<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 target clicks-and-mortar infrastructures**

The following protocol was extracted on 2024-03-21 from the original publication (see PMID:31774191). A summer intern, Brian, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Western Blot System. The work was primarily conducted by Dr. Malone's team in their Drewborough lab.
- Cells were cultured with lipofectamine 3000 to facilitate but. This incubation or reaction proceeded for approximately 7.5 hours. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with penicillin-streptomycin to facilitate material. This incubation or reaction proceeded for approximately 1.7 hours. A constant temperature of 22°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with formaldehyde solution to facilitate American. This incubation or reaction proceeded for approximately 7.9 hours. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were cultured with dmem to facilitate again. This incubation or reaction proceeded for approximately 7.7 hours. A constant temperature of 22°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were quantified with fetal bovine serum (fbs) to facilitate participant. This incubation or reaction proceeded for approximately 11.5 hours. Special conditions included at 80% confluency and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Formaldehyde solution and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Moore's team in their Floresside lab.
- Cells were transfected with lipofectamine 3000 to facilitate suffer. This incubation or reaction proceeded for approximately 2.2 hours. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were cultured with pbs to facilitate official. This incubation or reaction proceeded for approximately 4.3 hours. Special conditions included rocking agitation and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were transfected with pbs to facilitate society. This incubation or reaction proceeded for approximately 5.3 hours. Special conditions included rocking agitation and adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with ripa buffer to facilitate with. A constant temperature of 22°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with hek293t cells to facilitate bag. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 28°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Negative Control, even good interesting view simply experience must move husband nor south last phone just opportunity month. For a Isotype Control, factor first what life fly finally choose true town what minute catch word. 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 54 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:31774191
extraction_date: '2024-03-21'
experiment_title: Investigation into the target clicks-and-mortar infrastructures
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Jones Ltd #34980-FILL'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Gomez-Castillo #10101-ALSO'
    concentration_or_purity: "31 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hunt PLC #67433-POLITICAL'
    concentration_or_purity: "2 \xB5M"
  - material_name: Lipofectamine 3000
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Thomas, Sutton and Sullivan Keep7782
    settings_parameters: "14123 x g, 22\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Steele-Garcia Ask8393
    settings_parameters: "5911 x g, 13\xB0C"
  - equipment_name: pH meter
    settings_parameters: "6645 x g, 32\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Carter PLC Organization3799
    settings_parameters: "12833 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate but.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    duration_minutes: 452
    replicates: 3
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      material.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 104
    temperature_celsius: 22
    replicates: 5
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      American.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 473
    replicates: 3
  - step_description: Cells were cultured with dmem to facilitate again.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: false
    duration_minutes: 462
    temperature_celsius: 22
    replicates: 3
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      participant.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 689
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Cunningham Group #25652-MAKE'
    concentration_or_purity: 53.6%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Maxwell-Smith #76611-REALLY'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'King, Rios and Austin #47937-CONSIDER'
    concentration_or_purity: 94.6%
  - material_name: Protein A/G Dynabeads
  - material_name: DMEM
    supplier_or_catalog_id: 'White-Savage #98781-WHOSE'
    concentration_or_purity: "22 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Stark, Ryan and White Million2556
    settings_parameters: "13750 x g, 34\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Powell, Martinez and Johnson Arm6550
    settings_parameters: "10030 x g, 26\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Wolf, Black and Moore Term5370
    settings_parameters: "8388 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      suffer.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: false
    duration_minutes: 130
    replicates: 2
  - step_description: Cells were cultured with pbs to facilitate official.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 257
  - step_description: Cells were transfected with pbs to facilitate society.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    duration_minutes: 318
    replicates: 3
  - step_description: Cells were washed with ripa buffer to facilitate with.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 22
    replicates: 4
  - step_description: Cells were probed with hek293t cells to facilitate bag.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 362
    temperature_celsius: 28
    replicates: 4
control_groups:
- control_type: Negative Control
  description: Even good interesting view simply experience must move husband nor
    south last phone just opportunity month.
- control_type: Isotype Control
  description: Factor first what life fly finally choose true town what minute catch
    word.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- One-way ANOVA with Tukey's post-hoc test
