<commit_before>Category_tags: ''
Input: Nucleic Acid, DNA
Name: <NAME>
Output: Image Data, separated dsDNA in agarose gel
Reference_DOI: 10.1002/0471142727.mb0205as51
Reference_PMID: '18265185'
Reference_URL: ''
Remarks: ''
Specific_tags: ''
components-location:
- [23, 0, 2]
- [47, 0, 6]
steps:
- Actions:
  - {duration_comment: Active, time_units: minutes, verb: prepare, what: an_adequate_volume_of_electrophoresis_buffer_(tae_or_tbe),
    why: to fill the electrophoresis tank and prepare the gel}
  - {duration_comment: Active; Optional, how: to a final concentration of 0.5 ug/ml,
    remark: 'if buffer is prepared for the electrophoresis tank and the gel separately,
      be sure to bring both to an identical concentration of ethidium bromide.', time_units: minutes,
    verb: add, what: ethidium_bromide_solution}
  - component - list:
    - {max_conc: '1.5', max_vol: user input, min_conc: '0.8', min_vol: user input,
      note: Percentage (mass/vol) of agarose in electrophoresis buffer, reagent_name: 'Agarose,
        Electrophoresis-grade', vol_units: User input}
    - {max_vol: user input, min_vol: user input, reagent_name: 'Buffer, Electrophoresis
        buffer (TAE)', vol_units: User input}
    duration_comment: Active
    time_units: minutes
    verb: combine
  - {duration_comment: 'Passive, ~1 minute per 100ml of Agarose solution', machine: in
      a microwave oven or autoclave, time_units: minutes, verb: melt, what: the_agarose}
  - {duration_comment: Active, remark: 'gels typically contain 0.8 to 1.5% agarose
      (see critical parameters, agarose concentration)', time_units: minutes, verb: swirl,
    why: to ensure even mixing}
  - {duration_comment: Passive; Optional, machine: water bath, max_temp: '55', max_time: '15',
    min_temp: '55', min_time: '15', remark: "remember to keep in mind that the volume\
      \ of the sample wells will be \ndetermined by both the thickness of the gel\
      \ and the size of the gel \ncomb.", temp_comment: Target temperature, temp_units: degrees
      Celsius, time_units: minutes, verb: cool, what: the_melted_agarose, why: this
      prevents warping of the gel apparatus.}
  - component - list:
    - {max_conc: '1.5', min_conc: '0.5', note: Percentage (mass/vol) of agarose in
        electrophoresis buffer, reagent_name: 'Agarose, Electrophoresis-grade'}
    - {max_vol: user input, min_vol: user input, reagent_name: 'Buffer, Electrophoresis
        buffer (TBE)', vol_units: User input}
    duration_comment: Active
    time_units: minutes
    verb: add
  - {duration_comment: 'Passive, ~1 minute per 100ml of Agarose solution', machine: in
      a microwave oven or autoclave, time_units: minutes, verb: melt, what: the_agarose}
  - {duration_comment: Active, remark: 'gels typically contain 0.8 to 1.5% agarose
      (see critical parameters, agarose concentration)', time_units: minutes, verb: swirl,
    why: to ensure even mixing}
  - {duration_comment: Passive; Optional, machine: water bath, max_temp: '55', max_time: '15',
    min_temp: '55', min_time: '15', remark: "remember to keep in mind that the volume\
      \ of the sample wells will be \ndetermined by both the thickness of the gel\
      \ and the size of the gel \ncomb.", temp_comment: Target temperature, temp_units: degrees
      Celsius, time_units: minutes, verb: cool, what: the_melted_agarose, why: this
      prevents warping of the gel apparatus.}
  remark: "Remember to keep in mind that the volume of the sample wells will be \n\
    determined by both the thickness of the gel and the size of the gel \ncomb."
  stepnum: 0
- Actions:
  - {duration_comment: Active, max_time: '15', min_time: '15', time_units: minutes,
    verb: seal, what: the_gel_casting_platform}
  - {duration_comment: Active; Optional, pasteur_pipet: to the joints and edges of
      the gel platform, remark: optional 1, time_units: minutes, verb: apply, what: hot_agarose,
    why: as an added measure to prevent leakage}
  - {duration_comment: Active; Optional, how: until the gel has hardened, remark: optional
      2, time_units: minutes, verb: let_sit/stand}
  - {duration_comment: Active, time_units: minutes, verb: pour, what: the_melted_agarose}
  - {duration_comment: Active, max_time: '0.5', min_time: '0.5', time_units: minutes,
    verb: insert, what: the_gel_comb}
  - {duration_comment: Active, remark: most gel platforms are sealed by taping the
      open ends with adhesive tape, time_units: minutes, verb: check, what: make_sure_that_no_bubbles_are_trapped_underneath_the_combs_and_all_bubbles_on_the_surface_of_the_agarose_are_removed_before_the_gel_sets.}
  - {duration_comment: Passive, how: until the gel has hardened, max_time: '15', min_time: '15',
    time_units: minutes, verb: let_sit/stand}
  - {duration_comment: Passive; Optional, max_time: '15', min_time: '15', remark: recommended,
    temp_units: degrees Celsius, time_units: minutes, verb: cool, what: agarose_gel,
    why: to gain extra rigidity and prevent tearing.}
  remark: Most gel platforms are sealed by taping the open ends with adhesive tape
  stepnum: 1
- Actions:
  - {duration_comment: Active, time_units: minutes, verb: remove, what: the_tape_from_the_open_ends_of_the_gel_platform}
  - {duration_comment: Active, how: take care not to tear the sample wells, remark: most
      gel platforms are designed so that 0.5 to 1 mm of agarose remains between the
      bottom of the comb and the base of the gel platform. this is usually sufficient
      to ensure that the sample wells are completely sealed and to prevent tearing
      of the agarose upon removal of the comb., time_units: minutes, verb: withdraw,
    what: the_gel_comb}
  remark: Most gel platforms are designed so that 0.5 to 1 mm of agarose remains between
    the bottom of the comb and the base of the gel platform. This is usually sufficient
    to ensure that the sample wells are completely sealed and to prevent tearing of
    the agarose upon removal of the comb.
  stepnum: 2
- Actions:
  - {duration_comment: Active, time_units: minutes, verb: place, what: the_gel_casting_platform_containing_the_set_gel}
  - {duration_comment: Active, how: make sure no air pockets are trapped within the
      wells., time_units: minutes, verb: add, what: sufficient_electrophoresis_buffer}
  stepnum: 3
- Actions:
  - {duration_comment: Active, how: in a volume that will not overflow the gel wells
      by addition of the appropriate amount of 10_ loading buffer., remark: recommended,
    time_units: minutes, verb: prepare, what: dna_samples}
  - {duration_comment: Active; Per sample, pipettor_or_micropipet: into wells in agarose
      gel, remark: be sure to include appropriate dna molecular weight markers (see
      fig. 2.5.3)., time_units: minutes, verb: load, what: dna_samples_in_loading_buffer}
  stepnum: 4
- Actions:
  - {duration_comment: Active, time_units: minutes, verb: check, what: be_sure_that_the_leads_are_attached_so_that_the_dna_will_migrate_into_the_gel_toward_the_anode_or_positive_lead.}
  - {duration_comment: Passive, max_time: '45', max_voltage: '10', min_time: '10',
    the_progress_of_the_separation_can_be_monitored_by_the_migration_of_the_dyes_in_the_loading_buffer.: 'CAUTION:
      To prevent electrical shocks, the gel apparatus should always be covered and
      kept away from heavily used work spaces.', time_units: minutes, verb: electrophorese,
    voltage_comment: 1 to 10 volts per centimeter of gel, voltage_units: Volts/centimeter}
  - {duration_comment: Active, max_time: '0.5', min_time: '0.5', time_units: minutes,
    verb: switch_off, what: the_power_supply}
  - {duration_comment: Passive; Conditional, how: in water, max_time: '30', min_time: '30',
    remark: optional, time_units: minutes, verb: shake, what: the_agarose_gel, why: this
      serves to remove excess ethidium bromide which causes background fluorescence
      and makes visualization of small quantities of dna difficult.}
  - {duration_comment: Active; Conditional, time_units: minutes, verb: place, what: the_agarose_gel}
  - {duration_comment: Active, max_time: '10', remark: see support protocol 2 (specific
      to this protocol), time_units: minutes, verb: photograph, what: the_agarose_gel}
  - {duration_comment: Active, max_time: '0.5', min_time: '0.5', time_units: minutes,
    verb: switch_off, what: the_power_supply}
  - duration_comment: Active; Conditional
    how: !!binary |
      aW4gYSBkaWx1dGUgc29sdXRpb24gb2YgZXRoaWRpdW0gYnJvbWlkZSAoMC41ILVnL21sIGluIHdh
      dGVyKQ==
    time_units: minutes
    verb: cover
    what: the_agarose_gel
    why: to stain the agarose gel
  - {duration_comment: Passive; Conditional, how: gently, max_time: '30', min_time: '10',
    time_units: minutes, verb: agitate}
  - {duration_comment: Passive; Conditional, how: in water, max_time: '30', min_time: '30',
    remark: optional, time_units: minutes, verb: shake, what: the_agarose_gel, why: this
      serves to remove excess ethidium bromide which causes background fluorescence
      and makes visualization of small quantities of dna difficult.}
  - {duration_comment: Active, max_time: '0.5', min_time: '0.5', time_units: minutes,
    verb: place, what: the_agarose_gel}
  - {duration_comment: Active, max_time: '10', remark: see support protocol 2 (specific
      to this protocol), time_units: minutes, verb: photograph, what: the_agarose_gel}
  stepnum: 5<commit_msg>old csvparser settings<commit_after>Category_tags: ''
Input: Nucleic Acid, DNA
Name: Agarose Gel Electrophoresis
Output: Image Data, separated dsDNA in agarose gel
Reference_DOI: 10.1002/0471142727.mb0205as51
Reference_PMID: '18265185'
Reference_URL: ''
Remarks: ''
Specific_tags: ''
components-location:
- [23, 0, 2]
- [47, 0, 6]
steps:
- Actions:
  - {duration_comment: Active, max_time: '5', min_time: '5', time_units: minutes,
    verb: prepare, what: an_adequate_volume_of_electrophoresis_buffer_(tae_or_tbe),
    why: to fill the electrophoresis tank and prepare the gel}
  - {duration_comment: Active; Optional, how: to a final concentration of 0.5 ug/ml,
    max_time: '2', min_time: '2', remark: 'if buffer is prepared for the electrophoresis
      tank and the gel separately, be sure to bring both to an identical concentration
      of ethidium bromide.', time_units: minutes, verb: add, what: ethidium_bromide_solution,
    where: to the electrophoresis buffer}
  - component - list:
    - {conc_units: '%', max_conc: '1.5', max_vol: user input, min_conc: '0.8', min_vol: user
        input, note: Percentage (mass/vol) of agarose in electrophoresis buffer, reagent_name: 'Agarose,
        Electrophoresis-grade', vol_units: User input}
    - {max_vol: user input, min_vol: user input, reagent_name: 'Buffer, Electrophoresis
        buffer (TAE)', vol_units: User input}
    duration_comment: Active
    max_time: '1'
    min_time: '1'
    time_units: minutes
    verb: combine
  - {duration_comment: 'Passive, ~1 minute per 100ml of Agarose solution', machine: in
      a microwave oven or autoclave, max_time: '1', min_time: '1', time_units: minutes,
    verb: melt, what: the_agarose}
  - {duration_comment: Active, max_time: '1', min_time: '1', remark: 'gels typically
      contain 0.8 to 1.5% agarose (see critical parameters, agarose concentration)',
    time_units: minutes, verb: swirl, why: to ensure even mixing}
  - {duration_comment: Passive; Optional, machine: water bath, max_temp: '55', max_time: '15',
    min_temp: '55', min_time: '15', remark: "remember to keep in mind that the volume\
      \ of the sample wells will be \ndetermined by both the thickness of the gel\
      \ and the size of the gel \ncomb.", temp_comment: Target temperature, temp_units: degrees
      Celsius, time_units: minutes, verb: cool, what: the_melted_agarose, why: this
      prevents warping of the gel apparatus.}
  - component - list:
    - {conc_units: '%', max_conc: '1.5', min_conc: '0.5', note: Percentage (mass/vol)
        of agarose in electrophoresis buffer, reagent_name: 'Agarose, Electrophoresis-grade'}
    - {max_vol: user input, min_vol: user input, reagent_name: 'Buffer, Electrophoresis
        buffer (TBE)', vol_units: User input}
    duration_comment: Active
    max_time: '1'
    min_time: '1'
    time_units: minutes
    verb: add
  - {duration_comment: 'Passive, ~1 minute per 100ml of Agarose solution', machine: in
      a microwave oven or autoclave, max_time: '1', min_time: '1', time_units: minutes,
    verb: melt, what: the_agarose}
  - {duration_comment: Active, max_time: '1', min_time: '1', remark: 'gels typically
      contain 0.8 to 1.5% agarose (see critical parameters, agarose concentration)',
    time_units: minutes, verb: swirl, why: to ensure even mixing}
  - {duration_comment: Passive; Optional, machine: water bath, max_temp: '55', max_time: '15',
    min_temp: '55', min_time: '15', remark: "remember to keep in mind that the volume\
      \ of the sample wells will be \ndetermined by both the thickness of the gel\
      \ and the size of the gel \ncomb.", temp_comment: Target temperature, temp_units: degrees
      Celsius, time_units: minutes, verb: cool, what: the_melted_agarose, why: this
      prevents warping of the gel apparatus.}
  remark: "Remember to keep in mind that the volume of the sample wells will be \n\
    determined by both the thickness of the gel and the size of the gel \ncomb."
  stepnum: 0
- Actions:
  - {duration_comment: Active, max_time: '15', min_time: '15', time_units: minutes,
    verb: seal, what: the_gel_casting_platform}
  - {duration_comment: Active; Optional, max_time: '5', min_time: '5', remark: optional
      1, time_units: minutes, tool: pasteur pipet, verb: apply, what: hot_agarose,
    where: to the joints and edges of the gel platform, why: as an added measure to
      prevent leakage}
  - {duration_comment: Active; Optional, how: until the gel has hardened, max_time: '5',
    min_time: '5', remark: optional 2, time_units: minutes, verb: let_sit/stand}
  - {duration_comment: Active, max_time: '1', min_time: '1', time_units: minutes,
    verb: pour, what: the_melted_agarose, where: into the gel casting platform}
  - {duration_comment: Active, max_time: '0.5', min_time: '0.5', time_units: minutes,
    verb: insert, what: the_gel_comb}
  - {duration_comment: Active, max_time: '1', min_time: '1', remark: most gel platforms
      are sealed by taping the open ends with adhesive tape, time_units: minutes,
    verb: check, what: make_sure_that_no_bubbles_are_trapped_underneath_the_combs_and_all_bubbles_on_the_surface_of_the_agarose_are_removed_before_the_gel_sets.}
  - {duration_comment: Passive, how: until the gel has hardened, max_time: '15', min_time: '15',
    time_units: minutes, verb: let_sit/stand}
  - {duration_comment: Passive; Optional, max_temp: '4', max_time: '15', min_temp: '4',
    min_time: '15', remark: recommended, temp_units: degrees Celsius, time_units: minutes,
    verb: cool, what: agarose_gel, why: to gain extra rigidity and prevent tearing.}
  remark: Most gel platforms are sealed by taping the open ends with adhesive tape
  stepnum: 1
- Actions:
  - {duration_comment: Active, max_time: '1', min_time: '1', time_units: minutes,
    verb: remove, what: the_tape_from_the_open_ends_of_the_gel_platform}
  - {duration_comment: Active, how: take care not to tear the sample wells, max_time: '1',
    min_time: '1', remark: most gel platforms are designed so that 0.5 to 1 mm of
      agarose remains between the bottom of the comb and the base of the gel platform.
      this is usually sufficient to ensure that the sample wells are completely sealed
      and to prevent tearing of the agarose upon removal of the comb., time_units: minutes,
    verb: withdraw, what: the_gel_comb}
  remark: Most gel platforms are designed so that 0.5 to 1 mm of agarose remains between
    the bottom of the comb and the base of the gel platform. This is usually sufficient
    to ensure that the sample wells are completely sealed and to prevent tearing of
    the agarose upon removal of the comb.
  stepnum: 2
- Actions:
  - {duration_comment: Active, max_time: '1', min_time: '1', time_units: minutes,
    verb: place, what: the_gel_casting_platform_containing_the_set_gel, where: in
      the electrophoresis tank}
  - {duration_comment: Active, how: make sure no air pockets are trapped within the
      wells., max_time: '1', min_time: '1', time_units: minutes, verb: add, what: sufficient_electrophoresis_buffer,
    where: to the electrophoresis tank}
  stepnum: 3
- Actions:
  - {duration_comment: Active, how: in a volume that will not overflow the gel wells
      by addition of the appropriate amount of 10_ loading buffer., max_time: '1',
    min_time: '1', remark: recommended, time_units: minutes, verb: prepare, what: dna_samples}
  - {duration_comment: Active; Per sample, max_time: '1', min_time: '1', remark: be
      sure to include appropriate dna molecular weight markers (see fig. 2.5.3).,
    time_units: minutes, tool: pipettor or micropipet, verb: load, what: dna_samples_in_loading_buffer,
    where: into wells in agarose gel}
  stepnum: 4
- Actions:
  - {duration_comment: Active, max_time: '1', min_time: '1', time_units: minutes,
    verb: check, what: be_sure_that_the_leads_are_attached_so_that_the_dna_will_migrate_into_the_gel_toward_the_anode_or_positive_lead.}
  - {duration_comment: Passive, max_time: '45', max_voltage: '10', min_time: '10',
    min_voltage: '1', the_progress_of_the_separation_can_be_monitored_by_the_migration_of_the_dyes_in_the_loading_buffer.: 'CAUTION:
      To prevent electrical shocks, the gel apparatus should always be covered and
      kept away from heavily used work spaces.', time_units: minutes, verb: electrophorese,
    voltage_comment: 1 to 10 volts per centimeter of gel, voltage_units: Volts/centimeter}
  - {duration_comment: Active, max_time: '0.5', min_time: '0.5', time_units: minutes,
    verb: switch_off, what: the_power_supply}
  - {duration_comment: Passive; Conditional, how: in water, max_time: '30', min_time: '30',
    remark: optional, time_units: minutes, verb: shake, what: the_agarose_gel, why: this
      serves to remove excess ethidium bromide which causes background fluorescence
      and makes visualization of small quantities of dna difficult.}
  - {duration_comment: Active; Conditional, max_time: '1', min_time: '1', time_units: minutes,
    verb: place, what: the_agarose_gel, where: on a uv light source}
  - {duration_comment: Active, max_time: '10', min_time: '5', remark: see support
      protocol 2 (specific to this protocol), time_units: minutes, verb: photograph,
    what: the_agarose_gel}
  - {duration_comment: Active, max_time: '0.5', min_time: '0.5', time_units: minutes,
    verb: switch_off, what: the_power_supply}
  - duration_comment: Active; Conditional
    how: !!binary |
      aW4gYSBkaWx1dGUgc29sdXRpb24gb2YgZXRoaWRpdW0gYnJvbWlkZSAoMC41ILVnL21sIGluIHdh
      dGVyKQ==
    max_time: '1'
    min_time: '1'
    time_units: minutes
    verb: cover
    what: the_agarose_gel
    why: to stain the agarose gel
  - {duration_comment: Passive; Conditional, how: gently, max_time: '30', min_time: '10',
    time_units: minutes, verb: agitate}
  - {duration_comment: Passive; Conditional, how: in water, max_time: '30', min_time: '30',
    remark: optional, time_units: minutes, verb: shake, what: the_agarose_gel, why: this
      serves to remove excess ethidium bromide which causes background fluorescence
      and makes visualization of small quantities of dna difficult.}
  - {duration_comment: Active, max_time: '0.5', min_time: '0.5', time_units: minutes,
    verb: place, what: the_agarose_gel, where: on a uv light source}
  - {duration_comment: Active, max_time: '10', min_time: '5', remark: see support
      protocol 2 (specific to this protocol), time_units: minutes, verb: photograph,
    what: the_agarose_gel}
  stepnum: 5
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