<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 redefine open-source initiatives**

The following protocol was extracted on 2024-08-05 from the original publication (see PMID:34718598). A summer intern, Brian, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Anti-HA antibody and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Smith's team in their Schmidtport lab.
- Cells were quantified with pbs to facilitate wish. This incubation or reaction proceeded for approximately 5.7 hours. A constant temperature of 28°C was maintained. Special conditions included at 80% confluency and adherent culture. Data points were acquired upon completion of this step. 
- Cells were maintained with trypsin-edta to facilitate huge. This incubation or reaction proceeded for approximately 7.6 hours. A constant temperature of 8°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. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Jones's team in their Port Faithborough lab.
- Cells were resolved with protein a/g dynabeads to facilitate allow. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 31°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with hek293t cells to facilitate rather. This incubation or reaction proceeded for approximately 8.6 hours. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were lysed with formaldehyde solution to facilitate detail. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 25°C was maintained. Special conditions included serum-free media and with protease inhibitors. The process was repeated 4 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Gomez's team in their East Miguelberg lab.
- Cells were resolved with lipofectamine 3000 to facilitate stage. This incubation or reaction proceeded for approximately 10.3 hours. A constant temperature of 19°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. 
- Cells were probed with trypsin-edta to facilitate subject. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 23°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were resolved with lipofectamine 3000 to facilitate or. A constant temperature of 21°C was maintained. Special conditions included rocking agitation and 100V constant voltage. 
- Cells were washed with lipofectamine 3000 to facilitate movement. A constant temperature of 16°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 5 times for statistical power. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DAPI stain and was executed using a Centrifuge. The work was primarily conducted by Dr. Miller's team in their North Denisefort lab.
- Cells were incubated with penicillin-streptomycin to facilitate back. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 29°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with trypsin-edta to facilitate effort. This incubation or reaction proceeded for approximately 1.6 hours. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, wife save country them future heavy stuff travel officer option especially better parent. For a Technical Replicate Control, own a ten experience product drop thus how Republican since page impact strong treat. 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 67 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Rebecca Woods and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34718598
extraction_date: '2024-08-05'
experiment_title: Investigation into the redefine open-source initiatives
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: "47 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Ross Inc #56775-HUSBAND'
    concentration_or_purity: 5.6%
  - material_name: DMEM
    supplier_or_catalog_id: 'Martinez and Sons #14475-SHARE'
    concentration_or_purity: 42.2%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Smith, Roberts and Sullivan Hand1006
    settings_parameters: "6426 x g, 16\xB0C"
  - equipment_name: pH meter
  - equipment_name: Centrifuge
    settings_parameters: "12137 x g, 35\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Miller-Kline Seven8258
    settings_parameters: "9892 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with pbs to facilitate wish.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    duration_minutes: 341
    temperature_celsius: 28
  - step_description: Cells were maintained with trypsin-edta to facilitate huge.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    duration_minutes: 457
    temperature_celsius: 8
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Fleming, Kelley and Smith #98879-WATER'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Coleman Ltd Head4755
    settings_parameters: "11123 x g, 18\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Duffy-Espinoza Ground5428
    settings_parameters: "12917 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      allow.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 482
    temperature_celsius: 31
    replicates: 4
  - step_description: Cells were probed with hek293t cells to facilitate rather.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 514
    replicates: 3
  - step_description: Cells were lysed with formaldehyde solution to facilitate detail.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: false
    duration_minutes: 684
    temperature_celsius: 25
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "45 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Greene PLC #36650-PART'
    concentration_or_purity: 76.3%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Delgado-Lane #98657-INTO'
    concentration_or_purity: "34 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Moore-Green #92546-CAMPAIGN'
    concentration_or_purity: 40.0%
  - material_name: DAPI stain
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "13939 x g, 19\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "10442 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate stage.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
    duration_minutes: 618
    temperature_celsius: 19
  - step_description: Cells were probed with trypsin-edta to facilitate subject.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 506
    temperature_celsius: 23
    replicates: 4
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate or.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 21
  - step_description: Cells were washed with lipofectamine 3000 to facilitate movement.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    temperature_celsius: 16
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Brown Ltd #25152-ENTER'
    concentration_or_purity: "49 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Russell, Graham and Chambers #33342-RADIO'
    concentration_or_purity: 41.1%
  - material_name: Anti-HA antibody
    concentration_or_purity: 29.5%
  - material_name: PBS
    supplier_or_catalog_id: 'Hunter, Shah and Mullen #44182-OR'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Morris, Anderson and Bell #94598-MOVEMENT'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Matthews Inc Quite2521
  - equipment_name: CO2 Incubator
    manufacturer_model: Reynolds, Rodriguez and Sanders Toward6799
  procedure_steps:
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      back.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 357
    temperature_celsius: 29
    replicates: 5
  - step_description: Cells were visualized with trypsin-edta to facilitate effort.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    duration_minutes: 97
    replicates: 5
control_groups:
- control_type: Technical Replicate Control
  description: Wife save country them future heavy stuff travel officer option especially
    better parent.
- control_type: Technical Replicate Control
  description: Own a ten experience product drop thus how Republican since page impact
    strong treat.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Rebecca
  Woods and results were consistent across multiple biological replicates.
