 5 column 1
# - dispense to `cols` in position 1
# - pick up isopropanol from position 5 column 2
# - dispense to `cols` in position 1
# - return tip at end
ipa_remaining, ipa_wells = add_buffer(pipette_left, ipa_wells, mag_plate,
cols, 300, 18000 / 8)
protocol.pause('Decap and return spun-down strip tube plate to position '
'4. \n\nPress continue when ready.')
# ### Transfer lysate to new plate
# # This should:
# - pick up tips in position 7
# - pick up 180 µL lysate from plate in position 4
# - air gap
# - dispense into corresponding well in position 1
# - blow out and touch tip
# - repeat
# - return tip to position 7
# this needs to be modified to position transfer aspirate
# location accurately.
protocol.comment('Transferring lysate to wash plate.')
for col in cols:
# do first transfer.
pipette_left.pick_up_tip(tiprack_wash.wells_by_name()[col])
pipette_left.aspirate(180,
lysate[col].bottom(z=min_height + 5),
rate=0.25)
pipette_left.air_gap(10)
pipette_left.dispense(190, mag_plate[col].top(z=-5))
pipette_left.blow_out()
pipette_left.touch_tip(v_offset=-1)
# do second transfer.
pipette_left.aspirate(180, lysate[col].bottom(z=min_height), rate=0.25)
pipette_left.air_gap(10)
pipette_left.dispense(190, mag_plate[col].top(z=-5))
pipette_left.blow_out()
pipette_left.touch_tip(v_offset=-1)
pipette_left.mix(5, 250, mag_plate[col].bottom(z=1))
pipette_left.blow_out(mag_plate[col].top(z=-2))
pipette_left.return_tip()
# bind
protocol.comment('Binding DNA to beads.')
protocol.delay(seconds=pause_bind)
# mix
for col in cols:
pipette_left.pick_up_tip(tiprack_wash.wells_by_name()[col])
pipette_left.mix(5, 250, mag_plate[col].bottom(z=1))
pipette_left.blow_out(mag_plate[col].top(z=-2))
pipette_left.touch_tip()
pipette_left.return_tip()
# bind for specified length of time
protocol.comment('Binding beads to magnet.')
magblock.engage(height_from_base=mag_engage_height)
protocol.delay(seconds=pause_mag)
# ### Do first wash
protocol.comment('Doing wash #1.')
ipa_remaining, ipa_wells = bead_wash(
# global arguments
protocol,
magblock,
pipette_left,
mag_plate,
cols,
# super arguments
waste['A1'],
tiprack_wash,
# wash buffer arguments
ipa_wells,
18000 / 8,
# mix arguments
tiprack_wash,
# optional arguments
super_vol=700,
drop_super_tip=False,
mix_n=wash_mix,
mix_vol=250,
remaining=ipa_remaining,
mag_engage_height=mag_engage_height)
# ### Do second wash
protocol.comment('Doing wash #2.')
eth_remaining, eth_wells = bead_wash(
# global arguments
protocol,
magblock,
pipette_left,
mag_plate,
cols,
# super arguments
waste['A1'],
tiprack_wash,
# wash buffer arguments
eth_wells,
18000 / 8,
# mix arguments
tiprack_wash,
# optional arguments,
super_vol=300,
drop_super_tip=False,
mix_n=wash_mix,
mix_vol=250,
remaining=None,
mag_engage_height=mag_engage_height)
# ### Do third wash
protocol.comment('Doing wash #3.')
eth_remaining, eth_wells = bead_wash(
# global arguments
protocol,
magblock,
pipette_left,
mag_plate,
cols,
# super arguments
waste['A1'],
tiprack_wash,
# wash buffer arguments
eth_wells,
18000 / 8,
# mix arguments
tiprack_wash,
# optional arguments,
super_vol=300,
drop_super_tip=False,
mix_n=wash_mix,
mix_vol=250,
remaining=eth_remaining,
mag_engage_height=mag_engage_height)
# ### Dry
protocol.comment('Removing wash and drying beads.')
# This should:
# - pick up tip in position 8
# - pick up supernatant from magplate
# - dispense in waste, position 11
# - repeat
# - trash tip
# - leave magnet engaged
# remove supernatant
remove_supernatant(pipette_left,
mag_plate,
cols,
tiprack_wash,
waste['A1'],
super_vol=380,
rate=bead_flow,
bottom_offset=.5,
drop_tip=True)
# dry
protocol.delay(seconds=pause_dry)
# ### Elute
protocol.comment('Eluting DNA from beads.')
# This should:
# - disengage magnet
# - pick up tip from position 6
# - pick up reagents from column 2 of position 9
# - dispense into magplate
# - mix 10 times
# - blow out, touch tip
# - return tip to position 6
# - wait (5 seconds)
# - engage magnet
# - wait (5 seconds)
# - pick up tip from position 6
# - aspirate from magplate
# - dispense to position 3
# - trash tip
# transfer elution buffer to mag plate
magblock.disengage()
# add elution buffer and mix
for col in cols:
pipette_left.pick_up_tip(tiprack_elution_1.wells_by_name()[col])
pipette_left.aspirate(50, reagents['A2'], rate=1)
pipette_left.dispense(50, mag_plate[col].bottom(z=1))
pipette_left.mix(10, 40, mag_plate[col].bottom(z=1))
pipette_left.blow_out(mag_plate[col].top())
pipette_left.touch_tip()
# we'll use these same tips for final transfer
pipette_left.return_tip()
protocol.delay(seconds=pause_elute)
# # start timer
# t0 = clock()
# # mix again
# t_mix = 0
# while t_mix < pause_elute():
for col in cols:
pipette_left.pick_up_tip(tiprack_elution_1.wells_by_name()[col])
pipette_left.mix(10, 40, mag_plate[col].bottom(z=1))
pipette_left.blow_out(mag_plate[col].top())
pipette_left.touch_tip()
# we'll use these same tips for final transfer
pipette_left.drop_tip()
# t_mix = clock() - t0
# bind to magnet
protocol.comment('Binding beads to magnet.')
magblock.engage(height_from_base=mag_engage_height)
protocol.delay(seconds=pause_mag)
protocol.comment('Transferring eluted DNA to final plate.')
for col in cols:
pipette_left.pick_up_tip(tiprack_elution_2.wells_by_name()[col])
pipette_left.aspirate(50, mag_plate[col].bottom(z=2), rate=bead_flow)
pipette_left.dispense(50, eluate[col])
pipette_left.blow_out(eluate[col].top())
pipette_left.touch_tip()
# we're done with these tips now
pipette_left.drop_tip()
magblock.disengage()