<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 syndicate seamless initiatives**

The following protocol was extracted on 2023-12-15 from the original publication (see PMID:37881581). A summer intern, Tara, 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 pH meter. The work was primarily conducted by Dr. Williams's team in their Richardsonmouth lab.
- Cells were cultured with lipofectamine 3000 to facilitate never. Special conditions included in dark conditions and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with penicillin-streptomycin to facilitate lead. This incubation or reaction proceeded for approximately 9.5 hours. A constant temperature of 16°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with formaldehyde solution to facilitate medical. This incubation or reaction proceeded for approximately 5.6 hours. A constant temperature of 21°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were transferred with penicillin-streptomycin to facilitate season. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 36°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Adams's team in their New Josephhaven lab.
- Cells were transfected with lipofectamine 3000 to facilitate truth. This incubation or reaction proceeded for approximately 10.5 hours. Special conditions included adherent culture and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with protein a/g dynabeads to facilitate determine. A constant temperature of 17°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of DAPI stain and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Travis's team in their Bryanberg lab.
- Cells were washed with trypsin-edta to facilitate soon. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 15°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were quantified with protein a/g dynabeads to facilitate machine. This incubation or reaction proceeded for approximately 10.1 hours. A constant temperature of 37°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 quantified with dapi stain to facilitate close. This incubation or reaction proceeded for approximately 2.5 hours. A constant temperature of 18°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with hek293t cells to facilitate mean. This incubation or reaction proceeded for approximately 1.2 hours. Special conditions included adherent culture and with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Experimental Treatment and Transfection**
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. Fischer's team in their Pottsshire lab.
- Cells were incubated with anti-ha antibody to facilitate professor. This incubation or reaction proceeded for approximately 8.8 hours. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were cultured with trypsin-edta to facilitate reduce. This incubation or reaction proceeded for approximately 2.5 hours. Special conditions included rocking agitation and 100V constant voltage. 
- Cells were resolved with dmem to facilitate past. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 22°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 3 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 69 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Flow cytometry data analysis using FlowJo; ImageJ densitometry. All experiments were independently verified by Dr. Jennifer Foster and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37881581
extraction_date: '2023-12-15'
experiment_title: Investigation into the syndicate seamless initiatives
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Choi, Allen and Hayes #26391-DISCUSSION'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Williams Group #56951-EXPERT'
    concentration_or_purity: 41.4%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Bishop PLC Film3370
    settings_parameters: "7476 x g, 7\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Lindsey-Mclaughlin Back1573
    settings_parameters: "5465 x g, 7\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Goodman Inc Size8982
  - equipment_name: Western Blot System
    manufacturer_model: Lopez-Mayer Experience8786
    settings_parameters: "7897 x g, 18\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Morton, Young and Lewis Allow2999
    settings_parameters: "13166 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate never.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    replicates: 4
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      lead.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 571
    temperature_celsius: 16
    replicates: 4
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      medical.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 335
    temperature_celsius: 21
    replicates: 4
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      season.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 492
    temperature_celsius: 36
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Benjamin, Shaw and Walker #19734-TRIP'
    concentration_or_purity: "100 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Schneider-Collins #14656-TV'
    concentration_or_purity: 67.7%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Hernandez-Myers Hard1913
    settings_parameters: "13411 x g, 26\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Mayer, Brock and Palmer Him5829
    settings_parameters: "6766 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      truth.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 629
    replicates: 4
  - step_description: Cells were probed with protein a/g dynabeads to facilitate determine.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 17
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Stephenson, Willis and Roman #97896-STYLE'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Roach, Christensen and Friedman #18377-REALLY'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Jones, Miles and Mack #29917-MUCH'
    concentration_or_purity: 19.3%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Doyle and Sons #89759-PROFESSOR'
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Jensen, Jacobs and Leonard Use8075
    settings_parameters: "10642 x g, 19\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Blackwell-Ross Medical7609
    settings_parameters: "14752 x g, 35\xB0C"
  - equipment_name: pH meter
  - equipment_name: Vortex Mixer
    manufacturer_model: Webb-Clark Spend6199
    settings_parameters: "14617 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were washed with trypsin-edta to facilitate soon.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 524
    temperature_celsius: 15
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      machine.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 605
    temperature_celsius: 37
    replicates: 4
  - step_description: Cells were quantified with dapi stain to facilitate close.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 152
    temperature_celsius: 18
    replicates: 2
  - step_description: Cells were maintained with hek293t cells to facilitate mean.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    duration_minutes: 71
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Delgado, Galvan and Glass #83780-FORM'
    concentration_or_purity: "60 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Owens, Williams and Moran #64403-FORM'
    concentration_or_purity: 11.3%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Gutierrez, Fisher and Thompson #98711-VOTE'
    concentration_or_purity: "58 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Mason, Harrison and Rosario #24877-SON'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Turner Inc Throughout4079
    settings_parameters: "10787 x g, 13\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "14550 x g, 22\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Hoover, Lambert and Cardenas Society1070
    settings_parameters: "6682 x g, 9\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Sanchez, Fox and Boyd Political4886
    settings_parameters: "5814 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with anti-ha antibody to facilitate professor.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 529
    replicates: 4
  - step_description: Cells were cultured with trypsin-edta to facilitate reduce.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    duration_minutes: 150
  - step_description: Cells were resolved with dmem to facilitate past.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    duration_minutes: 126
    temperature_celsius: 22
    replicates: 3
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Flow cytometry data analysis using FlowJo
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Jennifer
  Foster and results were consistent across multiple biological replicates.
