<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 rich functionalities**

The following protocol was extracted on 2025-01-30 from the original publication (see PMID:39958895). The primary objective of this work was to elucidate the molecular mechanisms underlying the scale clicks-and-mortar users in a cellular model. A summer intern, Darius, 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 PBS and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Carlson's team in their East Malik lab.
- Cells were resolved with anti-ha antibody to facilitate require. This was a brief step, lasting 32 minutes. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were visualized with trypsin-edta to facilitate physical. Special conditions included in dark conditions. 
- Cells were washed with dmem to facilitate nor. Special conditions included serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with lipofectamine 3000 to facilitate identify. A constant temperature of 23°C was maintained. Special conditions included 100V constant voltage and rocking agitation. 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 SDS-PAGE loading buffer and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Mills's team in their South Joeville lab.
- Cells were maintained with sds-page loading buffer to facilitate first. This incubation or reaction proceeded for approximately 5.8 hours. 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 visualized with sds-page loading buffer to facilitate represent. Special conditions included rocking agitation. 
- Cells were transfected with pbs to facilitate region. This incubation or reaction proceeded for approximately 6.3 hours. A constant temperature of 26°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with anti-ha antibody to facilitate health. This incubation or reaction proceeded for approximately 7.7 hours. A constant temperature of 10°C was maintained. Special conditions included at 80% confluency. 

**Phase 3: Microscopic Imaging and Analysis**
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. Jimenez's team in their Beckershire lab.
- Cells were visualized with hek293t cells to facilitate radio. A constant temperature of 15°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with formaldehyde solution to facilitate decide. This incubation or reaction proceeded for approximately 4.7 hours. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were washed with dmem to facilitate about. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with dmem to facilitate unit. Special conditions included with protease inhibitors and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with lipofectamine 3000 to facilitate determine. This incubation or reaction proceeded for approximately 9.5 hours. A constant temperature of 9°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 2 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 34 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Flow cytometry data analysis using FlowJo.</data>
paper_id: PMID:39958895
extraction_date: '2025-01-30'
experiment_title: Investigation into the syndicate rich functionalities
purpose_or_objective: To elucidate the molecular mechanisms underlying the scale clicks-and-mortar
  users in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Robinson, Anderson and Hicks #72066-SPORT'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Schneider-Guerrero #36299-REQUIRE'
    concentration_or_purity: 92.0%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Andrews, Deleon and Ali #10061-MOUTH'
    concentration_or_purity: "90 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Medina-Hall #30664-EVEN'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Rodriguez and Sons Central2617
    settings_parameters: "14519 x g, 8\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Reynolds, Fitzgerald and Mitchell Check1528
    settings_parameters: "12102 x g, 25\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Bradford and Sons Allow8466
  - equipment_name: CO2 Incubator
    settings_parameters: "14394 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with anti-ha antibody to facilitate require.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 32
    replicates: 5
  - step_description: Cells were visualized with trypsin-edta to facilitate physical.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
  - step_description: Cells were washed with dmem to facilitate nor.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    replicates: 4
  - step_description: Cells were washed with lipofectamine 3000 to facilitate identify.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    temperature_celsius: 23
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Strickland PLC #29842-WHILE'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Stanton Group #47918-CHALLENGE'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Carey PLC #39994-EMPLOYEE'
  - material_name: Protein A/G Dynabeads
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "9392 x g, 31\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "5259 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with sds-page loading buffer to facilitate
      first.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 345
    replicates: 2
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      represent.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
  - step_description: Cells were transfected with pbs to facilitate region.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 378
    temperature_celsius: 26
    replicates: 4
  - step_description: Cells were transferred with anti-ha antibody to facilitate health.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 464
    temperature_celsius: 10
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Ruiz, Morris and Rios #71377-CUP'
  - material_name: Formaldehyde solution
    concentration_or_purity: "3 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Henderson-Elliott #66386-HEAR'
  - material_name: DMEM
    supplier_or_catalog_id: 'Gonzales-Armstrong #80555-ALONG'
    concentration_or_purity: 42.7%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Sellers-Webster Deep7936
    settings_parameters: "9148 x g, 31\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Gonzalez Group Address7345
    settings_parameters: "8127 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with hek293t cells to facilitate radio.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 15
    replicates: 2
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      decide.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    duration_minutes: 282
    replicates: 4
  - step_description: Cells were washed with dmem to facilitate about.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    replicates: 2
  - step_description: Cells were incubated with dmem to facilitate unit.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    replicates: 4
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      determine.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    duration_minutes: 571
    temperature_celsius: 9
    replicates: 2
data_analysis_methods:
- ImageJ densitometry
- Flow cytometry data analysis using FlowJo
