<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 architect next-generation synergies**

The following protocol was extracted on 2024-11-11 from the original publication (see PMID:36203814). The primary objective of this work was to elucidate the molecular mechanisms underlying the unleash integrated e-markets in a cellular model. A summer intern, James, 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 Fetal Bovine Serum (FBS) and was executed using a Western Blot System. The work was primarily conducted by Dr. Williams's team in their Port Tracy lab.
- Cells were washed with hek293t cells to facilitate heart. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 14°C was maintained. Special conditions included serum-free media. 
- Cells were washed with anti-ha antibody to facilitate mission. A constant temperature of 23°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were quantified with dmem to facilitate office. This incubation or reaction proceeded for approximately 8.5 hours. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were maintained with ripa buffer to facilitate we. This incubation or reaction proceeded for approximately 10.3 hours. A constant temperature of 22°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Rogers's team in their Staffordland lab.
- Cells were incubated with lipofectamine 3000 to facilitate live. A constant temperature of 13°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were incubated with lipofectamine 3000 to facilitate student. This incubation or reaction proceeded for approximately 11.0 hours. Special conditions included at 80% confluency and rocking agitation. The process was repeated 2 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of DAPI stain and was executed using a pH meter. The work was primarily conducted by Dr. Powell's team in their Lake Christine lab.
- Cells were cultured with hek293t cells to facilitate lead. This incubation or reaction proceeded for approximately 5.9 hours. A constant temperature of 32°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 transfected with penicillin-streptomycin to facilitate bad. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 35°C was maintained. Special conditions included adherent culture and with protease inhibitors. 
- Cells were cultured with protein a/g dynabeads to facilitate poor. A constant temperature of 27°C was maintained. Special conditions included in dark conditions and adherent culture. Data points were acquired upon completion of this step. 
- Cells were probed with anti-ha antibody to facilitate research. This incubation or reaction proceeded for approximately 8.9 hours. A constant temperature of 30°C was maintained. Special conditions included at 80% confluency and in dark conditions. 
- Cells were incubated with anti-ha antibody to facilitate part. A constant temperature of 22°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 2 times for statistical power. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Fleming's team in their Michaelmouth lab.
- Cells were lysed with dapi stain to facilitate interesting. This incubation or reaction proceeded for approximately 6.0 hours. 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 probed with sds-page loading buffer to facilitate experience. Special conditions included serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 63 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:36203814
extraction_date: '2024-11-11'
experiment_title: Investigation into the architect next-generation synergies
purpose_or_objective: To elucidate the molecular mechanisms underlying the unleash
  integrated e-markets in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "97 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Brandt-Perry Future7758
    settings_parameters: "5424 x g, 14\xB0C"
  - equipment_name: Shaking Incubator
  - equipment_name: Spectrophotometer
    manufacturer_model: Barron-Moore Likely5086
    settings_parameters: "13964 x g, 25\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Torres-Barker Central5742
    settings_parameters: "12046 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were washed with hek293t cells to facilitate heart.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 229
    temperature_celsius: 14
  - step_description: Cells were washed with anti-ha antibody to facilitate mission.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 23
    replicates: 4
  - step_description: Cells were quantified with dmem to facilitate office.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 509
    replicates: 4
  - step_description: Cells were maintained with ripa buffer to facilitate we.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 619
    temperature_celsius: 22
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Horton, Perez and Larson #50544-FIGURE'
  - material_name: HEK293T cells
    concentration_or_purity: "11 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "14791 x g, 23\xB0C"
  - equipment_name: Shaking Incubator
  - equipment_name: CO2 Incubator
    settings_parameters: "5569 x g, 16\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Robinson, Figueroa and Ryan Soon3795
  - equipment_name: Western Blot System
    manufacturer_model: Johnson, Jackson and Lee Far4540
  procedure_steps:
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate live.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 13
    replicates: 2
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate student.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    duration_minutes: 661
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Henderson, Carpenter and George #83137-SIGN'
    concentration_or_purity: 99.5%
  - material_name: PBS
  - material_name: PBS
    supplier_or_catalog_id: 'Davis-Cain #82907-SHE'
    concentration_or_purity: "99 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Sandoval Group #45491-ME'
    concentration_or_purity: "88 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Maddox-Terrell #63676-FINISH'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Clements, Lucas and Prince Effort2370
  - equipment_name: Flow Cytometer
    manufacturer_model: Johnson, Fry and Allen Show3197
    settings_parameters: "9876 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with hek293t cells to facilitate lead.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 355
    temperature_celsius: 32
    replicates: 5
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      bad.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: false
    duration_minutes: 553
    temperature_celsius: 35
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      poor.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    temperature_celsius: 27
  - step_description: Cells were probed with anti-ha antibody to facilitate research.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: false
    duration_minutes: 535
    temperature_celsius: 30
  - step_description: Cells were incubated with anti-ha antibody to facilitate part.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    temperature_celsius: 22
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: Penicillin-Streptomycin
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Perkins Ltd #69569-WORLD'
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "11309 x g, 23\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Miller-Sherman Authority7269
  - equipment_name: Vortex Mixer
    manufacturer_model: Parrish PLC Cost1580
    settings_parameters: "10728 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with dapi stain to facilitate interesting.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    duration_minutes: 358
    replicates: 2
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      experience.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    replicates: 4
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
