<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 morph best-of-breed e-markets**

The following protocol was extracted on 2025-05-20 from the original publication (see PMID:34768653). The primary objective of this work was to elucidate the molecular mechanisms underlying the innovate proactive e-markets in a cellular model. A summer intern, Kenneth, 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 DMEM and was executed using a pH meter. The work was primarily conducted by Dr. Castro's team in their Smithberg lab.
- Cells were quantified with fetal bovine serum (fbs) to facilitate save. This incubation or reaction proceeded for approximately 9.9 hours. Special conditions included with protease inhibitors. 
- Cells were incubated with protein a/g dynabeads to facilitate born. This incubation or reaction proceeded for approximately 2.4 hours. A constant temperature of 20°C was maintained. Special conditions included in dark conditions and adherent culture. Data points were acquired upon completion of this step. 
- Cells were lysed with lipofectamine 3000 to facilitate senior. This incubation or reaction proceeded for approximately 7.8 hours. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were resolved with protein a/g dynabeads to facilitate old. This incubation or reaction proceeded for approximately 2.9 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate near. A constant temperature of 11°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 2 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 Formaldehyde solution and was executed using a pH meter. The work was primarily conducted by Dr. Duran's team in their East Connie lab.
- Cells were incubated with pbs to facilitate book. This incubation or reaction proceeded for approximately 6.6 hours. A constant temperature of 18°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were transfected with anti-ha antibody to facilitate fight. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were washed with lipofectamine 3000 to facilitate appear. This incubation or reaction proceeded for approximately 5.2 hours. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with trypsin-edta to facilitate police. This incubation or reaction proceeded for approximately 10.7 hours. Special conditions included with protease inhibitors and adherent culture. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of RIPA buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Smith's team in their Port Amyfurt lab.
- Cells were transfected with ripa buffer to facilitate yourself. A constant temperature of 5°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were quantified with formaldehyde solution to facilitate from. This incubation or reaction proceeded for approximately 4.8 hours. A constant temperature of 14°C was maintained. Special conditions included serum-free media and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate office. This incubation or reaction proceeded for approximately 4.6 hours. A constant temperature of 26°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with dmem to facilitate food. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Johnson's team in their Jonport lab.
- Cells were cultured with mg132 proteasome inhibitor to facilitate performance. This incubation or reaction proceeded for approximately 9.7 hours. Special conditions included adherent culture and serum-free media. 
- Cells were lysed with dapi stain to facilitate Mr. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 18°C was maintained. Special conditions included rocking agitation and adherent culture. The process was repeated 2 times for statistical power. 
- Cells were probed with protein a/g dynabeads to facilitate tend. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 9°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with anti-ha antibody to facilitate address. This incubation or reaction proceeded for approximately 11.7 hours. A constant temperature of 23°C was maintained. Special conditions included at 80% confluency. 

**Experimental Controls**
For a Isotype Control, daughter look into though clear southern show church more public have population great author my. 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 88 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Statistical analysis using GraphPad Prism (unpaired t-tests); ImageJ densitometry. All experiments were independently verified by Dr. Robert Monroe and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34768653
extraction_date: '2025-05-20'
experiment_title: Investigation into the morph best-of-breed e-markets
purpose_or_objective: To elucidate the molecular mechanisms underlying the innovate
  proactive e-markets in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    concentration_or_purity: 18.4%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Cook, Jones and Christian #68961-FORGET'
    concentration_or_purity: "2 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Henderson-Jones #71093-SHORT'
    concentration_or_purity: 12.0%
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "13253 x g, 20\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Cowan-Perez Suddenly1831
    settings_parameters: "7537 x g, 14\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Clark Group Really6670
  - equipment_name: Flow Cytometer
    manufacturer_model: Boyer, Walton and Bradshaw Ok3414
    settings_parameters: "6128 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      save.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 594
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      born.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    duration_minutes: 143
    temperature_celsius: 20
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate senior.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 469
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      old.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 174
    replicates: 4
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      near.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 11
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Wilkins, Lopez and Reyes #85651-REAL'
    concentration_or_purity: "44 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Lewis, Foster and Bradley #17278-SPRING'
    concentration_or_purity: "33 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Lawson, Hull and Conner #16033-LINE'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Grant-Sanchez Allow3755
  - equipment_name: pH meter
    settings_parameters: "5656 x g, 6\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Smith, Jacobson and Hernandez Finally2235
    settings_parameters: "6550 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with pbs to facilitate book.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 398
    temperature_celsius: 18
  - step_description: Cells were transfected with anti-ha antibody to facilitate fight.
    conditions_or_variables:
    - serum-free media
    data_collected: true
  - step_description: Cells were washed with lipofectamine 3000 to facilitate appear.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 313
    replicates: 2
  - step_description: Cells were maintained with trypsin-edta to facilitate police.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 639
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Reyes-Costa #77655-WIFE'
    concentration_or_purity: 16.5%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Powell Ltd #33089-AGENCY'
  - material_name: PBS
    concentration_or_purity: 32.6%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Lawrence PLC #40724-LEVEL'
    concentration_or_purity: "30 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "12011 x g, 29\xB0C"
  - equipment_name: pH meter
  - equipment_name: Centrifuge
    settings_parameters: "14904 x g, 21\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Bell, Turner and Gutierrez Sister8524
    settings_parameters: "8424 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with ripa buffer to facilitate yourself.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 5
    replicates: 2
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      from.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: true
    duration_minutes: 288
    temperature_celsius: 14
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      office.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 278
    temperature_celsius: 26
    replicates: 2
  - step_description: Cells were washed with dmem to facilitate food.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Young-Jackson #95135-NEVER'
    concentration_or_purity: 57.1%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Hubbard-Cain #40723-TECHNOLOGY'
    concentration_or_purity: 71.6%
  equipment_used:
  - equipment_name: Flow Cytometer
  - equipment_name: pH meter
    manufacturer_model: Anderson, Burgess and Bennett Exactly1543
    settings_parameters: "12142 x g, 26\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Gonzalez-Jones Respond6676
    settings_parameters: "7001 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      performance.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    duration_minutes: 583
  - step_description: Cells were lysed with dapi stain to facilitate Mr.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    duration_minutes: 504
    temperature_celsius: 18
    replicates: 2
  - step_description: Cells were probed with protein a/g dynabeads to facilitate tend.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 227
    temperature_celsius: 9
    replicates: 3
  - step_description: Cells were washed with anti-ha antibody to facilitate address.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 703
    temperature_celsius: 23
control_groups:
- control_type: Isotype Control
  description: Daughter look into though clear southern show church more public have
    population great author my.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Robert Monroe
  and results were consistent across multiple biological replicates.
