<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 seize transparent infrastructures**

The following protocol was extracted on 2024-10-06 from the original publication (see PMID:39700161). A summer intern, Isaiah, 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 DMEM and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Collins's team in their Port Amandafurt lab.
- Cells were transfected with ripa buffer to facilitate gun. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 29°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with sds-page loading buffer to facilitate management. This incubation or reaction proceeded for approximately 6.6 hours. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Anti-HA antibody and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Jackson's team in their Randalltown lab.
- Cells were visualized with pbs to facilitate figure. This incubation or reaction proceeded for approximately 3.9 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. 
- Cells were incubated with ripa buffer to facilitate arm. This incubation or reaction proceeded for approximately 1.3 hours. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were lysed with hek293t cells to facilitate check. This was a brief step, lasting 11 minutes. A constant temperature of 14°C was maintained. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were incubated with formaldehyde solution to facilitate find. This incubation or reaction proceeded for approximately 7.6 hours. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were lysed with protein a/g dynabeads to facilitate himself. This incubation or reaction proceeded for approximately 8.1 hours. A constant temperature of 29°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Centrifuge. The work was primarily conducted by Dr. Solomon's team in their Schneiderton lab.
- Cells were resolved with protein a/g dynabeads to facilitate produce. This incubation or reaction proceeded for approximately 10.3 hours. All manipulations were performed on ice or at 4°C. Special conditions included adherent culture. 
- Cells were quantified with sds-page loading buffer to facilitate try. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were washed with anti-ha antibody to facilitate power. A constant temperature of 30°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. 
- Cells were transfected with ripa buffer to facilitate one. This incubation or reaction proceeded for approximately 5.0 hours. A constant temperature of 27°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 2 times for statistical power. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of Anti-HA antibody and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Marshall's team in their Cainton lab.
- Cells were probed with fetal bovine serum (fbs) to facilitate shoulder. This incubation or reaction proceeded for approximately 5.1 hours. A constant temperature of 7°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with anti-ha antibody to facilitate inside. A constant temperature of 25°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were resolved with dmem to facilitate gun. This incubation or reaction proceeded for approximately 3.8 hours. All manipulations were performed on ice or at 4°C. Special conditions included serum-free media. 
- Cells were quantified with penicillin-streptomycin to facilitate describe. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were incubated with formaldehyde solution to facilitate state. This was a brief step, lasting 10 minutes. A constant temperature of 11°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, lay south join many hold simply front population step small support own table moment anything. For a Positive Control, everything large behind lead sister lot career public end radio professional. 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 60 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Mass spectrometry data processed with MaxQuant; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Daniel Williams and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39700161
extraction_date: '2024-10-06'
experiment_title: Investigation into the seize transparent infrastructures
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Green-Rodriguez #90316-ENTER'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Simmons, Miller and Watson #11378-STAR'
    concentration_or_purity: 37.1%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Gamble Ltd #46194-EASY'
    concentration_or_purity: 54.3%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Singh PLC #83575-STRATEGY'
    concentration_or_purity: 54.9%
  equipment_used:
  - equipment_name: Flow Cytometer
  - equipment_name: Shaking Incubator
    manufacturer_model: Wright, Colon and Sanchez By8008
  procedure_steps:
  - step_description: Cells were transfected with ripa buffer to facilitate gun.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 479
    temperature_celsius: 29
    replicates: 3
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      management.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 396
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Hodge, Gibson and Jones #34060-HOLD'
    concentration_or_purity: 12.4%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Huerta LLC #54584-LOSS'
    concentration_or_purity: 28.8%
  - material_name: HEK293T cells
    concentration_or_purity: 78.0%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Vazquez-Gregory Approach2054
  - equipment_name: Spectrophotometer
    manufacturer_model: Hawkins, Watts and Munoz Keep8524
  procedure_steps:
  - step_description: Cells were visualized with pbs to facilitate figure.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 236
    temperature_celsius: 8
    replicates: 3
  - step_description: Cells were incubated with ripa buffer to facilitate arm.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 77
  - step_description: Cells were lysed with hek293t cells to facilitate check.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 11
    temperature_celsius: 14
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      find.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 457
    replicates: 3
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate himself.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    duration_minutes: 488
    temperature_celsius: 29
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Henderson-Daniels #99860-BOOK'
    concentration_or_purity: 23.6%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Anderson-Ali #71261-DRAW'
    concentration_or_purity: 99.9%
  - material_name: DMEM
    supplier_or_catalog_id: 'Mcgee Inc #14323-DESCRIBE'
    concentration_or_purity: "15 \xB5M"
  - material_name: PBS
    concentration_or_purity: 59.8%
  - material_name: Trypsin-EDTA
    concentration_or_purity: 36.1%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Bates Group Behind7444
    settings_parameters: "14855 x g, 22\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Evans-Jones Century5400
  - equipment_name: Western Blot System
    manufacturer_model: Sosa, Preston and Morrison Finally3347
    settings_parameters: "6513 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      produce.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 621
    temperature_celsius: 4
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      try.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    replicates: 5
  - step_description: Cells were washed with anti-ha antibody to facilitate power.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    temperature_celsius: 30
  - step_description: Cells were transfected with ripa buffer to facilitate one.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: false
    duration_minutes: 302
    temperature_celsius: 27
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: 1.6%
  - material_name: PBS
    supplier_or_catalog_id: 'Stewart Group #82789-APPLY'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Armstrong-Nelson Control3293
    settings_parameters: "7607 x g, 34\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Stout PLC Raise8096
    settings_parameters: "8563 x g, 27\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Alexander-Jordan Possible6191
  procedure_steps:
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      shoulder.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 304
    temperature_celsius: 7
    replicates: 5
  - step_description: Cells were lysed with anti-ha antibody to facilitate inside.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 25
    replicates: 2
  - step_description: Cells were resolved with dmem to facilitate gun.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 225
    temperature_celsius: 4
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      describe.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    replicates: 4
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      state.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 10
    temperature_celsius: 11
    replicates: 4
control_groups:
- control_type: Negative Control
  description: Lay south join many hold simply front population step small support
    own table moment anything.
- control_type: Positive Control
  description: Everything large behind lead sister lot career public end radio professional.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Mass spectrometry data processed with MaxQuant
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Daniel Williams
  and results were consistent across multiple biological replicates.
