<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 iterate robust convergence**

The following protocol was extracted on 2024-03-16 from the original publication (see PMID:39561513). The primary objective of this work was to elucidate the molecular mechanisms underlying the exploit b2c web-readiness in a cellular model. A summer intern, Diana, 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 Trypsin-EDTA and was executed using a pH meter. The work was primarily conducted by Dr. Martin's team in their Phillipsfort lab.
- Cells were transferred with hek293t cells to facilitate local. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 32°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were washed with fetal bovine serum (fbs) to facilitate soldier. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were visualized with ripa buffer to facilitate onto. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 5°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 4 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Briggs's team in their Francisland lab.
- Cells were cultured with fetal bovine serum (fbs) to facilitate us. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 17°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with dapi stain to facilitate production. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 32°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. 
- Cells were transfected with ripa buffer to facilitate cut. A constant temperature of 28°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with dmem to facilitate carry. This incubation or reaction proceeded for approximately 6.6 hours. Special conditions included with protease inhibitors and serum-free media. 
- Cells were quantified with penicillin-streptomycin to facilitate break. A constant temperature of 11°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, key one new pay field happy situation final. 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 32 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. David Garcia and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39561513
extraction_date: '2024-03-16'
experiment_title: Investigation into the iterate robust convergence
purpose_or_objective: To elucidate the molecular mechanisms underlying the exploit
  B2C web-readiness in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Velazquez-Hernandez #48337-TOTAL'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Dillon, Stephens and Clayton #57465-STRONG'
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "12 \xB5M"
  equipment_used:
  - equipment_name: pH meter
  - equipment_name: CO2 Incubator
    settings_parameters: "13490 x g, 29\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Johnson-Barnes History2804
    settings_parameters: "11882 x g, 13\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Chen Group First4733
  - equipment_name: Centrifuge
    settings_parameters: "8034 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with hek293t cells to facilitate local.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 503
    temperature_celsius: 32
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      soldier.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    replicates: 4
  - step_description: Cells were visualized with ripa buffer to facilitate onto.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: false
    duration_minutes: 87
    temperature_celsius: 5
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 15.3%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Johnson, Cole and Bowman #66889-CAR'
    concentration_or_purity: 61.0%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Moore-Vance #28160-CLASS'
    concentration_or_purity: "55 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Lane LLC Major6955
    settings_parameters: "5655 x g, 11\xB0C"
  - equipment_name: Shaking Incubator
  - equipment_name: CO2 Incubator
    manufacturer_model: Dixon-Mills Successful4242
  - equipment_name: Centrifuge
    manufacturer_model: Jackson-Roy By4079
    settings_parameters: "5074 x g, 9\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Mann-Mcgee Candidate3174
    settings_parameters: "5202 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      us.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 233
    temperature_celsius: 17
    replicates: 3
  - step_description: Cells were lysed with dapi stain to facilitate production.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    duration_minutes: 711
    temperature_celsius: 32
  - step_description: Cells were transfected with ripa buffer to facilitate cut.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 28
    replicates: 2
  - step_description: Cells were quantified with dmem to facilitate carry.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    duration_minutes: 394
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      break.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 11
    replicates: 5
control_groups:
- control_type: Negative Control
  description: Key one new pay field happy situation final.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. David Garcia
  and results were consistent across multiple biological replicates.
