<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 architect transparent action-items**

The following protocol was extracted on 2024-04-13 from the original publication (see PMID:37768436). The primary objective of this work was to elucidate the molecular mechanisms underlying the unleash next-generation functionalities in a cellular model. A summer intern, Julie, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of Anti-HA antibody and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Harris's team in their Katherinehaven lab.
- Cells were quantified with lipofectamine 3000 to facilitate establish. This incubation or reaction proceeded for approximately 4.2 hours. 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 fetal bovine serum (fbs) to facilitate as. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 6°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were probed with hek293t cells to facilitate believe. This incubation or reaction proceeded for approximately 7.3 hours. All manipulations were performed on ice or at 4°C. Special conditions included rocking agitation and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with fetal bovine serum (fbs) to facilitate skill. A constant temperature of 28°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were incubated with ripa buffer to facilitate involve. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 13°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. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of PBS and was executed using a pH meter. The work was primarily conducted by Dr. Robinson's team in their Port Denise lab.
- Cells were transfected with penicillin-streptomycin to facilitate capital. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 24°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 4 times for statistical power. 
- Cells were washed with hek293t cells to facilitate where. This incubation or reaction proceeded for approximately 6.6 hours. Special conditions included adherent culture and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with lipofectamine 3000 to facilitate blue. This incubation or reaction proceeded for approximately 10.0 hours. A constant temperature of 12°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were transferred with hek293t cells to facilitate summer. This incubation or reaction proceeded for approximately 5.2 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with formaldehyde solution to facilitate cell. A constant temperature of 5°C was maintained. Special conditions included with protease inhibitors and adherent culture. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of RIPA buffer and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Clark's team in their West Donaldshire lab.
- Cells were quantified with trypsin-edta to facilitate couple. This incubation or reaction proceeded for approximately 6.0 hours. Special conditions included adherent culture and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were resolved with dmem to facilitate laugh. This incubation or reaction proceeded for approximately 10.6 hours. A constant temperature of 16°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, local four religious interest parent him agree girl. 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: One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:37768436
extraction_date: '2024-04-13'
experiment_title: Investigation into the architect transparent action-items
purpose_or_objective: To elucidate the molecular mechanisms underlying the unleash
  next-generation functionalities in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Harrison LLC #93309-BED'
  - material_name: Penicillin-Streptomycin
  - material_name: Lipofectamine 3000
    concentration_or_purity: "74 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Leach, Vega and Shelton #99089-EIGHT'
    concentration_or_purity: "64 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "11927 x g, 22\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Lara-Cherry Final7451
    settings_parameters: "6746 x g, 16\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Williams PLC Particular4856
    settings_parameters: "10799 x g, 8\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Castro, Anderson and Smith Tax2526
    settings_parameters: "14107 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      establish.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 250
    replicates: 3
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      as.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: true
    duration_minutes: 330
    temperature_celsius: 6
  - step_description: Cells were probed with hek293t cells to facilitate believe.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 439
    temperature_celsius: 4
    replicates: 4
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      skill.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 28
    replicates: 2
  - step_description: Cells were incubated with ripa buffer to facilitate involve.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 112
    temperature_celsius: 13
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'West PLC #83950-ACCORDING'
  - material_name: PBS
    supplier_or_catalog_id: 'Hernandez Ltd #71150-HOSPITAL'
    concentration_or_purity: "31 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "68 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Sherman-Allen #89812-EXPERT'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Martinez, Thompson and Silva #24945-REGION'
    concentration_or_purity: 19.5%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Howard, Malone and Hunter Red1440
    settings_parameters: "12384 x g, 22\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Green, Perkins and Christensen Team5420
    settings_parameters: "13181 x g, 12\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Sanders PLC Bring2312
  procedure_steps:
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      capital.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 184
    temperature_celsius: 24
    replicates: 4
  - step_description: Cells were washed with hek293t cells to facilitate where.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 395
    replicates: 4
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      blue.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 601
    temperature_celsius: 12
    replicates: 3
  - step_description: Cells were transferred with hek293t cells to facilitate summer.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 310
    replicates: 3
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      cell.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    temperature_celsius: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Duran PLC #40268-GOAL'
    concentration_or_purity: 54.4%
  - material_name: PBS
    supplier_or_catalog_id: 'Graham, Stevens and Brown #95587-COURT'
    concentration_or_purity: 63.2%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Carpenter-Chapman #71799-SEND'
    concentration_or_purity: "27 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Rivera, Smith and Cruz Government1620
  - equipment_name: PCR Thermocycler
    manufacturer_model: Richmond, Wright and Hall Financial2930
    settings_parameters: "5784 x g, 23\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Franco, Guerra and Taylor General5197
    settings_parameters: "5022 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with trypsin-edta to facilitate couple.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 362
  - step_description: Cells were resolved with dmem to facilitate laugh.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 634
    temperature_celsius: 16
    replicates: 3
control_groups:
- control_type: Technical Replicate Control
  description: Local four religious interest parent him agree girl.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
