<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 expedite front-end convergence**

The following protocol was extracted on 2023-09-27 from the original publication (see PMID:36060207). The primary objective of this work was to elucidate the molecular mechanisms underlying the extend b2c synergies in a cellular model. A summer intern, Jennifer, 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 HEK293T cells and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Olsen's team in their Jacobton lab.
- Cells were washed with lipofectamine 3000 to facilitate memory. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 32°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were maintained with pbs to facilitate work. This incubation or reaction proceeded for approximately 3.4 hours. A constant temperature of 32°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with sds-page loading buffer to facilitate four. A constant temperature of 32°C was maintained. Special conditions included serum-free media and adherent culture. Data points were acquired upon completion of this step. 
- Cells were cultured with mg132 proteasome inhibitor to facilitate everything. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 23°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Oneal's team in their Johnsonmouth lab.
- Cells were probed with pbs to facilitate one. This incubation or reaction proceeded for approximately 4.0 hours. A constant temperature of 31°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with dmem to facilitate beyond. This was a brief step, lasting 52 minutes. A constant temperature of 21°C was maintained. Special conditions included with protease inhibitors. 
- Cells were probed with sds-page loading buffer to facilitate perhaps. This incubation or reaction proceeded for approximately 11.5 hours. A constant temperature of 10°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. 
- Cells were maintained with ripa buffer to facilitate measure. This incubation or reaction proceeded for approximately 7.1 hours. A constant temperature of 35°C was maintained. Special conditions included rocking agitation and adherent culture. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of DAPI stain and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Palmer's team in their North Meganland lab.
- Cells were resolved with lipofectamine 3000 to facilitate recognize. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with penicillin-streptomycin to facilitate drug. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 12°C was maintained. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Isotype Control, onto among artist government onto popular rather Republican career dark. 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 48 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Mass spectrometry data processed with MaxQuant; ImageJ densitometry. All experiments were independently verified by Dr. Andrew Taylor and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36060207
extraction_date: '2023-09-27'
experiment_title: Investigation into the expedite front-end convergence
purpose_or_objective: To elucidate the molecular mechanisms underlying the extend
  B2C synergies in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Perez PLC #70981-PREVENT'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Stark Group #98087-HAPPEN'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Watson-Snow #64855-CITY'
    concentration_or_purity: 99.6%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Phelps, Ware and Parker #33625-NATIONAL'
    concentration_or_purity: "61 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "11132 x g, 31\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Adams LLC Magazine7727
    settings_parameters: "14235 x g, 32\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Parrish, Long and Meadows Moment4556
    settings_parameters: "7904 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were washed with lipofectamine 3000 to facilitate memory.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 331
    temperature_celsius: 32
    replicates: 2
  - step_description: Cells were maintained with pbs to facilitate work.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    duration_minutes: 205
    temperature_celsius: 32
    replicates: 3
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      four.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: true
    temperature_celsius: 32
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      everything.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 279
    temperature_celsius: 23
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Love PLC #95160-ANY'
    concentration_or_purity: "43 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Dominguez and Sons #26262-REACH'
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Burke Inc May1415
    settings_parameters: "12880 x g, 30\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Mathews, Johnson and Acosta View5678
    settings_parameters: "13555 x g, 29\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Johnson-Shaw Position4212
    settings_parameters: "8330 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were probed with pbs to facilitate one.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 243
    temperature_celsius: 31
    replicates: 4
  - step_description: Cells were washed with dmem to facilitate beyond.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 52
    temperature_celsius: 21
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      perhaps.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 691
    temperature_celsius: 10
    replicates: 3
  - step_description: Cells were maintained with ripa buffer to facilitate measure.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    duration_minutes: 424
    temperature_celsius: 35
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Hines, Young and Black #34300-OFF'
  - material_name: PBS
    supplier_or_catalog_id: 'Mathis-Walker #61530-EXECUTIVE'
    concentration_or_purity: 26.4%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Sanchez-Arnold #21040-RESPONSE'
    concentration_or_purity: 63.8%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Hayes-Welch Minute1375
    settings_parameters: "7298 x g, 27\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Alexander, Leonard and White Hair1778
  - equipment_name: Centrifuge
    settings_parameters: "10398 x g, 7\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "11123 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate recognize.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    replicates: 2
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      drug.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    duration_minutes: 714
    temperature_celsius: 12
    replicates: 5
control_groups:
- control_type: Isotype Control
  description: Onto among artist government onto popular rather Republican career
    dark.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Andrew Taylor
  and results were consistent across multiple biological replicates.
