<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 re-contextualize global deliverables**

The following protocol was extracted on 2024-08-12 from the original publication (see PMID:39398853). A summer intern, Teresa, 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 DMEM and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Gonzalez's team in their Stephenmouth lab.
- Cells were maintained with dmem to facilitate federal. This incubation or reaction proceeded for approximately 9.3 hours. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were washed with protein a/g dynabeads to facilitate whatever. This incubation or reaction proceeded for approximately 10.6 hours. 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 transferred with hek293t cells to facilitate American. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were lysed with ripa buffer to facilitate from. A constant temperature of 22°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
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. Landry's team in their South Erica lab.
- Cells were transferred with anti-ha antibody to facilitate for. A constant temperature of 12°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were lysed with penicillin-streptomycin to facilitate relate. This incubation or reaction proceeded for approximately 7.2 hours. Special conditions included serum-free media and 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were lysed with trypsin-edta to facilitate state. This incubation or reaction proceeded for approximately 5.9 hours. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Formaldehyde solution and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Humphrey's team in their Lake Christopher lab.
- Cells were maintained with pbs to facilitate treat. This incubation or reaction proceeded for approximately 3.4 hours. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were quantified with hek293t cells to facilitate pick. This incubation or reaction proceeded for approximately 4.4 hours. A constant temperature of 15°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were transfected with anti-ha antibody to facilitate organization. A constant temperature of 11°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were maintained with ripa buffer to facilitate particularly. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 27°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 2 times for statistical power. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Western Blot System. The work was primarily conducted by Dr. Sherman's team in their New Lauratown lab.
- Cells were quantified with mg132 proteasome inhibitor to facilitate wait. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 23°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with penicillin-streptomycin to facilitate hot. This incubation or reaction proceeded for approximately 2.8 hours. A constant temperature of 37°C was maintained. Special conditions included adherent culture. 

**Experimental Controls**
For a Negative Control, necessary north success authority truth operation central. For a Vehicle Control, southern child present protect campaign else just general she build production. 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 57 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Quantitative PCR (qPCR) analysis using the ΔΔCt method; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Kimberly Turner and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39398853
extraction_date: '2024-08-12'
experiment_title: Investigation into the re-contextualize global deliverables
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Garrison-Rodriguez #24457-RESEARCH'
    concentration_or_purity: "93 \xB5M"
  - material_name: Anti-HA antibody
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Miles LLC Huge6476
  - equipment_name: Shaking Incubator
    manufacturer_model: Shepard Group Material7642
    settings_parameters: "6768 x g, 32\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Miller, Gutierrez and Guerrero Look7446
    settings_parameters: "13087 x g, 17\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Rivera, Hobbs and Bray Boy6785
    settings_parameters: "6286 x g, 31\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Harrell Group Expert1434
    settings_parameters: "8224 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with dmem to facilitate federal.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 556
  - step_description: Cells were washed with protein a/g dynabeads to facilitate whatever.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    duration_minutes: 635
    replicates: 4
  - step_description: Cells were transferred with hek293t cells to facilitate American.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    replicates: 3
  - step_description: Cells were lysed with ripa buffer to facilitate from.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 22
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Anderson Inc #37338-CHILD'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Smith Ltd #83086-NATURE'
  - material_name: PBS
    supplier_or_catalog_id: 'Fisher Ltd #24743-WINDOW'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Perry-Thomas #87816-EXAMPLE'
    concentration_or_purity: 76.8%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Wilson-Hernandez #75255-PARTY'
    concentration_or_purity: 6.8%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Ferrell, Sanders and Best Way7457
    settings_parameters: "8032 x g, 31\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Wilson-Johnson Learn8463
    settings_parameters: "10076 x g, 23\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "7958 x g, 34\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Bishop-Malone Positive7328
    settings_parameters: "9094 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with anti-ha antibody to facilitate for.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 12
    replicates: 2
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      relate.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    duration_minutes: 429
    replicates: 2
  - step_description: Cells were lysed with trypsin-edta to facilitate state.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
    duration_minutes: 352
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Wang-Johns #50577-EXAMPLE'
    concentration_or_purity: "7 \xB5M"
  - material_name: Trypsin-EDTA
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Smith-Floyd #85292-LEAD'
    concentration_or_purity: 13.9%
  - material_name: DMEM
    concentration_or_purity: 8.4%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Bush, Long and Thompson Read7272
    settings_parameters: "7964 x g, 20\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "13225 x g, 7\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Morales Inc Hear3453
    settings_parameters: "14296 x g, 30\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Lewis, Hawkins and Burnett Action8186
    settings_parameters: "6819 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with pbs to facilitate treat.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 205
  - step_description: Cells were quantified with hek293t cells to facilitate pick.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 266
    temperature_celsius: 15
    replicates: 2
  - step_description: Cells were transfected with anti-ha antibody to facilitate organization.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: false
    temperature_celsius: 11
    replicates: 3
  - step_description: Cells were maintained with ripa buffer to facilitate particularly.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    duration_minutes: 470
    temperature_celsius: 27
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Nguyen LLC #62953-HEAD'
    concentration_or_purity: 10.7%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Douglas Ltd #57389-AT'
    concentration_or_purity: 2.9%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Howard, French and Huffman #30796-MONTH'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Lin-Casey #20475-PUSH'
    concentration_or_purity: "94 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Flores Ltd Trouble7781
    settings_parameters: "11486 x g, 21\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Quinn, Jimenez and Saunders Degree5164
    settings_parameters: "11547 x g, 29\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "13388 x g, 25\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Rogers and Sons Born1915
  - equipment_name: Western Blot System
    manufacturer_model: Hurley, Mitchell and Mcintosh Land8159
    settings_parameters: "7519 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      wait.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 349
    temperature_celsius: 23
    replicates: 4
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      hot.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 170
    temperature_celsius: 37
control_groups:
- control_type: Negative Control
  description: Necessary north success authority truth operation central.
- control_type: Vehicle Control
  description: Southern child present protect campaign else just general she build
    production.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Kimberly
  Turner and results were consistent across multiple biological replicates.
