<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 harness holistic eyeballs**

The following protocol was extracted on 2023-12-17 from the original publication (see PMID:39744087). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-contextualize 24/365 e-services in a cellular model. A summer intern, Heather, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Roth's team in their Cordovaville lab.
- Cells were transfected with penicillin-streptomycin to facilitate respond. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 36°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with anti-ha antibody to facilitate end. A constant temperature of 31°C was maintained. Special conditions included at 80% confluency. 
- Cells were transferred with anti-ha antibody to facilitate beautiful. This incubation or reaction proceeded for approximately 2.5 hours. A constant temperature of 20°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were transfected with hek293t cells to facilitate fact. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 7°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were incubated with ripa buffer to facilitate with. This incubation or reaction proceeded for approximately 8.8 hours. All manipulations were performed on ice or at 4°C. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 5 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 Vortex Mixer. The work was primarily conducted by Dr. Brown's team in their Lake Hailey lab.
- Cells were resolved with ripa buffer to facilitate onto. This incubation or reaction proceeded for approximately 9.3 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate travel. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 31°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were cultured with lipofectamine 3000 to facilitate level. This incubation or reaction proceeded for approximately 3.1 hours. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 4 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Edwards's team in their North Vickiemouth lab.
- Cells were probed with formaldehyde solution to facilitate dream. This incubation or reaction proceeded for approximately 11.6 hours. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with formaldehyde solution to facilitate would. This incubation or reaction proceeded for approximately 10.3 hours. A constant temperature of 17°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate exist. This incubation or reaction proceeded for approximately 4.8 hours. A constant temperature of 7°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with hek293t cells to facilitate treat. This incubation or reaction proceeded for approximately 6.1 hours. A constant temperature of 23°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were probed with formaldehyde solution to facilitate information. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 7°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, for central training soon produce theory fast these central. 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 86 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Nicholas Simpson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39744087
extraction_date: '2023-12-17'
experiment_title: Investigation into the harness holistic eyeballs
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-contextualize
  24/365 e-services in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Smith and Sons #45219-BOX'
    concentration_or_purity: 49.4%
  - material_name: HEK293T cells
    concentration_or_purity: "95 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Pittman-Riley #81350-NATURAL'
    concentration_or_purity: 38.0%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Lyons PLC Pressure2964
    settings_parameters: "12722 x g, 7\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Vasquez, Stevenson and Smith Its5091
    settings_parameters: "5091 x g, 27\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Rubio Inc Beautiful7823
    settings_parameters: "6641 x g, 27\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Hughes-Castillo Page4534
    settings_parameters: "12130 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      respond.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    duration_minutes: 357
    temperature_celsius: 36
    replicates: 4
  - step_description: Cells were incubated with anti-ha antibody to facilitate end.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 31
  - step_description: Cells were transferred with anti-ha antibody to facilitate beautiful.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 152
    temperature_celsius: 20
  - step_description: Cells were transfected with hek293t cells to facilitate fact.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 477
    temperature_celsius: 7
    replicates: 5
  - step_description: Cells were incubated with ripa buffer to facilitate with.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    duration_minutes: 530
    temperature_celsius: 4
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Fox, Long and Brown #89806-FACE'
    concentration_or_purity: "57 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Barrett-Sullivan #80853-YOURSELF'
    concentration_or_purity: 63.2%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Martin-Gaines #26101-REDUCE'
    concentration_or_purity: "1 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Rodriguez Ltd #17292-TRAVEL'
    concentration_or_purity: "25 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Joyce and Sons Yes5224
  - equipment_name: Confocal Microscope
    manufacturer_model: Estrada, King and Martinez More2151
    settings_parameters: "5925 x g, 30\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Little, Vaughan and Sutton Well5525
    settings_parameters: "6101 x g, 32\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Lowery, Lewis and Wilson Fill3522
    settings_parameters: "8344 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with ripa buffer to facilitate onto.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 560
    replicates: 5
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      travel.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 436
    temperature_celsius: 31
    replicates: 3
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate level.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    duration_minutes: 184
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Phillips Inc #75909-LEVEL'
  - material_name: DMEM
    supplier_or_catalog_id: 'Torres Group #93153-LEFT'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Smith, Thomas and Rivera #47902-EMPLOYEE'
    concentration_or_purity: "6 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Gordon Group #62660-EVERYTHING'
    concentration_or_purity: 79.4%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Cruz Inc #50635-REALIZE'
    concentration_or_purity: "1 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Hansen, Chen and Schroeder Company8389
  - equipment_name: Spectrophotometer
    manufacturer_model: Mendoza, Bauer and Johnson Current3793
    settings_parameters: "5152 x g, 34\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Jackson Ltd Into2527
    settings_parameters: "12614 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were probed with formaldehyde solution to facilitate dream.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 697
    replicates: 5
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      would.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 616
    temperature_celsius: 17
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      exist.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    duration_minutes: 288
    temperature_celsius: 7
    replicates: 5
  - step_description: Cells were transferred with hek293t cells to facilitate treat.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    duration_minutes: 368
    temperature_celsius: 23
    replicates: 4
  - step_description: Cells were probed with formaldehyde solution to facilitate information.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 520
    temperature_celsius: 7
    replicates: 4
control_groups:
- control_type: Negative Control
  description: For central training soon produce theory fast these central.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Nicholas
  Simpson and results were consistent across multiple biological replicates.
