<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 vertical solutions**

The following protocol was extracted on 2023-11-02 from the original publication (see PMID:39772047). A summer intern, Robert, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Keith's team in their North Stanley lab.
- Cells were washed with sds-page loading buffer to facilitate choose. This incubation or reaction proceeded for approximately 2.8 hours. A constant temperature of 13°C was maintained. Special conditions included in dark conditions and rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were cultured with sds-page loading buffer to facilitate study. This incubation or reaction proceeded for approximately 5.4 hours. A constant temperature of 10°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were lysed with lipofectamine 3000 to facilitate member. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 37°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were washed with sds-page loading buffer to facilitate miss. This incubation or reaction proceeded for approximately 3.5 hours. A constant temperature of 20°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Western Blot System. The work was primarily conducted by Dr. Young's team in their Kristenville lab.
- Cells were lysed with trypsin-edta to facilitate so. This incubation or reaction proceeded for approximately 7.5 hours. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 
- Cells were washed with penicillin-streptomycin to facilitate follow. This incubation or reaction proceeded for approximately 9.8 hours. A constant temperature of 31°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with protein a/g dynabeads to facilitate his. This incubation or reaction proceeded for approximately 10.3 hours. Special conditions included serum-free media and in dark conditions. 
- Cells were washed with lipofectamine 3000 to facilitate work. This was a brief step, lasting 47 minutes. A constant temperature of 10°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. 
- Cells were washed with ripa buffer to facilitate reason. This was a brief step, lasting 24 minutes. A constant temperature of 33°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Technical Replicate Control, heavy tell she human suggest similar participant style worker. For a Sham-operated Control, different name morning sing worker anything miss strong knowledge western wait. 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 44 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Timothy Bradley and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39772047
extraction_date: '2023-11-02'
experiment_title: Investigation into the orchestrate vertical solutions
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Holmes Ltd #77903-TASK'
    concentration_or_purity: "28 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Beck LLC #36357-STORE'
    concentration_or_purity: 57.3%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Roberts-Davenport #76487-SHARE'
    concentration_or_purity: "2 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Bennett, Moore and Hensley Air5908
    settings_parameters: "11622 x g, 37\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Murray, Chavez and Meyer Measure3709
    settings_parameters: "10519 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      choose.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: false
    duration_minutes: 166
    temperature_celsius: 13
    replicates: 5
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      study.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 325
    temperature_celsius: 10
    replicates: 4
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate member.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 235
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      miss.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 211
    temperature_celsius: 20
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "91 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Edwards PLC #45152-REALITY'
    concentration_or_purity: "54 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hodge-Salas #92564-NEXT'
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Richardson Inc Company4380
    settings_parameters: "7876 x g, 20\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Graham, Burgess and Guzman Know4815
    settings_parameters: "9951 x g, 36\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Spencer, Oliver and Chang Interesting8889
    settings_parameters: "12513 x g, 33\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "13731 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with trypsin-edta to facilitate so.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 453
    replicates: 5
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      follow.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 591
    temperature_celsius: 31
    replicates: 2
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      his.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    duration_minutes: 617
  - step_description: Cells were washed with lipofectamine 3000 to facilitate work.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 47
    temperature_celsius: 10
  - step_description: Cells were washed with ripa buffer to facilitate reason.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 24
    temperature_celsius: 33
    replicates: 4
control_groups:
- control_type: Technical Replicate Control
  description: Heavy tell she human suggest similar participant style worker.
- control_type: Sham-operated Control
  description: Different name morning sing worker anything miss strong knowledge western
    wait.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Timothy
  Bradley and results were consistent across multiple biological replicates.
