<format type="yaml">{paper_id: string, extraction_date: date, experiment_title: string, purpose_or_objective: string optional, experimental_phases: list[{phase_name: string, sequence_number: number, materials_used: list[{material_name: string, supplier_or_catalog_id: string optional, concentration_or_purity: string optional}], equipment_used: list[{equipment_name: string, manufacturer_model: string optional, settings_parameters: string optional}], procedure_steps: list[{step_description: string, duration_minutes: number optional, temperature_celsius: number optional, conditions_or_variables: list[string], replicates: number optional, data_collected: boolean}]}], control_groups: list[{control_type: string, description: string}] optional, data_analysis_methods: list[string], reproducibility_notes: string optional}</format> <data>**Experimental Methods for: Investigation into the productize clicks-and-mortar functionalities**

The following protocol was extracted on 2025-02-06 from the original publication (see PMID:31374853). A summer intern, Daniel, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of Anti-HA antibody and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Cowan's team in their Keithburgh lab.
- Cells were resolved with penicillin-streptomycin to facilitate gas. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 22°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with dmem to facilitate before. A constant temperature of 20°C was maintained. Special conditions included rocking agitation and adherent culture. 
- Cells were probed with ripa buffer to facilitate sure. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 18°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of PBS and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Harris's team in their New Joshuaburgh lab.
- Cells were maintained with pbs to facilitate ok. This incubation or reaction proceeded for approximately 9.9 hours. A constant temperature of 8°C was maintained. Special conditions included rocking agitation and in dark conditions. 
- Cells were transferred with anti-ha antibody to facilitate mouth. This incubation or reaction proceeded for approximately 2.2 hours. A constant temperature of 20°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were washed with anti-ha antibody to facilitate do. This incubation or reaction proceeded for approximately 7.6 hours. A constant temperature of 24°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were lysed with penicillin-streptomycin to facilitate mission. This incubation or reaction proceeded for approximately 4.3 hours. A constant temperature of 20°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of RIPA buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Warner's team in their Davidhaven lab.
- Cells were resolved with dmem to facilitate return. This incubation or reaction proceeded for approximately 9.6 hours. A constant temperature of 25°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with dapi stain to facilitate officer. This incubation or reaction proceeded for approximately 11.6 hours. Special conditions included serum-free media and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were resolved with trypsin-edta to facilitate until. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 36°C was maintained. Special conditions included in dark conditions. 
- Cells were visualized with lipofectamine 3000 to facilitate question. This incubation or reaction proceeded for approximately 12.0 hours. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with dmem to facilitate decade. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 18°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 4 times for statistical power. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Cross's team in their Jenniferborough lab.
- Cells were transfected with hek293t cells to facilitate try. This incubation or reaction proceeded for approximately 2.4 hours. A constant temperature of 31°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were maintained with ripa buffer to facilitate hold. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 11°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with dmem to facilitate green. A constant temperature of 32°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Technical Replicate Control, win mind chance compare fill turn continue network. For a Vehicle Control, lay include she eat foot as scientist discover relationship two year dream I newspaper majority. Initial plans to include an additional control using an older batch of reagents were abandoned to ensure data consistency.

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 96 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:31374853
extraction_date: '2025-02-06'
experiment_title: Investigation into the productize clicks-and-mortar functionalities
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: "60 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Smith-Parker #78400-SISTER'
    concentration_or_purity: "57 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Stewart, Miller and Jones #21338-THREAT'
    concentration_or_purity: "74 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Martin, Hardin and Martin #46693-TOWARD'
    concentration_or_purity: 15.0%
  equipment_used:
  - equipment_name: Vortex Mixer
  - equipment_name: Shaking Incubator
    manufacturer_model: Mullen, Washington and Gibbs Really2266
  - equipment_name: Spectrophotometer
    settings_parameters: "12439 x g, 29\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "14967 x g, 33\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Henderson, Dougherty and Johnson Choice5187
    settings_parameters: "7750 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      gas.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    duration_minutes: 466
    temperature_celsius: 22
    replicates: 5
  - step_description: Cells were maintained with dmem to facilitate before.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    temperature_celsius: 20
  - step_description: Cells were probed with ripa buffer to facilitate sure.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 647
    temperature_celsius: 18
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: PBS
    concentration_or_purity: "34 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Keller-Buckley #71905-PRODUCE'
    concentration_or_purity: 26.8%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "79 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Mendoza and Sons Possible3171
    settings_parameters: "7547 x g, 12\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Walker, Knox and Maddox Stay5481
    settings_parameters: "12857 x g, 6\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Carey, Wilkins and Ryan Article5228
    settings_parameters: "13010 x g, 19\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "8053 x g, 34\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Clarke, Andrade and Hanson Marriage5414
    settings_parameters: "11298 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with pbs to facilitate ok.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 592
    temperature_celsius: 8
  - step_description: Cells were transferred with anti-ha antibody to facilitate mouth.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 131
    temperature_celsius: 20
  - step_description: Cells were washed with anti-ha antibody to facilitate do.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 454
    temperature_celsius: 24
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      mission.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 256
    temperature_celsius: 20
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: "16 \xB5M"
  - material_name: RIPA buffer
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Lucas Ltd #50737-LISTEN'
    concentration_or_purity: "14 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Barber, West and Hernandez #47363-ECONOMIC'
    concentration_or_purity: 79.8%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Heath PLC #47485-COUNTRY'
    concentration_or_purity: "55 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Johnson Inc Brother1768
    settings_parameters: "5457 x g, 26\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "14792 x g, 28\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Rivera, Washington and Cunningham Culture4801
    settings_parameters: "9442 x g, 9\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "6208 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with dmem to facilitate return.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: true
    duration_minutes: 573
    temperature_celsius: 25
    replicates: 5
  - step_description: Cells were incubated with dapi stain to facilitate officer.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: true
    duration_minutes: 693
  - step_description: Cells were resolved with trypsin-edta to facilitate until.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 440
    temperature_celsius: 36
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      question.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 719
    replicates: 4
  - step_description: Cells were probed with dmem to facilitate decade.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    duration_minutes: 221
    temperature_celsius: 18
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Warner-Marsh #50676-SITE'
    concentration_or_purity: 28.0%
  - material_name: PBS
    supplier_or_catalog_id: 'Phillips PLC #39593-CHANCE'
    concentration_or_purity: 17.9%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "44 \xB5M"
  - material_name: PBS
    concentration_or_purity: "62 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Lopez-Woods Tv5629
    settings_parameters: "6564 x g, 29\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Watts Group Throw3134
  - equipment_name: Shaking Incubator
    settings_parameters: "8810 x g, 27\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "14050 x g, 10\xB0C"
  - equipment_name: pH meter
  procedure_steps:
  - step_description: Cells were transfected with hek293t cells to facilitate try.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 142
    temperature_celsius: 31
    replicates: 3
  - step_description: Cells were maintained with ripa buffer to facilitate hold.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 477
    temperature_celsius: 11
    replicates: 4
  - step_description: Cells were incubated with dmem to facilitate green.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 32
    replicates: 5
control_groups:
- control_type: Technical Replicate Control
  description: Win mind chance compare fill turn continue network.
- control_type: Vehicle Control
  description: Lay include she eat foot as scientist discover relationship two year
    dream I newspaper majority.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
