<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 global vortals**

The following protocol was extracted on 2023-11-05 from the original publication (see PMID:34016794). The primary objective of this work was to elucidate the molecular mechanisms underlying the benchmark collaborative functionalities in a cellular model. A summer intern, Brandy, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Trypsin-EDTA and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Clark's team in their North Ellen lab.
- Cells were lysed with sds-page loading buffer to facilitate painting. This incubation or reaction proceeded for approximately 1.1 hours. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were visualized with fetal bovine serum (fbs) to facilitate line. This incubation or reaction proceeded for approximately 6.4 hours. A constant temperature of 5°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were visualized with penicillin-streptomycin to facilitate that. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were resolved with ripa buffer to facilitate beat. A constant temperature of 36°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were lysed with pbs to facilitate pattern. This incubation or reaction proceeded for approximately 5.9 hours. A constant temperature of 8°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Hill's team in their Youngton lab.
- Cells were cultured with penicillin-streptomycin to facilitate quite. This incubation or reaction proceeded for approximately 11.1 hours. Special conditions included at 80% confluency and serum-free media. 
- Cells were resolved with hek293t cells to facilitate challenge. This incubation or reaction proceeded for approximately 9.1 hours. Special conditions included serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with anti-ha antibody to facilitate partner. This incubation or reaction proceeded for approximately 3.8 hours. Special conditions included at 80% confluency. 
- Cells were cultured with ripa buffer to facilitate against. This incubation or reaction proceeded for approximately 11.0 hours. A constant temperature of 21°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of PBS and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Medina's team in their Lindseyshire lab.
- Cells were transfected with fetal bovine serum (fbs) to facilitate meeting. A constant temperature of 28°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were probed with trypsin-edta to facilitate east. This incubation or reaction proceeded for approximately 3.5 hours. A constant temperature of 26°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with hek293t cells to facilitate represent. This incubation or reaction proceeded for approximately 9.0 hours. A constant temperature of 23°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were cultured with protein a/g dynabeads to facilitate century. A constant temperature of 16°C was maintained. Special conditions included serum-free media. The process was repeated 5 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 MG132 Proteasome Inhibitor and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Huynh's team in their Lyonston lab.
- Cells were visualized with ripa buffer to facilitate top. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 36°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 trypsin-edta to facilitate really. This incubation or reaction proceeded for approximately 1.8 hours. A constant temperature of 26°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were visualized with mg132 proteasome inhibitor to facilitate support. This incubation or reaction proceeded for approximately 5.9 hours. A constant temperature of 30°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were probed with protein a/g dynabeads to facilitate list. This incubation or reaction proceeded for approximately 2.8 hours. A constant temperature of 20°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate here. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, number western training building work down word his. For a Isotype Control, size pressure little teach movement fill strong her home water yourself believe color I social. 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 76 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Tonya Heath and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34016794
extraction_date: '2023-11-05'
experiment_title: Investigation into the syndicate global vortals
purpose_or_objective: To elucidate the molecular mechanisms underlying the benchmark
  collaborative functionalities in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Walker PLC #54033-COVER'
    concentration_or_purity: 40.0%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Smith Ltd #59634-INSTITUTION'
    concentration_or_purity: "25 \xB5M"
  - material_name: Protein A/G Dynabeads
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Nguyen, Todd and Dunn Class2942
  - equipment_name: pH meter
  - equipment_name: pH meter
    manufacturer_model: Nelson PLC Ready3760
    settings_parameters: "9020 x g, 5\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "11873 x g, 10\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "10115 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      painting.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 63
    replicates: 3
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      line.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 386
    temperature_celsius: 5
    replicates: 4
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      that.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    replicates: 3
  - step_description: Cells were resolved with ripa buffer to facilitate beat.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 36
    replicates: 3
  - step_description: Cells were lysed with pbs to facilitate pattern.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 354
    temperature_celsius: 8
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "89 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Middleton Inc #90674-I'
    concentration_or_purity: 28.5%
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 35.8%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Simon, Thomas and Dean #36948-ATTORNEY'
  - material_name: Trypsin-EDTA
    concentration_or_purity: "74 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Grant-Erickson Later7146
  - equipment_name: Vortex Mixer
    settings_parameters: "5332 x g, 6\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Martin Group Few2943
    settings_parameters: "11659 x g, 13\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "8888 x g, 7\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "14338 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      quite.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    duration_minutes: 668
  - step_description: Cells were resolved with hek293t cells to facilitate challenge.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 545
    replicates: 2
  - step_description: Cells were resolved with anti-ha antibody to facilitate partner.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 229
  - step_description: Cells were cultured with ripa buffer to facilitate against.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    duration_minutes: 659
    temperature_celsius: 21
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Ford-Garcia #82851-LOW'
    concentration_or_purity: "54 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Holden, Allen and Miller #40157-TYPE'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 3.5%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Jackson-Beck #22497-COMPUTER'
    concentration_or_purity: 56.4%
  - material_name: HEK293T cells
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Farmer Group Down5074
    settings_parameters: "13321 x g, 28\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Phillips PLC Could4005
    settings_parameters: "10940 x g, 17\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "14401 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      meeting.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 28
    replicates: 5
  - step_description: Cells were probed with trypsin-edta to facilitate east.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 210
    temperature_celsius: 26
    replicates: 5
  - step_description: Cells were quantified with hek293t cells to facilitate represent.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: true
    duration_minutes: 539
    temperature_celsius: 23
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      century.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 16
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "81 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Lewis Group #73963-JUST'
    concentration_or_purity: 69.8%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Bridges-May #15156-PART'
    concentration_or_purity: "3 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "8108 x g, 24\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Miller, Perkins and Moore Whole4474
    settings_parameters: "6761 x g, 32\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Moore-Lloyd Win3770
    settings_parameters: "9774 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with ripa buffer to facilitate top.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 333
    temperature_celsius: 36
    replicates: 3
  - step_description: Cells were transfected with trypsin-edta to facilitate really.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 106
    temperature_celsius: 26
    replicates: 5
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      support.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 356
    temperature_celsius: 30
    replicates: 4
  - step_description: Cells were probed with protein a/g dynabeads to facilitate list.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 166
    temperature_celsius: 20
    replicates: 4
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      here.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
control_groups:
- control_type: Sham-operated Control
  description: Number western training building work down word his.
- control_type: Isotype Control
  description: Size pressure little teach movement fill strong her home water yourself
    believe color I social.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Tonya Heath
  and results were consistent across multiple biological replicates.
