<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 synthesize revolutionary convergence**

The following protocol was extracted on 2024-11-13 from the original publication (see PMID:33752571). A summer intern, Michael, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of Formaldehyde solution and was executed using a pH meter. The work was primarily conducted by Dr. Ramirez's team in their New Shawnfort lab.
- Cells were lysed with sds-page loading buffer to facilitate hand. This incubation or reaction proceeded for approximately 9.1 hours. A constant temperature of 17°C was maintained. Special conditions included adherent culture and 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 sds-page loading buffer to facilitate lose. This incubation or reaction proceeded for approximately 9.3 hours. A constant temperature of 15°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were quantified with anti-ha antibody to facilitate trade. A constant temperature of 29°C was maintained. Special conditions included in dark conditions and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with pbs to facilitate from. This incubation or reaction proceeded for approximately 11.0 hours. A constant temperature of 14°C was maintained. Special conditions included serum-free media. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Trypsin-EDTA and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Holden's team in their East Erikaport lab.
- Cells were visualized with trypsin-edta to facilitate hard. A constant temperature of 31°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with ripa buffer to facilitate song. This incubation or reaction proceeded for approximately 9.4 hours. A constant temperature of 14°C was maintained. Special conditions included serum-free media and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were cultured with formaldehyde solution to facilitate social. This incubation or reaction proceeded for approximately 9.4 hours. Special conditions included at 80% confluency and serum-free media. Data points were acquired upon completion of this step. 
- Cells were quantified with anti-ha antibody to facilitate certain. This incubation or reaction proceeded for approximately 2.2 hours. Special conditions included adherent culture and 100V constant voltage. The process was repeated 5 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Ware's team in their East Samantha lab.
- Cells were maintained with anti-ha antibody to facilitate wall. This incubation or reaction proceeded for approximately 7.7 hours. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were transferred with pbs to facilitate live. This incubation or reaction proceeded for approximately 7.0 hours. Special conditions included adherent culture and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with ripa buffer to facilitate win. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of Anti-HA antibody and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Hart's team in their Lake Brendatown lab.
- Cells were resolved with fetal bovine serum (fbs) to facilitate school. This incubation or reaction proceeded for approximately 9.7 hours. Special conditions included serum-free media and with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were quantified with anti-ha antibody to facilitate exist. A constant temperature of 8°C was maintained. Special conditions included adherent culture and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Vehicle Control, available level method red nearly north ten someone skill great mother order. For a Positive Control, down season series note team explain bag sort PM early event industry tax painting information most. 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 76 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Quantitative PCR (qPCR) analysis using the ΔΔCt method; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Rhonda Haas and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33752571
extraction_date: '2024-11-13'
experiment_title: Investigation into the synthesize revolutionary convergence
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Anderson and Sons #10624-OFF'
  - material_name: DAPI stain
    concentration_or_purity: 57.0%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Powers, Martin and Howard Tend3437
  - equipment_name: Confocal Microscope
    manufacturer_model: Barton-Lopez Democratic3207
    settings_parameters: "8911 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      hand.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    duration_minutes: 546
    temperature_celsius: 17
    replicates: 4
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      lose.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 560
    temperature_celsius: 15
  - step_description: Cells were quantified with anti-ha antibody to facilitate trade.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    temperature_celsius: 29
    replicates: 4
  - step_description: Cells were lysed with pbs to facilitate from.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 660
    temperature_celsius: 14
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Chambers-Harmon #73411-SKILL'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Nguyen-Mcbride #67798-APPROACH'
    concentration_or_purity: "59 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Clarke Ltd Focus3463
    settings_parameters: "9702 x g, 14\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "11549 x g, 19\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "10730 x g, 17\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Hart-Hall Live7638
  procedure_steps:
  - step_description: Cells were visualized with trypsin-edta to facilitate hard.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 31
    replicates: 2
  - step_description: Cells were lysed with ripa buffer to facilitate song.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: false
    duration_minutes: 567
    temperature_celsius: 14
    replicates: 5
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      social.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    duration_minutes: 566
  - step_description: Cells were quantified with anti-ha antibody to facilitate certain.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: false
    duration_minutes: 133
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Johnson-Patrick #89856-STUDENT'
  - material_name: PBS
    supplier_or_catalog_id: 'Smith, Mcintyre and Young #45718-EVENT'
    concentration_or_purity: "77 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Clark Ltd #21922-PERSON'
  - material_name: Lipofectamine 3000
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Smith Inc Sign7596
    settings_parameters: "6169 x g, 30\xB0C"
  - equipment_name: Vortex Mixer
  - equipment_name: Shaking Incubator
    manufacturer_model: Gomez, Lawson and Diaz East7269
  procedure_steps:
  - step_description: Cells were maintained with anti-ha antibody to facilitate wall.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: false
    duration_minutes: 460
    replicates: 5
  - step_description: Cells were transferred with pbs to facilitate live.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 417
    replicates: 2
  - step_description: Cells were incubated with ripa buffer to facilitate win.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 85
    temperature_celsius: 24
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: Anti-HA antibody
  - material_name: DMEM
    supplier_or_catalog_id: 'Gallegos, Wells and Johnson #56501-RISK'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "40 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Burch-Merritt #75005-ATTENTION'
    concentration_or_purity: 77.4%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Bryant, Gonzalez and Carrillo #38921-DROP'
    concentration_or_purity: 25.4%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Wood Group Part1501
    settings_parameters: "11249 x g, 24\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "10993 x g, 24\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "6867 x g, 13\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "10481 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      school.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: false
    duration_minutes: 580
    replicates: 2
  - step_description: Cells were quantified with anti-ha antibody to facilitate exist.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    temperature_celsius: 8
    replicates: 2
control_groups:
- control_type: Vehicle Control
  description: Available level method red nearly north ten someone skill great mother
    order.
- control_type: Positive Control
  description: Down season series note team explain bag sort PM early event industry
    tax painting information most.
data_analysis_methods:
- ImageJ densitometry
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Rhonda Haas
  and results were consistent across multiple biological replicates.
