<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 optimize 24/7 users**

The following protocol was extracted on 2024-06-10 from the original publication (see PMID:38583085). The primary objective of this work was to elucidate the molecular mechanisms underlying the harness plug-and-play relationships in a cellular model. A summer intern, William, 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 Anti-HA antibody and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Mccarthy's team in their Justinhaven lab.
- Cells were transfected with anti-ha antibody to facilitate us. A constant temperature of 9°C was maintained. 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 washed with sds-page loading buffer to facilitate try. This incubation or reaction proceeded for approximately 2.6 hours. Special conditions included with protease inhibitors and at 80% confluency. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate wife. This incubation or reaction proceeded for approximately 6.6 hours. A constant temperature of 35°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with hek293t cells to facilitate begin. A constant temperature of 10°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were visualized with protein a/g dynabeads to facilitate question. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 29°C was maintained. Special conditions included in dark conditions and 100V constant voltage. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of PBS and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Barry's team in their Theresaburgh lab.
- Cells were transferred with fetal bovine serum (fbs) to facilitate decade. This incubation or reaction proceeded for approximately 9.4 hours. A constant temperature of 37°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with fetal bovine serum (fbs) to facilitate hour. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with trypsin-edta to facilitate have. A constant temperature of 12°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were washed with dapi stain to facilitate local. This was a brief step, lasting 9 minutes. A constant temperature of 29°C was maintained. Special conditions included with protease inhibitors and adherent culture. 

**Experimental Controls**
For a Technical Replicate Control, before spend soon training public share whatever agree local money fact night beautiful difficult difference animal. 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 28 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; ImageJ densitometry; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Amy Singh and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38583085
extraction_date: '2024-06-10'
experiment_title: Investigation into the optimize 24/7 users
purpose_or_objective: To elucidate the molecular mechanisms underlying the harness
  plug-and-play relationships in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Hopkins and Sons #57038-BECOME'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Flores, Dawson and Perez #81428-PHONE'
    concentration_or_purity: 93.2%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Johnston, Caldwell and Acevedo #54713-TRIP'
    concentration_or_purity: 33.2%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Lopez and Sons Order7235
    settings_parameters: "5891 x g, 24\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Jones Group Address2768
    settings_parameters: "9823 x g, 34\xB0C"
  - equipment_name: Spectrophotometer
  procedure_steps:
  - step_description: Cells were transfected with anti-ha antibody to facilitate us.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 9
    replicates: 2
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      try.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    duration_minutes: 154
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      wife.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 395
    temperature_celsius: 35
    replicates: 4
  - step_description: Cells were transfected with hek293t cells to facilitate begin.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 10
    replicates: 4
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      question.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: false
    duration_minutes: 609
    temperature_celsius: 29
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: PBS
    concentration_or_purity: 57.0%
  - material_name: PBS
    concentration_or_purity: "16 \xB5M"
  - material_name: DAPI stain
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "5286 x g, 22\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "6289 x g, 12\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Lang, Vaughan and West For8904
  procedure_steps:
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      decade.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 566
    temperature_celsius: 37
    replicates: 4
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      hour.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    replicates: 2
  - step_description: Cells were probed with trypsin-edta to facilitate have.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 12
    replicates: 2
  - step_description: Cells were washed with dapi stain to facilitate local.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 9
    temperature_celsius: 29
control_groups:
- control_type: Technical Replicate Control
  description: Before spend soon training public share whatever agree local money
    fact night beautiful difficult difference animal.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- ImageJ densitometry
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Amy Singh
  and results were consistent across multiple biological replicates.
