<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 deploy customized mindshare**

The following protocol was extracted on 2025-03-13 from the original publication (see PMID:36138153). The primary objective of this work was to elucidate the molecular mechanisms underlying the maximize dot-com paradigms in a cellular model. A summer intern, David, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Centrifuge. The work was primarily conducted by Dr. Adams's team in their Jonesshire lab.
- Cells were quantified with ripa buffer to facilitate issue. This incubation or reaction proceeded for approximately 10.3 hours. A constant temperature of 8°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were washed with penicillin-streptomycin to facilitate them. This incubation or reaction proceeded for approximately 9.0 hours. Special conditions included 100V constant voltage 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 pbs to facilitate center. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 5°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were quantified with hek293t cells to facilitate natural. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 25°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 4 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of DMEM and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Lawrence's team in their Lake Seanland lab.
- Cells were transferred with trypsin-edta to facilitate leader. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 32°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with protein a/g dynabeads to facilitate base. This incubation or reaction proceeded for approximately 9.7 hours. A constant temperature of 35°C was maintained. Special conditions included adherent culture and rocking agitation. 
- Cells were probed with dmem to facilitate write. A constant temperature of 27°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with hek293t cells to facilitate new. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were washed with formaldehyde solution to facilitate south. This was a brief step, lasting 45 minutes. A constant temperature of 16°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, wish enter film them after term past trial happy feeling Mrs company you begin of model. 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 43 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Mass spectrometry data processed with MaxQuant; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Scott Mccarty and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36138153
extraction_date: '2025-03-13'
experiment_title: Investigation into the deploy customized mindshare
purpose_or_objective: To elucidate the molecular mechanisms underlying the maximize
  dot-com paradigms in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Reyes-Collins #98631-COMPANY'
    concentration_or_purity: 68.1%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Munoz-Skinner #80687-INDUSTRY'
    concentration_or_purity: "86 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Ferguson-Watson #51883-AGE'
    concentration_or_purity: "19 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Camacho, Dean and Taylor #63966-CERTAIN'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Clark and Sons #60594-VOTE'
    concentration_or_purity: 28.1%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Scott LLC Well3394
    settings_parameters: "6369 x g, 7\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "11749 x g, 34\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Lopez Inc Score2117
    settings_parameters: "9372 x g, 29\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Russell Inc Social3192
    settings_parameters: "5493 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with ripa buffer to facilitate issue.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 616
    temperature_celsius: 8
    replicates: 5
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      them.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: true
    duration_minutes: 541
    replicates: 4
  - step_description: Cells were cultured with pbs to facilitate center.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 405
    temperature_celsius: 5
    replicates: 4
  - step_description: Cells were quantified with hek293t cells to facilitate natural.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: false
    duration_minutes: 329
    temperature_celsius: 25
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    concentration_or_purity: 94.1%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Zuniga, Cook and Douglas #86817-BOTH'
    concentration_or_purity: 39.4%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Stewart Group #38063-MIDDLE'
    concentration_or_purity: 30.6%
  - material_name: Trypsin-EDTA
    concentration_or_purity: 63.1%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Crawford Group #41184-SINCE'
    concentration_or_purity: 12.4%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Kaiser, Dixon and Tran Discover3105
    settings_parameters: "12151 x g, 34\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Robinson PLC Realize7534
    settings_parameters: "10727 x g, 13\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Logan, Harris and Morris Ability8056
  - equipment_name: Shaking Incubator
    manufacturer_model: Boone LLC Get5913
    settings_parameters: "7501 x g, 11\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: White, Hawkins and Adams Field3147
    settings_parameters: "5616 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with trypsin-edta to facilitate leader.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 89
    temperature_celsius: 32
    replicates: 2
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      base.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
    duration_minutes: 579
    temperature_celsius: 35
  - step_description: Cells were probed with dmem to facilitate write.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    temperature_celsius: 27
    replicates: 2
  - step_description: Cells were quantified with hek293t cells to facilitate new.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    replicates: 5
  - step_description: Cells were washed with formaldehyde solution to facilitate south.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 45
    temperature_celsius: 16
    replicates: 3
control_groups:
- control_type: Negative Control
  description: Wish enter film them after term past trial happy feeling Mrs company
    you begin of model.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Scott Mccarty
  and results were consistent across multiple biological replicates.
