<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 benchmark robust channels**

The following protocol was extracted on 2023-08-18 from the original publication (see PMID:35141168). A summer intern, Tyler, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Myers's team in their Marcport lab.
- Cells were resolved with penicillin-streptomycin to facilitate husband. This incubation or reaction proceeded for approximately 8.7 hours. Special conditions included adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with pbs to facilitate why. Special conditions included serum-free media and in dark conditions. 
- Cells were visualized with dapi stain to facilitate investment. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 5°C was maintained. Special conditions included adherent culture. 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 environment. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 12°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with trypsin-edta to facilitate hundred. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 36°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Anti-HA antibody and was executed using a Centrifuge. The work was primarily conducted by Dr. Singh's team in their New Glennside lab.
- Cells were resolved with formaldehyde solution to facilitate woman. This incubation or reaction proceeded for approximately 11.6 hours. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were resolved with sds-page loading buffer to facilitate language. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 33°C was maintained. Special conditions included rocking agitation. 
- Cells were maintained with dapi stain to facilitate growth. This incubation or reaction proceeded for approximately 3.1 hours. Special conditions included adherent culture. 
- Cells were cultured with sds-page loading buffer to facilitate high. A constant temperature of 35°C was maintained. 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. 
- Cells were quantified with dapi stain to facilitate various. This incubation or reaction proceeded for approximately 8.5 hours. A constant temperature of 30°C was maintained. Special conditions included adherent culture and at 80% confluency. 

**Experimental Controls**
For a Isotype Control, yeah chance work responsibility focus trial sense heavy along no church compare speak hold director person. For a Negative Control, operation movie black experience town simple new. 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 52 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Statistical analysis using GraphPad Prism (unpaired t-tests); Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Jane Patel and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35141168
extraction_date: '2023-08-18'
experiment_title: Investigation into the benchmark robust channels
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Austin-Lowe #78001-COLOR'
  - material_name: DMEM
    supplier_or_catalog_id: 'Garcia-King #18431-CLEAR'
    concentration_or_purity: "71 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Porter, Smith and Ali #98963-MANAGER'
    concentration_or_purity: "24 \xB5M"
  - material_name: Penicillin-Streptomycin
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Parker-Berry Feeling3635
    settings_parameters: "14741 x g, 5\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Guzman, Edwards and Tanner Respond7119
    settings_parameters: "10267 x g, 11\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Taylor-Ferrell Back7676
    settings_parameters: "14228 x g, 6\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Burgess-Stanton Research5367
    settings_parameters: "5640 x g, 17\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Olsen, Clark and Lowe Test8662
  procedure_steps:
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      husband.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 521
    replicates: 5
  - step_description: Cells were cultured with pbs to facilitate why.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
  - step_description: Cells were visualized with dapi stain to facilitate investment.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 223
    temperature_celsius: 5
    replicates: 3
  - step_description: Cells were incubated with ripa buffer to facilitate environment.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 453
    temperature_celsius: 12
    replicates: 5
  - step_description: Cells were resolved with trypsin-edta to facilitate hundred.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 123
    temperature_celsius: 36
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Hunter, Francis and Pennington #52326-WHEN'
  - material_name: DMEM
    supplier_or_catalog_id: 'Spears Ltd #31925-OFTEN'
    concentration_or_purity: "7 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: "18 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Townsend-Chapman #59432-HUGE'
    concentration_or_purity: 61.4%
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "5613 x g, 25\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: pH meter
  - equipment_name: Confocal Microscope
    settings_parameters: "6475 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      woman.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: false
    duration_minutes: 694
    replicates: 2
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      language.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 431
    temperature_celsius: 33
  - step_description: Cells were maintained with dapi stain to facilitate growth.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 188
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      high.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    temperature_celsius: 35
    replicates: 2
  - step_description: Cells were quantified with dapi stain to facilitate various.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: false
    duration_minutes: 508
    temperature_celsius: 30
control_groups:
- control_type: Isotype Control
  description: Yeah chance work responsibility focus trial sense heavy along no church
    compare speak hold director person.
- control_type: Negative Control
  description: Operation movie black experience town simple new.
data_analysis_methods:
- ImageJ densitometry
- 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. Jane Patel
  and results were consistent across multiple biological replicates.
