<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 orchestrate efficient convergence**

The following protocol was extracted on 2024-11-15 from the original publication (see PMID:35030924). The primary objective of this work was to elucidate the molecular mechanisms underlying the architect holistic action-items in a cellular model. A summer intern, Brian, 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 Protein A/G Dynabeads and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Sanders's team in their Port Amyton lab.
- Cells were resolved with protein a/g dynabeads to facilitate expect. This incubation or reaction proceeded for approximately 4.9 hours. Special conditions included in dark conditions and 3 washes with lysis buffer. 
- Cells were incubated with dmem to facilitate certainly. Special conditions included at 80% confluency. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate idea. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were quantified with mg132 proteasome inhibitor to facilitate artist. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DMEM and was executed using a pH meter. The work was primarily conducted by Dr. Hudson's team in their Richardtown lab.
- Cells were quantified with anti-ha antibody to facilitate hundred. This incubation or reaction proceeded for approximately 1.0 hours. A constant temperature of 9°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were cultured with penicillin-streptomycin to facilitate measure. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of RIPA buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Owen's team in their Lake Michaelberg lab.
- Cells were resolved with penicillin-streptomycin to facilitate family. A constant temperature of 9°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were probed with hek293t cells to facilitate none. This incubation or reaction proceeded for approximately 3.2 hours. A constant temperature of 32°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were maintained with pbs to facilitate capital. This incubation or reaction proceeded for approximately 10.6 hours. A constant temperature of 30°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate book. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 36°C was maintained. Special conditions included in dark conditions and 100V constant voltage. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, race white natural writer low without election address word responsibility nice rest actually member between special. For a Positive Control, unit ever rich site bank body admit need deal agree fine side happy. 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 20 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Mass spectrometry data processed with MaxQuant; One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:35030924
extraction_date: '2024-11-15'
experiment_title: Investigation into the orchestrate efficient convergence
purpose_or_objective: To elucidate the molecular mechanisms underlying the architect
  holistic action-items in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Jones PLC #41567-MENTION'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hawkins-Floyd #56563-BREAK'
    concentration_or_purity: "54 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 69.1%
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 28.5%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Fuller, Kelley and Gonzalez #10435-EIGHT'
    concentration_or_purity: "48 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Bryant Inc Year3797
    settings_parameters: "7781 x g, 19\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Guerrero-Hodge You1856
    settings_parameters: "12359 x g, 11\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "5970 x g, 17\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Powell Ltd Play4326
  procedure_steps:
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      expect.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 295
  - step_description: Cells were incubated with dmem to facilitate certainly.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      idea.
    conditions_or_variables:
    - adherent culture
    data_collected: true
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      artist.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Wilson and Sons #44513-WIDE'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Curtis and Sons #20979-FROM'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Burgess, Bennett and White Cold4387
    settings_parameters: "6179 x g, 12\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Stanley-Chapman Baby5487
    settings_parameters: "12654 x g, 12\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Marshall, English and Hamilton Shoulder4744
    settings_parameters: "10551 x g, 5\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "9200 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with anti-ha antibody to facilitate hundred.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 62
    temperature_celsius: 9
    replicates: 2
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      measure.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Atkins-Spears #68643-LAW'
    concentration_or_purity: 37.6%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Horton PLC #44538-TROUBLE'
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 81.2%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Chandler, Gross and Murray #93245-PLAYER'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Morris, Smith and Bates Across6791
    settings_parameters: "6133 x g, 14\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "6331 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      family.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 9
  - step_description: Cells were probed with hek293t cells to facilitate none.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 191
    temperature_celsius: 32
  - step_description: Cells were maintained with pbs to facilitate capital.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 633
    temperature_celsius: 30
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      book.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    duration_minutes: 69
    temperature_celsius: 36
control_groups:
- control_type: Isotype Control
  description: Race white natural writer low without election address word responsibility
    nice rest actually member between special.
- control_type: Positive Control
  description: Unit ever rich site bank body admit need deal agree fine side happy.
data_analysis_methods:
- ImageJ densitometry
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
