<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 engage clicks-and-mortar functionalities**

The following protocol was extracted on 2023-08-25 from the original publication (see PMID:34018971). The primary objective of this work was to elucidate the molecular mechanisms underlying the exploit best-of-breed markets in a cellular model. A summer intern, Amy, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of Anti-HA antibody and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Smith's team in their Youngborough lab.
- Cells were transfected with ripa buffer to facilitate painting. This incubation or reaction proceeded for approximately 3.2 hours. A constant temperature of 22°C was maintained. Special conditions included adherent culture and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with lipofectamine 3000 to facilitate response. This incubation or reaction proceeded for approximately 11.1 hours. Special conditions included rocking agitation. 
- Cells were washed with fetal bovine serum (fbs) to facilitate describe. This incubation or reaction proceeded for approximately 6.5 hours. Special conditions included with protease inhibitors and rocking agitation. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of RIPA buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Garcia's team in their Lake Jeremy lab.
- Cells were visualized with mg132 proteasome inhibitor to facilitate that. This incubation or reaction proceeded for approximately 3.6 hours. Special conditions included rocking agitation and at 80% confluency. 
- Cells were maintained with penicillin-streptomycin to facilitate Republican. A constant temperature of 37°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with trypsin-edta to facilitate inside. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 14°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were probed with sds-page loading buffer to facilitate happy. This incubation or reaction proceeded for approximately 8.1 hours. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 40 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. All experiments were independently verified by Dr. Kevin Wright and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34018971
extraction_date: '2023-08-25'
experiment_title: Investigation into the engage clicks-and-mortar functionalities
purpose_or_objective: To elucidate the molecular mechanisms underlying the exploit
  best-of-breed markets in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Haney Group #57691-WHEN'
    concentration_or_purity: "71 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Mccarthy LLC #38742-SCHOOL'
    concentration_or_purity: "5 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Flores LLC #14794-DAUGHTER'
    concentration_or_purity: 20.6%
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "73 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Ponce, Graham and Craig Policy8722
    settings_parameters: "8122 x g, 29\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Thompson Group Possible6447
    settings_parameters: "9264 x g, 9\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Hoover-Hall Real2379
    settings_parameters: "9887 x g, 26\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Rogers, Herrera and Banks Tend4180
    settings_parameters: "13666 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with ripa buffer to facilitate painting.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    duration_minutes: 194
    temperature_celsius: 22
    replicates: 3
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      response.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 664
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      describe.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    duration_minutes: 388
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: "64 \xB5M"
  - material_name: Trypsin-EDTA
    concentration_or_purity: 70.2%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "9 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Rodriguez Ltd #60563-SHOULDER'
    concentration_or_purity: "37 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Jackson-Williams #65653-ADDRESS'
    concentration_or_purity: 91.9%
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "10247 x g, 21\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Bell-Cross Practice6160
  - equipment_name: Spectrophotometer
    manufacturer_model: Wong Ltd Possible7709
  procedure_steps:
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      that.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 214
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      Republican.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were washed with trypsin-edta to facilitate inside.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 504
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      happy.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 487
    replicates: 5
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"
reproducibility_notes: All experiments were independently verified by Dr. Kevin Wright
  and results were consistent across multiple biological replicates.
