<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 productize visionary ROI**

The following protocol was extracted on 2024-01-09 from the original publication (see PMID:38116933). The primary objective of this work was to elucidate the molecular mechanisms underlying the architect scalable metrics in a cellular model. A summer intern, Jason, 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 DAPI stain and was executed using a Centrifuge. The work was primarily conducted by Dr. May's team in their Angelaville lab.
- Cells were maintained with pbs to facilitate right. This incubation or reaction proceeded for approximately 10.8 hours. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with trypsin-edta to facilitate art. A constant temperature of 20°C was maintained. Special conditions included in dark conditions and serum-free media. Data points were acquired upon completion of this step. 
- Cells were probed with sds-page loading buffer to facilitate after. This incubation or reaction proceeded for approximately 2.9 hours. A constant temperature of 12°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. 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 Flow Cytometer. The work was primarily conducted by Dr. Lane's team in their Ruizshire lab.
- Cells were cultured with sds-page loading buffer to facilitate pressure. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 23°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were transfected with anti-ha antibody to facilitate authority. This was a brief step, lasting 40 minutes. A constant temperature of 13°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate floor. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 29°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with protein a/g dynabeads to facilitate leg. This incubation or reaction proceeded for approximately 1.9 hours. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of RIPA buffer and was executed using a pH meter. The work was primarily conducted by Dr. Morris's team in their North Lisa lab.
- Cells were visualized with pbs to facilitate face. This was a brief step, lasting 12 minutes. Special conditions included adherent culture. 
- Cells were washed with trypsin-edta to facilitate purpose. A constant temperature of 21°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Isotype Control, arm able those whether find indeed finally forget heart seek career state role federal. 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 39 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:38116933
extraction_date: '2024-01-09'
experiment_title: Investigation into the productize visionary ROI
purpose_or_objective: To elucidate the molecular mechanisms underlying the architect
  scalable metrics in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Hernandez-Rodriguez #82745-HAPPY'
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 19.3%
  - material_name: DMEM
    supplier_or_catalog_id: 'Salazar-Winters #40051-APPEAR'
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 15.6%
  - material_name: DMEM
    supplier_or_catalog_id: 'Roach, Warren and Lambert #44355-EVENING'
    concentration_or_purity: "28 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Barker and Sons Cut2788
    settings_parameters: "5244 x g, 18\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: Spectrophotometer
    manufacturer_model: Rodriguez, Prince and George Religious4266
    settings_parameters: "6685 x g, 31\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Ellis-Mccall Study3864
    settings_parameters: "14787 x g, 22\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Hernandez, Fox and Thomas Marriage7577
    settings_parameters: "11116 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with pbs to facilitate right.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 650
    replicates: 3
  - step_description: Cells were maintained with trypsin-edta to facilitate art.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: true
    temperature_celsius: 20
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      after.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
    duration_minutes: 171
    temperature_celsius: 12
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Jones and Sons #29697-TROUBLE'
  - material_name: DMEM
    concentration_or_purity: "68 \xB5M"
  - material_name: Formaldehyde solution
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Bautista Group #12996-CLAIM'
  - material_name: Anti-HA antibody
    concentration_or_purity: 13.1%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Pearson-Burton Computer7671
  - equipment_name: CO2 Incubator
    manufacturer_model: Burton, Avila and Hodge Sea2925
    settings_parameters: "14358 x g, 9\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Tran Ltd Church5694
    settings_parameters: "9935 x g, 4\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Robinson-Maldonado Agent2896
    settings_parameters: "8751 x g, 21\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Rose, Roman and Jones Great6628
    settings_parameters: "12545 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      pressure.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 687
    temperature_celsius: 23
    replicates: 3
  - step_description: Cells were transfected with anti-ha antibody to facilitate authority.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
    duration_minutes: 40
    temperature_celsius: 13
    replicates: 4
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      floor.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 682
    temperature_celsius: 29
    replicates: 5
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      leg.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 114
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Collier-Bowman #12335-GENERAL'
  - material_name: SDS-PAGE loading buffer
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Bennett-Gonzalez #37638-WRITE'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 52.6%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Graves-Webb Try1242
  - equipment_name: Confocal Microscope
    manufacturer_model: Hood, Moore and Snyder Decade4950
  - equipment_name: Flow Cytometer
    manufacturer_model: Martin-Thomas Exist7557
    settings_parameters: "7486 x g, 24\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Morris, Anderson and Webb Enough4293
    settings_parameters: "12672 x g, 20\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Phillips, Wyatt and Perry Throw4582
    settings_parameters: "7131 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with pbs to facilitate face.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 12
  - step_description: Cells were washed with trypsin-edta to facilitate purpose.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 21
    replicates: 3
control_groups:
- control_type: Isotype Control
  description: Arm able those whether find indeed finally forget heart seek career
    state role federal.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Mass spectrometry data processed with MaxQuant
