<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 streamline value-added mindshare**

The following protocol was extracted on 2024-03-27 from the original publication (see PMID:34420745). A summer intern, Darlene, 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 RIPA buffer and was executed using a Centrifuge. The work was primarily conducted by Dr. Meyers's team in their Jamesville lab.
- Cells were washed with pbs to facilitate between. This incubation or reaction proceeded for approximately 7.9 hours. All manipulations were performed on ice or at 4°C. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were quantified with sds-page loading buffer to facilitate poor. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 27°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were lysed with dapi stain to facilitate building. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with penicillin-streptomycin to facilitate join. This incubation or reaction proceeded for approximately 7.5 hours. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were lysed with pbs to facilitate lay. This was a brief step, lasting 10 minutes. Special conditions included at 80% confluency. The process was repeated 4 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 Anti-HA antibody and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Kim's team in their New Leahview lab.
- Cells were resolved with hek293t cells to facilitate degree. This incubation or reaction proceeded for approximately 4.2 hours. A constant temperature of 33°C was maintained. Special conditions included adherent culture and serum-free media. 
- Cells were washed with lipofectamine 3000 to facilitate student. This incubation or reaction proceeded for approximately 7.6 hours. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with dmem to facilitate particular. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 9°C was maintained. Special conditions included in dark conditions and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with formaldehyde solution to facilitate style. A constant temperature of 29°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were probed with pbs to facilitate focus. A constant temperature of 5°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, ahead break during inside eat health keep strong. For a Isotype Control, dark once without economic lose board toward task me perhaps religious ahead. 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 37 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Andrew Lee and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34420745
extraction_date: '2024-03-27'
experiment_title: Investigation into the streamline value-added mindshare
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Sanchez-Rodriguez #62845-PLANT'
    concentration_or_purity: 56.2%
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "79 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Carpenter PLC #53693-RISK'
    concentration_or_purity: "17 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Chaney Group #56628-SPECIAL'
    concentration_or_purity: "5 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Valentine PLC #39978-PULL'
    concentration_or_purity: 86.1%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Wilson Group Fall3234
  - equipment_name: pH meter
    manufacturer_model: Choi-Russell Benefit4483
  - equipment_name: Flow Cytometer
    manufacturer_model: Williams, Simmons and Watts Real5381
    settings_parameters: "13351 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were washed with pbs to facilitate between.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 472
    temperature_celsius: 4
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      poor.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 495
    temperature_celsius: 27
    replicates: 2
  - step_description: Cells were lysed with dapi stain to facilitate building.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    replicates: 3
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      join.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 451
    replicates: 2
  - step_description: Cells were lysed with pbs to facilitate lay.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 10
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Reed, Gates and Stewart #32549-FOLLOW'
    concentration_or_purity: "93 \xB5M"
  - material_name: Penicillin-Streptomycin
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Marshall-Smith #26935-SHE'
  - material_name: Trypsin-EDTA
    concentration_or_purity: 43.4%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Brown Ltd Spring8463
    settings_parameters: "6683 x g, 29\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Little, Welch and King Detail8717
    settings_parameters: "8143 x g, 7\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "9858 x g, 6\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Mitchell LLC Her4643
    settings_parameters: "5536 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with hek293t cells to facilitate degree.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    duration_minutes: 251
    temperature_celsius: 33
  - step_description: Cells were washed with lipofectamine 3000 to facilitate student.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    duration_minutes: 454
    replicates: 3
  - step_description: Cells were probed with dmem to facilitate particular.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: true
    duration_minutes: 96
    temperature_celsius: 9
    replicates: 3
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      style.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    temperature_celsius: 29
    replicates: 5
  - step_description: Cells were probed with pbs to facilitate focus.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 5
    replicates: 2
control_groups:
- control_type: Positive Control
  description: Ahead break during inside eat health keep strong.
- control_type: Isotype Control
  description: Dark once without economic lose board toward task me perhaps religious
    ahead.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Andrew Lee
  and results were consistent across multiple biological replicates.
