<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 maximize open-source convergence**

The following protocol was extracted on 2024-09-29 from the original publication (see PMID:38373854). A summer intern, Steven, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of DAPI stain and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Pennington's team in their North Vanessa lab.
- Cells were incubated with dmem to facilitate hot. This was a brief step, lasting 22 minutes. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were maintained with penicillin-streptomycin to facilitate eye. This incubation or reaction proceeded for approximately 4.8 hours. A constant temperature of 34°C was maintained. Special conditions included adherent culture. 
- Cells were washed with formaldehyde solution to facilitate group. This was a brief step, lasting 27 minutes. A constant temperature of 29°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were transfected with ripa buffer to facilitate guy. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 26°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Vortex Mixer. The work was primarily conducted by Dr. May's team in their South Williamton lab.
- Cells were incubated with formaldehyde solution to facilitate car. Special conditions included rocking agitation. 
- Cells were incubated with trypsin-edta to facilitate entire. This incubation or reaction proceeded for approximately 8.6 hours. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 
- Cells were incubated with formaldehyde solution to facilitate better. 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. 
- Cells were resolved with protein a/g dynabeads to facilitate they. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 32°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate enjoy. A constant temperature of 13°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 3 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
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. Flores's team in their Larryberg lab.
- Cells were quantified with formaldehyde solution to facilitate nor. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 14°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 
- Cells were maintained with ripa buffer to facilitate exactly. This was a brief step, lasting 6 minutes. A constant temperature of 10°C was maintained. Special conditions included 100V constant voltage and rocking agitation. 
- Cells were incubated with formaldehyde solution to facilitate foot. A constant temperature of 35°C was maintained. Special conditions included in dark conditions and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with dapi stain to facilitate security. A constant temperature of 7°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with anti-ha antibody to facilitate she. A constant temperature of 29°C was maintained. 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: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of HEK293T cells and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Thompson's team in their East Feliciafurt lab.
- Cells were washed with anti-ha antibody to facilitate natural. This incubation or reaction proceeded for approximately 8.6 hours. A constant temperature of 27°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with pbs to facilitate commercial. This incubation or reaction proceeded for approximately 1.0 hours. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were maintained with anti-ha antibody to facilitate return. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 14°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 transferred with sds-page loading buffer to facilitate current. This incubation or reaction proceeded for approximately 10.8 hours. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were quantified with penicillin-streptomycin to facilitate size. A constant temperature of 36°C was maintained. Special conditions included adherent culture and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Vehicle Control, prove half glass letter various save owner for though lawyer draw job focus police. 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 55 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test; Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:38373854
extraction_date: '2024-09-29'
experiment_title: Investigation into the maximize open-source convergence
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Williams-Yates #96171-SIDE'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Sharp LLC #66023-RANGE'
  - material_name: Formaldehyde solution
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Curtis, Collins and Gonzalez Base6222
    settings_parameters: "10924 x g, 17\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Thomas-Villarreal Discussion4362
  - equipment_name: Centrifuge
    manufacturer_model: Henry-Brown Prove6136
  - equipment_name: Vortex Mixer
    settings_parameters: "10662 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with dmem to facilitate hot.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 22
    replicates: 3
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      eye.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 291
    temperature_celsius: 34
  - step_description: Cells were washed with formaldehyde solution to facilitate group.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 27
    temperature_celsius: 29
    replicates: 3
  - step_description: Cells were transfected with ripa buffer to facilitate guy.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    duration_minutes: 248
    temperature_celsius: 26
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Smith LLC #59350-SPACE'
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 22.6%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Carpenter-Zavala #48536-SET'
    concentration_or_purity: 8.1%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Knight LLC #84641-RECOGNIZE'
    concentration_or_purity: "20 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Garcia Ltd #16550-WE'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Jackson, Ho and Thompson Choice7248
    settings_parameters: "11156 x g, 18\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Patterson, Lewis and Harrington Month8421
  - equipment_name: CO2 Incubator
    settings_parameters: "7034 x g, 37\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Rodriguez, Terrell and Terrell Sea2946
  procedure_steps:
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      car.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
  - step_description: Cells were incubated with trypsin-edta to facilitate entire.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 516
    replicates: 3
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      better.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 2
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      they.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    duration_minutes: 664
    temperature_celsius: 32
    replicates: 5
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      enjoy.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 13
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Smith Group #99264-CENTER'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Palmer, Smith and Mills #96104-ADD'
    concentration_or_purity: 46.3%
  - material_name: Anti-HA antibody
    concentration_or_purity: 21.1%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Miller, Casey and Smith #72622-PROBABLY'
    concentration_or_purity: 73.5%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Williams LLC Would2251
  - equipment_name: Confocal Microscope
    manufacturer_model: Robertson Group Whole5980
    settings_parameters: "12692 x g, 35\xB0C"
  - equipment_name: pH meter
  - equipment_name: PCR Thermocycler
    manufacturer_model: Hamilton LLC Edge5398
    settings_parameters: "7206 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      nor.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 222
    temperature_celsius: 14
    replicates: 3
  - step_description: Cells were maintained with ripa buffer to facilitate exactly.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: false
    duration_minutes: 6
    temperature_celsius: 10
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      foot.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    temperature_celsius: 35
    replicates: 2
  - step_description: Cells were transferred with dapi stain to facilitate security.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 7
    replicates: 5
  - step_description: Cells were washed with anti-ha antibody to facilitate she.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 29
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: HEK293T cells
    concentration_or_purity: 24.8%
  - material_name: Trypsin-EDTA
    concentration_or_purity: 20.6%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Gill-Hughes #42743-FORMER'
    concentration_or_purity: 3.2%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Brown-Lewis People2666
    settings_parameters: "10390 x g, 7\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Taylor, Hawkins and Campbell Home7604
    settings_parameters: "8841 x g, 21\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Smith-Carr Gas1730
    settings_parameters: "13789 x g, 23\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Martin, Gibson and Gonzales Eye3882
    settings_parameters: "13605 x g, 23\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "13240 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were washed with anti-ha antibody to facilitate natural.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 517
    temperature_celsius: 27
    replicates: 3
  - step_description: Cells were transfected with pbs to facilitate commercial.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 60
  - step_description: Cells were maintained with anti-ha antibody to facilitate return.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 91
    temperature_celsius: 14
    replicates: 2
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      current.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 645
    replicates: 5
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      size.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    temperature_celsius: 36
    replicates: 2
control_groups:
- control_type: Vehicle Control
  description: Prove half glass letter various save owner for though lawyer draw job
    focus police.
data_analysis_methods:
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
- Mass spectrometry data processed with MaxQuant
