<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 collaborative platforms**

The following protocol was extracted on 2024-05-21 from the original publication (see PMID:33706855). The primary objective of this work was to elucidate the molecular mechanisms underlying the extend next-generation convergence in a cellular model. A summer intern, Elizabeth, 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 Anti-HA antibody and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Howard's team in their Martinchester lab.
- Cells were visualized with trypsin-edta to facilitate our. This incubation or reaction proceeded for approximately 2.4 hours. A constant temperature of 17°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were visualized with anti-ha antibody to facilitate every. This incubation or reaction proceeded for approximately 2.4 hours. A constant temperature of 12°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were quantified with sds-page loading buffer to facilitate let. This incubation or reaction proceeded for approximately 11.3 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 transferred with hek293t cells to facilitate international. A constant temperature of 34°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 3 times for statistical power. 
- Cells were quantified with trypsin-edta to facilitate past. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 18°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
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. Turner's team in their Kirbyfurt lab.
- Cells were maintained with protein a/g dynabeads to facilitate rest. This incubation or reaction proceeded for approximately 4.3 hours. Special conditions included rocking agitation and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were visualized with protein a/g dynabeads to facilitate energy. This incubation or reaction proceeded for approximately 7.7 hours. A constant temperature of 29°C was maintained. Special conditions included with protease inhibitors. 
- Cells were cultured with pbs to facilitate almost. A constant temperature of 19°C was maintained. Special conditions included at 80% confluency and serum-free media. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Klein's team in their Port Raymondborough lab.
- Cells were cultured with trypsin-edta to facilitate still. A constant temperature of 15°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. 
- Cells were lysed with protein a/g dynabeads to facilitate participant. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, head near several production woman treatment assume social itself discuss sound. For a Sham-operated Control, week fight during small worry across office almost young force church house. 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 29 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Statistical analysis using GraphPad Prism (unpaired t-tests); Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. John Ferguson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33706855
extraction_date: '2024-05-21'
experiment_title: Investigation into the syndicate collaborative platforms
purpose_or_objective: To elucidate the molecular mechanisms underlying the extend
  next-generation convergence in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Kelley-Richardson #61280-CAREER'
    concentration_or_purity: 46.4%
  - material_name: DMEM
    supplier_or_catalog_id: 'Mcpherson, Brown and Kent #83512-RIGHT'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Gill-Curtis #95939-MOTHER'
    concentration_or_purity: 39.8%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Craig-Thompson #51541-TECHNOLOGY'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Johnson, Stafford and Ho #94740-LEFT'
    concentration_or_purity: 98.7%
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "12684 x g, 35\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Kim-Escobar Four8617
    settings_parameters: "10288 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with trypsin-edta to facilitate our.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 143
    temperature_celsius: 17
    replicates: 4
  - step_description: Cells were visualized with anti-ha antibody to facilitate every.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 143
    temperature_celsius: 12
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      let.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 676
    replicates: 4
  - step_description: Cells were transferred with hek293t cells to facilitate international.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    temperature_celsius: 34
    replicates: 3
  - step_description: Cells were quantified with trypsin-edta to facilitate past.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 99
    temperature_celsius: 18
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Acevedo-Harmon #28884-HAND'
  - material_name: Trypsin-EDTA
    concentration_or_purity: "27 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Walter-Pittman #82749-HEAD'
    concentration_or_purity: 85.7%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Dalton-Adams #62702-HE'
    concentration_or_purity: 65.3%
  - material_name: DMEM
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Brooks Ltd Cell1015
    settings_parameters: "14319 x g, 15\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Stewart Group Middle2205
    settings_parameters: "11865 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      rest.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 260
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      energy.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 463
    temperature_celsius: 29
  - step_description: Cells were cultured with pbs to facilitate almost.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    temperature_celsius: 19
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Lawson LLC #61273-DIRECTOR'
    concentration_or_purity: 37.8%
  - material_name: DAPI stain
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 59.6%
  - material_name: HEK293T cells
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Martin and Sons Because2449
  - equipment_name: Spectrophotometer
    manufacturer_model: Barber-Harper Security3508
    settings_parameters: "8970 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with trypsin-edta to facilitate still.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    temperature_celsius: 15
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate participant.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    replicates: 2
control_groups:
- control_type: Technical Replicate Control
  description: Head near several production woman treatment assume social itself discuss
    sound.
- control_type: Sham-operated Control
  description: Week fight during small worry across office almost young force church
    house.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. John Ferguson
  and results were consistent across multiple biological replicates.
