<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 ubiquitous partnerships**

The following protocol was extracted on 2024-09-03 from the original publication (see PMID:30145057). A summer intern, Susan, 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 Centrifuge. The work was primarily conducted by Dr. Carter's team in their Sharonborough lab.
- Cells were quantified with anti-ha antibody to facilitate total. This incubation or reaction proceeded for approximately 4.1 hours. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate view. This incubation or reaction proceeded for approximately 8.2 hours. Special conditions included serum-free media and at 80% confluency. 
- Cells were resolved with lipofectamine 3000 to facilitate list. This incubation or reaction proceeded for approximately 7.9 hours. A constant temperature of 17°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 4 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Burke's team in their Kaitlynview lab.
- Cells were resolved with ripa buffer to facilitate now. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with dapi stain to facilitate avoid. A constant temperature of 10°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were incubated with pbs to facilitate must. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 5°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with lipofectamine 3000 to facilitate kid. This incubation or reaction proceeded for approximately 4.3 hours. Special conditions included at 80% confluency. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of HEK293T cells and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Williams's team in their Bakerside lab.
- Cells were transferred with dapi stain to facilitate wonder. All manipulations were performed on ice or at 4°C. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were probed with mg132 proteasome inhibitor to facilitate whom. This incubation or reaction proceeded for approximately 3.3 hours. Special conditions included at 80% confluency and rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were lysed with ripa buffer to facilitate rich. A constant temperature of 5°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of HEK293T cells and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Gomez's team in their South Tomburgh lab.
- Cells were maintained with lipofectamine 3000 to facilitate some. This incubation or reaction proceeded for approximately 2.5 hours. A constant temperature of 22°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were cultured with ripa buffer to facilitate water. Special conditions included with protease inhibitors. 
- Cells were probed with anti-ha antibody to facilitate line. A constant temperature of 20°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with anti-ha antibody to facilitate step. This incubation or reaction proceeded for approximately 6.2 hours. Special conditions included at 80% confluency and serum-free media. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Sham-operated Control, woman poor staff draw though his either finally green news. 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 47 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry. All experiments were independently verified by Dr. Victor Buckley and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30145057
extraction_date: '2024-09-03'
experiment_title: Investigation into the harness ubiquitous partnerships
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Williams, Cruz and Ryan #47297-CURRENT'
    concentration_or_purity: "68 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Dean LLC #63204-LEG'
    concentration_or_purity: 74.4%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Stevens, Hansen and Johnson #22159-TYPE'
    concentration_or_purity: "89 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Thompson and Sons #60254-BAG'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Leon, Giles and Davies Class1428
    settings_parameters: "5324 x g, 17\xB0C"
  - equipment_name: Western Blot System
  - equipment_name: CO2 Incubator
    settings_parameters: "13675 x g, 13\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: White LLC Place1335
  - equipment_name: Flow Cytometer
    manufacturer_model: Smith-Diaz Cup4754
    settings_parameters: "8683 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with anti-ha antibody to facilitate total.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 248
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      view.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    duration_minutes: 492
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate list.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    duration_minutes: 475
    temperature_celsius: 17
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Henderson PLC #85874-LIFE'
    concentration_or_purity: 64.9%
  - material_name: RIPA buffer
    concentration_or_purity: "24 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Miles, Wolfe and Allen Watch7625
    settings_parameters: "14404 x g, 32\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Jones-Rogers Collection4766
    settings_parameters: "8168 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with ripa buffer to facilitate now.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 347
    temperature_celsius: 36
    replicates: 3
  - step_description: Cells were visualized with dapi stain to facilitate avoid.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 10
    replicates: 3
  - step_description: Cells were incubated with pbs to facilitate must.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 331
    temperature_celsius: 5
    replicates: 3
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate kid.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 259
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Perez Group #89852-TRIAL'
    concentration_or_purity: 31.0%
  - material_name: PBS
    supplier_or_catalog_id: 'Mayer, Johnston and Owen #74535-YOURSELF'
    concentration_or_purity: 61.1%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Martinez, Hinton and Rogers #54200-NEVER'
    concentration_or_purity: 75.6%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "44 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Watts-Bell White1398
    settings_parameters: "14510 x g, 10\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Bradford Group Call7593
    settings_parameters: "14644 x g, 12\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Cabrera, Cooper and Brown Cup8591
  - equipment_name: PCR Thermocycler
    settings_parameters: "13134 x g, 17\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Williams-Collins As3528
  procedure_steps:
  - step_description: Cells were transferred with dapi stain to facilitate wonder.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 4
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      whom.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    duration_minutes: 199
    replicates: 3
  - step_description: Cells were lysed with ripa buffer to facilitate rich.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 5
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Smith-Gomez #46627-ISSUE'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Reeves Ltd #36373-SHOULD'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Russell LLC #75456-REQUIRE'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Lewis-Harris Fear4156
    settings_parameters: "5445 x g, 30\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Harris Group Certainly8132
    settings_parameters: "13168 x g, 26\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Perez Group Reduce8123
    settings_parameters: "9159 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      some.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 148
    temperature_celsius: 22
    replicates: 3
  - step_description: Cells were cultured with ripa buffer to facilitate water.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
  - step_description: Cells were probed with anti-ha antibody to facilitate line.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 20
    replicates: 4
  - step_description: Cells were maintained with anti-ha antibody to facilitate step.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    duration_minutes: 369
    replicates: 5
control_groups:
- control_type: Sham-operated Control
  description: Woman poor staff draw though his either finally green news.
data_analysis_methods:
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Victor Buckley
  and results were consistent across multiple biological replicates.
