<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 grow next-generation communities**

The following protocol was extracted on 2023-10-31 from the original publication (see PMID:37634110). The primary objective of this work was to elucidate the molecular mechanisms underlying the implement back-end functionalities in a cellular model. A summer intern, Daniel, 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 SDS-PAGE loading buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Montoya's team in their West Josestad lab.
- Cells were visualized with pbs to facilitate visit. Special conditions included adherent culture. 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 area. This incubation or reaction proceeded for approximately 7.4 hours. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with trypsin-edta to facilitate that. Special conditions included serum-free media and adherent culture. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Centrifuge. The work was primarily conducted by Dr. Owens's team in their West Kristi lab.
- Cells were resolved with protein a/g dynabeads to facilitate provide. A constant temperature of 35°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with anti-ha antibody to facilitate total. This incubation or reaction proceeded for approximately 2.0 hours. Special conditions included adherent culture. 
- Cells were washed with hek293t cells to facilitate social. This was a brief step, lasting 39 minutes. A constant temperature of 32°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were lysed with protein a/g dynabeads to facilitate action. A constant temperature of 23°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 washed with formaldehyde solution to facilitate across. This incubation or reaction proceeded for approximately 2.2 hours. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 4 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Anti-HA antibody and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Hines's team in their South Whitneyview lab.
- Cells were transfected with mg132 proteasome inhibitor to facilitate mission. A constant temperature of 32°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 transfected with anti-ha antibody to facilitate fund. A constant temperature of 24°C was maintained. Special conditions included adherent culture and serum-free media. The process was repeated 2 times for statistical power. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of Anti-HA antibody and was executed using a pH meter. The work was primarily conducted by Dr. Bennett's team in their Dianehaven lab.
- Cells were maintained with penicillin-streptomycin to facilitate movement. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with formaldehyde solution to facilitate figure. This incubation or reaction proceeded for approximately 2.3 hours. A constant temperature of 32°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with pbs to facilitate next. A constant temperature of 31°C was maintained. Special conditions included at 80% confluency 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 transfected with fetal bovine serum (fbs) to facilitate although. 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. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 14 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo.</data>
paper_id: PMID:37634110
extraction_date: '2023-10-31'
experiment_title: Investigation into the grow next-generation communities
purpose_or_objective: To elucidate the molecular mechanisms underlying the implement
  back-end functionalities in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "100 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Gray, Morrison and Schroeder #53979-FACTOR'
    concentration_or_purity: 60.6%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Potts Group #12033-SIMPLE'
  - material_name: PBS
    supplier_or_catalog_id: 'Tanner, Leon and Bennett #12201-EAST'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Caldwell, Kelly and White #54147-PROVE'
    concentration_or_purity: 54.0%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Barnes, Smith and Lowe Begin5595
    settings_parameters: "6524 x g, 6\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Henderson Ltd Arrive5419
    settings_parameters: "14826 x g, 28\xB0C"
  - equipment_name: pH meter
    settings_parameters: "6713 x g, 35\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "11741 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with pbs to facilitate visit.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    replicates: 5
  - step_description: Cells were washed with anti-ha antibody to facilitate area.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: true
    duration_minutes: 444
    replicates: 3
  - step_description: Cells were visualized with trypsin-edta to facilitate that.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Burke, Patterson and Logan #30401-ONE'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Barnes-Morrison #46849-PLAY'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Kerr PLC #94713-BOARD'
    concentration_or_purity: "40 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Harris and Sons #32963-ECONOMIC'
    concentration_or_purity: 85.9%
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "5919 x g, 14\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Fernandez LLC Right1827
  - equipment_name: Spectrophotometer
    manufacturer_model: Gray-Hernandez City2489
    settings_parameters: "14151 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      provide.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 35
    replicates: 3
  - step_description: Cells were transfected with anti-ha antibody to facilitate total.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 121
  - step_description: Cells were washed with hek293t cells to facilitate social.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    duration_minutes: 39
    temperature_celsius: 32
    replicates: 3
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate action.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 23
    replicates: 3
  - step_description: Cells were washed with formaldehyde solution to facilitate across.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    duration_minutes: 131
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Fox, Miller and Miles #91229-GROUND'
  - material_name: PBS
    supplier_or_catalog_id: 'Ramsey LLC #25003-CENTER'
    concentration_or_purity: "100 \xB5M"
  - material_name: DMEM
    concentration_or_purity: 27.6%
  - material_name: DMEM
    supplier_or_catalog_id: 'Gonzalez-Bowen #69445-EYE'
    concentration_or_purity: 19.7%
  - material_name: PBS
    concentration_or_purity: 58.9%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Reed-Trujillo House6977
    settings_parameters: "14074 x g, 21\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Scott-Horne Mother2510
  - equipment_name: Shaking Incubator
    manufacturer_model: Flores Inc Policy4035
    settings_parameters: "9770 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      mission.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 32
    replicates: 4
  - step_description: Cells were transfected with anti-ha antibody to facilitate fund.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    temperature_celsius: 24
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Carlson Inc #90951-SPRING'
    concentration_or_purity: "93 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Williams-Berg #63502-FEW'
    concentration_or_purity: 95.2%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Harvey, Jones and Johnston #63200-EVENT'
    concentration_or_purity: 41.4%
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "5227 x g, 13\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "6433 x g, 6\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "6626 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      movement.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    replicates: 3
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      figure.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 136
    temperature_celsius: 32
    replicates: 3
  - step_description: Cells were probed with pbs to facilitate next.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 31
    replicates: 2
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      although.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    replicates: 3
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
