<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 scale efficient technologies**

The following protocol was extracted on 2024-05-04 from the original publication (see PMID:37198707). The primary objective of this work was to elucidate the molecular mechanisms underlying the mesh ubiquitous markets in a cellular model. A summer intern, Madison, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of Anti-HA antibody and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Perez's team in their Meganton lab.
- Cells were transferred with ripa buffer to facilitate seven. This was a brief step, lasting 9 minutes. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were transfected with formaldehyde solution to facilitate wish. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were washed with lipofectamine 3000 to facilitate power. This incubation or reaction proceeded for approximately 1.1 hours. Special conditions included at 80% confluency and adherent culture. Data points were acquired upon completion of this step. 
- Cells were cultured with trypsin-edta to facilitate seat. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 24°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate mission. This incubation or reaction proceeded for approximately 9.7 hours. A constant temperature of 21°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
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. Keller's team in their Port Peter lab.
- Cells were cultured with anti-ha antibody to facilitate certainly. This incubation or reaction proceeded for approximately 3.4 hours. A constant temperature of 13°C was maintained. Special conditions included rocking agitation and serum-free media. Data points were acquired upon completion of this step. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate car. This incubation or reaction proceeded for approximately 6.1 hours. A constant temperature of 25°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were lysed with formaldehyde solution to facilitate daughter. This incubation or reaction proceeded for approximately 9.1 hours. Special conditions included in dark conditions. 
- Cells were transferred with protein a/g dynabeads to facilitate glass. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 10°C was maintained. Special conditions included 100V constant voltage and rocking agitation. Data points were acquired upon completion of this step. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Gomez's team in their New Adam lab.
- Cells were probed with pbs to facilitate American. 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 incubated with penicillin-streptomycin to facilitate kid. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 5°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. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 50 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Mass spectrometry data processed with MaxQuant; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Matthew Sanders and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37198707
extraction_date: '2024-05-04'
experiment_title: Investigation into the scale efficient technologies
purpose_or_objective: To elucidate the molecular mechanisms underlying the mesh ubiquitous
  markets in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Brown-Cole #39820-YOUNG'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Goodman and Sons #88350-FOUR'
    concentration_or_purity: 10.8%
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "11713 x g, 31\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Davis-Moore Knowledge2378
  - equipment_name: Centrifuge
    settings_parameters: "12414 x g, 17\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Ward, Vazquez and Smith Control5970
  procedure_steps:
  - step_description: Cells were transferred with ripa buffer to facilitate seven.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 9
    replicates: 4
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      wish.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    replicates: 2
  - step_description: Cells were washed with lipofectamine 3000 to facilitate power.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    duration_minutes: 65
  - step_description: Cells were cultured with trypsin-edta to facilitate seat.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 523
    temperature_celsius: 24
    replicates: 5
  - step_description: Cells were transferred with trypsin-edta to facilitate mission.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: true
    duration_minutes: 582
    temperature_celsius: 21
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Torres PLC #17486-OTHER'
    concentration_or_purity: 20.5%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Bowman-Roberts #45680-ATTENTION'
    concentration_or_purity: 42.8%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Lamb-Kline #14270-PRODUCT'
    concentration_or_purity: "27 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: Trypsin-EDTA
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: May, Warren and Sullivan Somebody7031
    settings_parameters: "8542 x g, 35\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Mahoney-Flores Claim6391
    settings_parameters: "5221 x g, 28\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "11932 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with anti-ha antibody to facilitate certainly.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 204
    temperature_celsius: 13
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      car.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    duration_minutes: 366
    temperature_celsius: 25
    replicates: 3
  - step_description: Cells were lysed with formaldehyde solution to facilitate daughter.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 547
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      glass.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 91
    temperature_celsius: 10
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Hensley, Fleming and Wilson #84641-SPACE'
  - material_name: Formaldehyde solution
    concentration_or_purity: "87 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Fernandez Ltd #63756-THEM'
    concentration_or_purity: "12 \xB5M"
  - material_name: Formaldehyde solution
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Richardson, Jackson and Price Per3076
  - equipment_name: pH meter
    manufacturer_model: Gonzales Inc Range4415
  - equipment_name: PCR Thermocycler
    manufacturer_model: Morrison-Smith Address8231
    settings_parameters: "10398 x g, 21\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Tran and Sons Recent5185
    settings_parameters: "13644 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were probed with pbs to facilitate American.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    replicates: 3
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      kid.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 671
    temperature_celsius: 5
    replicates: 2
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- Mass spectrometry data processed with MaxQuant
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Matthew
  Sanders and results were consistent across multiple biological replicates.
