def step(env, rxn, inputs=None):
'''DNA Ligation'''
env.rprotocol.step('ligation', 'DNA Ligation.')
lig = rxn.reactions[0]
s, t = relocate_volume(env, inputs, vol=5 * ureg.microliter)
s = react(env, lig.solution, lig.incubation, t)
return s
def step(env, rxn, inputs=None):
'''DNA Ligation'''
env.rprotocol.step('ligation', 'DNA Ligation.')
lig = rxn.reactions[0]
s, t = relocate_volume(env, inputs, vol=5*ureg.microliter)
s = react(env, lig.solution, lig.incubation, t)
return s
def step(env, rxn, inputs=None):
'''Bead purification of DNA using Agencourt AMPure XP magnetic beads.
Adapted from https://www.beckmancoulter.com/wsrportal/techdocs?docname=B37419AA
Presently the max volume for this step is set at 110 microliters.
Important - a strong magnet should be used. The magnet should be on the side of
the tube (?).
'''
env.rprotocol.step(
'purification',
'Bead purification of DNA using Agencourt AMPure XP magnetic beads..')
bnd, wsh, elu = rxn.reactions
bead_ratio = bnd.params.beadratio
bead_frac = bead_ratio / (1 + bead_ratio)
# ------- Binding to beads
s, t = relocate_volume(env, inputs, vol=5 * ureg.microliter)
s = dilute_dev(env, t, bnd.params.beads, ratio=bead_ratio)
s = mix(env, s, 10)
s = incubate(env, s, bnd.params.premagtemp, bnd.params.premagtime)
s = incubate(env, s, bnd.params.magtemp, bnd.params.magtime, mag=True)
# ------------------------
# -------- Ethanol wash
# Remove non-bead volume and discard
s, t = relocate_volume(env, s, fraction=1.0)
s = dilute_dev(env, s, wsh.params.etoh, wsh.params.etohvol)
s, t = relocate_volume(env, s, vol=wsh.params.etohvol)
s = plate_off_mag_adapter(env, s)
s = incubate(env, s, wsh.params.drytemp, wsh.params.drytime, mag=False)
# ---------------------
# --------- Re-suspension
s = dilute_dev(env, s, elu.solution.components, elu.params.eluentvol)
s = mix(env, s, 20)
#s = incubate(env, s, elu.params.premagtemp, elu.params.premagtime, mag=False)
s = incubate(env, s, elu.params.magtemp, elu.params.magtime, mag=True)
# ------------------------
s, t = relocate_volume(env, s, fraction=0.95)
return t
def step(env, rxn, inputs=None):
'''Reverse chromatin crosslinks'''
env.rprotocol.step('reversal', 'Reverse chromatin crosslinks')
rna, pk = rxn.reactions
s, t = relocate_volume(env, inputs, vol=5 * ureg.microliter)
s = react(env, rna.solution, rna.incubation, t)
s = react(env, pk.solution, pk.incubation, s)
return s
def step(env, rxn, inputs=None):
'''Reverse chromatin crosslinks'''
env.rprotocol.step('reversal', 'Reverse chromatin crosslinks')
rna, pk = rxn.reactions
s, t = relocate_volume(env, inputs, vol=5*ureg.microliter)
s = react(env, rna.solution, rna.incubation, t)
s = react(env, pk.solution, pk.incubation, s)
return s
def step(env, rxn, inputs=None):
'''Amplicon sequencing library prep from purified DNA.'''
env.rprotocol.step('amplicon_library', 'Amplicon sequencing library prep from purified DNA.')
amp, pur, quant = rxn.reactions
s, t = relocate_volume(env, inputs, vol=5*ureg.microliter)
s = pcr(env, amp, t)
s = purification(env, pur, s)
#s = quantification(env, quant, s)
return s
def step(env, rxn, inputs=None):
'''Bead purification of DNA using Agencourt AMPure XP magnetic beads.
Adapted from https://www.beckmancoulter.com/wsrportal/techdocs?docname=B37419AA
Presently the max volume for this step is set at 110 microliters.
Important - a strong magnet should be used. The magnet should be on the side of
the tube (?).
'''
env.rprotocol.step('purification', 'Bead purification of DNA using Agencourt AMPure XP magnetic beads..')
bnd, wsh, elu = rxn.reactions
bead_ratio = bnd.params.beadratio
bead_frac = bead_ratio/(1 + bead_ratio)
# ------- Binding to beads
s, t = relocate_volume(env, inputs, vol=5*ureg.microliter)
s = dilute_dev(env, t, bnd.params.beads, ratio=bead_ratio)
s = mix(env, s, 10)
s = incubate(env, s, bnd.params.premagtemp, bnd.params.premagtime)
s = incubate(env, s, bnd.params.magtemp, bnd.params.magtime, mag=True)
# ------------------------
# -------- Ethanol wash
# Remove non-bead volume and discard
s, t = relocate_volume(env, s, fraction=1.0)
s = dilute_dev(env, s, wsh.params.etoh, wsh.params.etohvol)
s, t = relocate_volume(env, s, vol=wsh.params.etohvol)
s = plate_off_mag_adapter(env, s)
s = incubate(env, s, wsh.params.drytemp, wsh.params.drytime, mag=False)
# ---------------------
# --------- Re-suspension
s = dilute_dev(env, s, elu.solution.components, elu.params.eluentvol)
s = mix(env, s, 20)
#s = incubate(env, s, elu.params.premagtemp, elu.params.premagtime, mag=False)
s = incubate(env, s, elu.params.magtemp, elu.params.magtime, mag=True)
# ------------------------
s, t = relocate_volume(env, s, fraction=0.95)
return t
def step(env, rxn, inputs=None):
'''Amplicon sequencing library prep from purified DNA.'''
env.rprotocol.step('amplicon_library',
'Amplicon sequencing library prep from purified DNA.')
amp, pur, quant = rxn.reactions
s, t = relocate_volume(env, inputs, vol=5 * ureg.microliter)
s = pcr(env, amp, t)
s = purification(env, pur, s)
#s = quantification(env, quant, s)
return s