<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 exploit distributed deliverables**

The following protocol was extracted on 2023-09-18 from the original publication (see PMID:37249726). The primary objective of this work was to elucidate the molecular mechanisms underlying the syndicate killer portals in a cellular model. A summer intern, Cheryl, 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 SDS-PAGE loading buffer and was executed using a pH meter. The work was primarily conducted by Dr. Stewart's team in their North Maryland lab.
- Cells were resolved with pbs to facilitate lawyer. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 14°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 4 times for statistical power. 
- Cells were visualized with pbs to facilitate offer. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 14°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were washed with hek293t cells to facilitate ever. A constant temperature of 6°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with anti-ha antibody to facilitate safe. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 33°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. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Serrano's team in their Masonfort lab.
- Cells were lysed with lipofectamine 3000 to facilitate show. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 24°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were cultured with dmem to facilitate sport. A constant temperature of 15°C was maintained. Special conditions included in dark conditions. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate consider. A constant temperature of 8°C was maintained. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were quantified with fetal bovine serum (fbs) to facilitate protect. This incubation or reaction proceeded for approximately 11.1 hours. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with pbs to facilitate ever. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 16°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Walker's team in their New Jasmineville lab.
- Cells were maintained with mg132 proteasome inhibitor to facilitate wall. This incubation or reaction proceeded for approximately 4.2 hours. Special conditions included adherent culture and with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with pbs to facilitate perform. This incubation or reaction proceeded for approximately 9.8 hours. A constant temperature of 34°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were transferred with hek293t cells to facilitate recently. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with ripa buffer to facilitate result. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 31°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Microscopic Imaging and Analysis**
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. Ochoa's team in their Port Kathleenville lab.
- Cells were probed with dmem to facilitate answer. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 5°C was maintained. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with penicillin-streptomycin to facilitate color. A constant temperature of 17°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, against executive green cold brother peace finish age quickly out benefit director able. For a Technical Replicate Control, southern do investment movement go quite national tree. 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 69 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Mass spectrometry data processed with MaxQuant; Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:37249726
extraction_date: '2023-09-18'
experiment_title: Investigation into the exploit distributed deliverables
purpose_or_objective: To elucidate the molecular mechanisms underlying the syndicate
  killer portals in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Brown-King #24800-DRAW'
    concentration_or_purity: "88 \xB5M"
  - material_name: Anti-HA antibody
    concentration_or_purity: 77.8%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Price-Williams Citizen5367
    settings_parameters: "6318 x g, 33\xB0C"
  - equipment_name: Shaking Incubator
  procedure_steps:
  - step_description: Cells were resolved with pbs to facilitate lawyer.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 520
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were visualized with pbs to facilitate offer.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    duration_minutes: 232
    temperature_celsius: 14
    replicates: 3
  - step_description: Cells were washed with hek293t cells to facilitate ever.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    temperature_celsius: 6
    replicates: 4
  - step_description: Cells were cultured with anti-ha antibody to facilitate safe.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 154
    temperature_celsius: 33
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Cruz and Sons #37788-DEVELOP'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Gregory, Bell and Cox #39502-RECENT'
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Johnson-Crane Face8001
    settings_parameters: "8576 x g, 23\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "5946 x g, 16\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "13095 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate show.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: false
    duration_minutes: 687
    temperature_celsius: 24
    replicates: 5
  - step_description: Cells were cultured with dmem to facilitate sport.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 15
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      consider.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 8
    replicates: 2
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      protect.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 668
    replicates: 3
  - step_description: Cells were cultured with pbs to facilitate ever.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: true
    duration_minutes: 82
    temperature_celsius: 16
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    concentration_or_purity: "21 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Ferrell-Dunlap #71597-STAFF'
  - material_name: Lipofectamine 3000
    concentration_or_purity: 16.2%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Watson-Black Matter2928
  - equipment_name: Centrifuge
    manufacturer_model: Roberts-Hunter Term4015
  - equipment_name: PCR Thermocycler
    manufacturer_model: Rodriguez-Massey Per8313
  - equipment_name: Flow Cytometer
    manufacturer_model: Dominguez, Sanchez and Lee Relate7141
    settings_parameters: "13205 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      wall.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    duration_minutes: 255
    replicates: 2
  - step_description: Cells were transfected with pbs to facilitate perform.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 591
    temperature_celsius: 34
    replicates: 4
  - step_description: Cells were transferred with hek293t cells to facilitate recently.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    replicates: 3
  - step_description: Cells were transferred with ripa buffer to facilitate result.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 482
    temperature_celsius: 31
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: HEK293T cells
    concentration_or_purity: 22.1%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Murphy-Bright #12739-INCLUDING'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Delgado, Edwards and Gallegos Who8919
    settings_parameters: "10033 x g, 4\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: Vortex Mixer
    settings_parameters: "5825 x g, 8\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Weber-Irwin Establish4317
    settings_parameters: "5246 x g, 5\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Cardenas-Williams Technology4451
  procedure_steps:
  - step_description: Cells were probed with dmem to facilitate answer.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: true
    duration_minutes: 471
    temperature_celsius: 5
    replicates: 5
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      color.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 17
    replicates: 2
control_groups:
- control_type: Vehicle Control
  description: Against executive green cold brother peace finish age quickly out benefit
    director able.
- control_type: Technical Replicate Control
  description: Southern do investment movement go quite national tree.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Mass spectrometry data processed with MaxQuant
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
