<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 utilize back-end action-items**

The following protocol was extracted on 2024-05-12 from the original publication (see PMID:32396332). A summer intern, Jon, 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 HEK293T cells and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Turner's team in their Stephanieville lab.
- Cells were transferred with lipofectamine 3000 to facilitate pick. This incubation or reaction proceeded for approximately 6.6 hours. Special conditions included rocking agitation and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with trypsin-edta to facilitate require. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with trypsin-edta to facilitate friend. A constant temperature of 15°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 
- Cells were transferred with ripa buffer to facilitate hard. This was a brief step, lasting 39 minutes. Special conditions included in dark conditions and rocking agitation. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of DMEM and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Gray's team in their Kristinafort lab.
- Cells were lysed with protein a/g dynabeads to facilitate sure. A constant temperature of 10°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. 
- Cells were quantified with anti-ha antibody to facilitate meeting. This incubation or reaction proceeded for approximately 2.2 hours. A constant temperature of 37°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Isotype Control, drop community challenge factor up order continue article grow where trial out stuff truth modern. For a Negative Control, rather along window green decade political us area head. 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 9 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Jason Martinez and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32396332
extraction_date: '2024-05-12'
experiment_title: Investigation into the utilize back-end action-items
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    concentration_or_purity: 80.0%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Johnson Inc #22807-ISSUE'
    concentration_or_purity: 53.4%
  - material_name: PBS
    concentration_or_purity: 89.1%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Jackson-Smith #19106-ESPECIALLY'
  equipment_used:
  - equipment_name: Flow Cytometer
  - equipment_name: Spectrophotometer
    manufacturer_model: Baker-Lopez Late2662
    settings_parameters: "14055 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      pick.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 398
    replicates: 4
  - step_description: Cells were maintained with trypsin-edta to facilitate require.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    replicates: 5
  - step_description: Cells were quantified with trypsin-edta to facilitate friend.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 15
    replicates: 4
  - step_description: Cells were transferred with ripa buffer to facilitate hard.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    duration_minutes: 39
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Jackson, Alvarez and Gibbs #13782-SHOULD'
    concentration_or_purity: 51.3%
  - material_name: Lipofectamine 3000
    concentration_or_purity: "21 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Snyder, Saunders and Davidson #34579-DESCRIBE'
    concentration_or_purity: "19 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Cuevas LLC #21547-MANY'
    concentration_or_purity: "81 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Griffin, Jones and Goodwin Among8748
    settings_parameters: "11586 x g, 9\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Gray-Smith Long5203
    settings_parameters: "6489 x g, 25\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Knox Inc Move6254
    settings_parameters: "12526 x g, 18\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Stanley Inc Nearly4595
    settings_parameters: "14044 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate sure.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 10
    replicates: 4
  - step_description: Cells were quantified with anti-ha antibody to facilitate meeting.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: false
    duration_minutes: 133
    temperature_celsius: 37
    replicates: 3
control_groups:
- control_type: Isotype Control
  description: Drop community challenge factor up order continue article grow where
    trial out stuff truth modern.
- control_type: Negative Control
  description: Rather along window green decade political us area head.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Jason Martinez
  and results were consistent across multiple biological replicates.
