@pikaa-ai/pikaa 0.3.1 → 0.3.4

package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-optimization.md

@@ -1,85 +0,0 @@
-# Cell Free Protein Expression Optimization
-
-**URL:** https://cloud.ginkgo.bio/protocols/cell-free-protein-expression-optimization
-**Status:** Ginkgo Certified
-**Price:** $199/sample
-**Turnaround:** up to 11 days
-
-## Overview
-
-Design of Experiment (DoE) approach to expressing protein targets in a proprietary reconstituted E. coli transcription-translation system. Each construct is evaluated in up to 24 reaction conditions per protein, including target-specific additives such as chaperones, disulfide-bond enhancers, and cofactors. Designed for difficult-to-express proteins including membrane proteins and targets with disulfide or cofactor requirements.
-
-## Input
-
-- **DNA sequence** in `.fasta` format
-
-## Output
-
-- **Comparative Yield:** Titer data mapped across all tested variables (lysates, temps, additives)
-- **Purity Profiling:** Target protein vs. background impurities to find highest quality yield
-- **Optimal Conditions:** Overlaid electropherograms pinpointing the exact formulation for a given sequence
-
-## Automated Workflow
-
-### Phase 1 - Reagent Prep
-
-1. Retrieve plates from 4 deg C
-2. Thaw at room temperature
-3. PBS backfill
-
-### Phase 2 - CFPS Reaction Setup & Incubation
-
-1. Retrieve plates from 4 deg C
-2. Dispense lysate
-3. QC plate read
-4. Incubate (shaking or static, condition-dependent)
-
-### Phase 3 - Quantification Prep & Read
-
-1. Dispense PBS
-2. Unseal plate
-3. LabChip quantification
-4. Seal plate
-5. Store at 4 deg C
-
-## Protocol Parameters
-
-- Payloads & Reagents
-- Bravo Stamp
-- HiG Centrifuge
-- Incubation & Storage
-
-## Optimization Variables
-
-The DoE matrix can span up to 24 conditions per protein, varying:
-
-- **Lysate composition** (different E. coli extract formulations)
-- **Temperature** (incubation temperature profiles)
-- **Additives:**
-  - Chaperones (for folding-challenged targets)
-  - Disulfide-bond enhancers (for targets requiring disulfide bridges)
-  - Cofactors (metal ions, coenzymes, prosthetic groups)
-  - Other target-specific supplements
-
-## Ordering
-
-- **Number of Proteins:** configurable
-- **Number of Replicates:** configurable
-- **File Upload:** CSV, Excel, FASTA, TXT, PDF, ZIP
-- **Additional Details:** free-text field for special requirements
-
-## Certification Milestones
-
-- Dry Run Complete
-- Wet Run Complete
-- Biovalidation Complete
-- App Note Complete
-
-## Use Cases
-
-- Optimizing expression of difficult-to-express proteins
-- Membrane protein expression screening
-- Identifying optimal conditions for disulfide-bonded proteins
-- Cofactor-dependent protein expression
-- Systematic exploration of expression parameter space
-- Finding the best formulation before scaling up production

package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-validation.md

@@ -1,71 +0,0 @@
-# Cell Free Protein Expression Validation
-
-**URL:** https://cloud.ginkgo.bio/protocols/cell-free-protein-expression-validation
-**Status:** Ginkgo Certified
-**Price:** $39/sample
-**Turnaround:** up to 10 days
-
-## Overview
-
-Fastest path from a protein sequence to a quantitative go/no-go readout on expression. Uses a proprietary reconstituted E. coli transcription-translation (cell-free protein synthesis, CFPS) system. Reactions complete in 4-16 hours. Designed for early-stage screening, novel construct evaluation, and rapid triage of candidate sequences before committing resources to downstream optimization or purification.
-
-## Input
-
-- **DNA sequence** in `.fasta` format
-- Sequences up to 1800 bp supported
-
-## Output
-
-- **Expression Confirmation:** Verification of target protein at expected molecular weight
-- **Baseline Titer:** Initial quantitative yield measurement (mg/L)
-- **Initial Purity:** Percentage of target protein vs. impurities, delivered with virtual gel images
-
-## Automated Workflow
-
-### Phase 1 - CFPS Reaction Setup & Incubation
-
-1. Retrieve plates
-2. Stamp DNA templates
-3. Seal plate
-4. Incubate shaking at 30 deg C
-
-### Phase 2 - Quantification Prep
-
-1. Dispense PBS diluent
-2. Seal plate
-3. Store at 4 deg C
-
-### Phase 3 - LabChip Quantification
-
-1. Unseal plate
-2. LabChip quantification
-3. Seal plate
-4. Store at 4 deg C
-
-## Protocol Parameters
-
-- Payloads & Reagents
-- Bravo Stamp
-- HiG Centrifuge
-- Incubation & Storage
-
-## Ordering
-
-- **Number of Proteins:** configurable
-- **Number of Replicates:** configurable
-- **File Upload:** CSV, Excel, FASTA, TXT, PDF, ZIP
-- **Additional Details:** free-text field for special requirements
-
-## Certification Milestones
-
-- Dry Run Complete
-- Wet Run Complete
-- Biovalidation Complete
-- App Note Complete
-
-## Use Cases
-
-- Screening candidate protein sequences for expressibility
-- Go/no-go decisions before investing in optimization
-- Evaluating novel constructs in a cell-free system
-- Comparing expression levels across sequence variants

package/skills/ginkgo-cloud-lab/references/cfps-expression-purification-quantification.md

@@ -1,60 +0,0 @@
-# Cell Free Protein Expression, Purification, and Quantification
-
-**URL:** https://cloud.ginkgo.bio/protocols/cfps-expression-purification-quantification
-**Status:** Ginkgo Certified
-**Price:** $159/sample
-**Turnaround:** up to 12 days
-**Throughput:** Up to 88 constructs per run (1 column reserved for controls), 96-well format
-
-## Overview
-
-End-to-end automated cell-free expression, Strep-tag purification, and quantification of StrepII-tagged proteins, combining A280 yield with LabChip purity/size assessment. Linear DNA templates are expressed in CFPS reactions for 8 hours, purified with magnetic beads on the Agilent Bravo, quantified by A280 on the BMG PHERAstar, then characterized for purity and apparent molecular weight on the Revvity LabChip.
-
-## Input
-
-- **DNA Input:** Linear DNA sequence (`.xlsx` template)
-- **Tag Orientation:** N-terminal or C-terminal fusion (validated with C-terminal tags; success is protein-dependent)
-- **Format:** Up to 88 constructs per run, 1 column of wells for controls
-
-## Output
-
-- **Expression Confirmation:** Verification of the target protein at the expected molecular weight
-- **Baseline Titer:** Initial quantitative yield measurement (mg/L)
-- **Initial Purity:** Percentage of target protein vs. impurities, delivered with virtual gel images
-
-## Automated Workflow
-
-### Phase 1 - CFPS Reaction Setup & Incubation
-
-1. Retrieve plates from storage (HRB TundraStore)
-2. Stamp DNA templates into CFPS reaction mix (Agilent Bravo 96)
-3. Seal plate (Agilent PlateLoc)
-4. Incubate shaking at 29-30 deg C (Thermo Cytomat)
-
-### Phase 2 - Mag Bead Purification & Quantification
-
-1. Dispense reagents and load samples (Biotek / Agilent)
-2. Bind sample to beads (Bravo Shaker)
-3. Wash beads (Agilent Bravo 96)
-4. Elute purified protein (Agilent Bravo 96)
-5. Transfer eluate to read plate (Agilent Bravo 96)
-6. Read A280 & fluorescence (BMG PHERAstar)
-
-### Phase 3 - LabChip Purity and Size Assessment
-
-1. LabChip assessment (Revvity LabChip)
-2. Seal plate (Agilent PlateLoc)
-3. Store at 4 deg C (HRB TundraStore)
-
-## Ordering
-
-- **Number of Proteins:** configurable
-- **Number of Replicates:** configurable
-- **File Upload:** CSV, Excel, FASTA, TXT, PDF, ZIP
-- **Additional Details:** free-text field for special requirements
-
-## Use Cases
-
-- Purified yield plus purity/size profiling in one cell-free run
-- Characterizing constructs before scale-up production
-- Comparing titer and purity across sequence variants

package/skills/ginkgo-cloud-lab/references/cfps-strep-purification-thermal-shift.md

@@ -1,63 +0,0 @@
-# Protein Expression and Thermal Shift Assay
-
-**URL:** https://cloud.ginkgo.bio/protocols/cfps-strep-purification-thermal-shift
-**Status:** Ginkgo Certified
-**Price:** $159/sample
-**Turnaround:** up to 12 days
-**Throughput:** Up to 88 constructs per run (1 column reserved for controls)
-
-## Overview
-
-Combines cell-free protein expression, Strep-tag magnetic bead purification, and a Protein Thermal Shift Assay using SYPRO Orange into a single end-to-end workflow. Starting from a DNA template plate, the protocol expresses protein in a CFPS reaction, purifies the tagged product via Strep-Tactin magnetic beads, and characterizes thermal unfolding of the purified protein by extrinsic fluorimetry.
-
-SYPRO Orange is a hydrophobic-binding dye whose fluorescence increases sharply as a protein unfolds and exposes buried hydrophobic regions during a controlled temperature ramp. Tracking fluorescence vs. temperature reports **Tonset** (where unfolding begins) plus up to three melting transitions (**TM1, TM2, TM3**) corresponding to distinct domains. These are standard developability parameters used to compare candidates, flag stability liabilities, and rank molecules for downstream development. Best suited for screening and ranking variants by thermal stability directly from DNA, where consistent Tm values across many samples matter more than absolute biophysical precision.
-
-## Input
-
-- **DNA Input:** Linear DNA sequence
-- **Tag Orientation:** N-terminal or C-terminal fusion (validated with C-terminal tags; success is protein-dependent)
-- **Format:** Up to 88 constructs per run, 1 column of wells for controls
-
-## Output
-
-- **Cell-Free Reaction:** 100 uL E. coli-based CFPS reaction per sample with process controls
-- **Yield Quantification:** Absolute protein yield in eluate via A280, converted to mg/mL
-- **Thermal Stability Measurement:** SYPRO Orange thermal shift in triplicate on purified eluate, reporting Tonset and up to three melting transitions (TM1, TM2, TM3) in deg C, where applicable
-- **Reporting & Data:** PDF report with yield data, thermogram plots, called TM values, reaction condition metadata, and QC status
-
-## Automated Workflow
-
-### Phase 1 - CFPS Reaction Setup
-
-1. Stamp DNA into CFPS mix (Agilent Bravo 96)
-2. Incubate (Cytomat / Inheco)
-
-### Phase 2 - Mag Bead Purification
-
-1. Dispense reagents and load samples (Biotek / Agilent)
-2. Bind sample to beads (Bravo Shaker)
-3. Wash beads (Agilent Bravo 96)
-4. Elute purified protein (Agilent Bravo 96)
-
-### Phase 3 - Assay Plate Preparation
-
-1. Transfer 1 uL SYPRO dye (Echo 525)
-2. Stamp purified protein (Agilent Bravo 96)
-
-### Phase 4 - Plate Sealing & Thermal Ramp
-
-1. Seal plate (Agilent PlateLoc)
-2. Execute melt-curve protocol (Bio-Rad CFX Opus thermal cycler)
-
-## Ordering
-
-- **Number of Proteins:** configurable
-- **Number of Replicates:** configurable
-- **File Upload:** CSV, Excel, FASTA, TXT, PDF, ZIP
-- **Additional Details:** free-text field for special requirements
-
-## Use Cases
-
-- Ranking protein variants by thermal stability (Tm/Tonset) directly from DNA
-- Developability screening and stability-liability flagging
-- Comparing domain unfolding across candidate libraries

package/skills/ginkgo-cloud-lab/references/cfps-strep-tag-purification-a280.md

@@ -1,55 +0,0 @@
-# Cell Free Protein Expression with Strep-tag Purification and Yield via A280
-
-**URL:** https://cloud.ginkgo.bio/protocols/cfps-strep-tag-purification-a280
-**Status:** Ginkgo Certified
-**Price:** $149/sample
-**Turnaround:** up to 11 days
-**Throughput:** Up to 88 constructs per run (1 column reserved for controls), 96-well format
-
-## Overview
-
-End-to-end automated expression and purification of StrepII-tagged proteins. Linear DNA templates are expressed in 100 uL CFPS reactions for 20 hours, purified with StreptactinXT magnetic beads on the Agilent Bravo, and quantified from the eluate by A280 absorbance on the BMG PHERAstar. Purity and size assessment are performed on the Revvity LabChip. Enables rapid, data-driven assessment of expressibility before larger-scale campaigns.
-
-## Input
-
-- **DNA Input:** Linear DNA sequence
-- **Tag Orientation:** N-terminal or C-terminal Strep-II tag fusion (validated with C-terminal tags; success is protein-dependent)
-- **Format:** Up to 88 constructs per run, 1 column of wells for controls
-
-## Output
-
-- **Yield Quantification:** A280 per well, converted to protein concentration (mg/mL) via the protein's molar extinction coefficient
-- **Expression Confirmation:** Fluorescence signal relative to controls
-- **Assay Quality Metrics:** Per-run quality summary with plate-level controls
-
-## Automated Workflow
-
-### Phase 1 - CFPS Reaction Setup
-
-1. Stamp DNA into CFPS mix (Agilent Bravo 96)
-2. Incubate (Cytomat / Inheco)
-
-### Phase 2 - Mag Bead Purification
-
-1. Dispense reagents and load samples (Biotek / Agilent)
-2. Bind sample to beads (Bravo Shaker)
-3. Wash beads (Agilent Bravo 96)
-4. Elute purified protein (Agilent Bravo 96)
-
-### Phase 3 - Detection & Quantification
-
-1. Transfer eluate to read plate (Agilent Bravo 96)
-2. Read A280 & fluorescence (BMG PHERAstar)
-
-## Ordering
-
-- **Number of Proteins:** configurable
-- **Number of Replicates:** configurable
-- **File Upload:** CSV, Excel, FASTA, TXT, PDF, ZIP
-- **Additional Details:** free-text field for special requirements
-
-## Use Cases
-
-- Purified-protein yield quantification from cell-free expression
-- Screening Strep-tagged constructs before scale-up
-- Comparing expression and purity across sequence variants

package/skills/ginkgo-cloud-lab/references/echo-ms-cfps-detection.md

@@ -1,49 +0,0 @@
-# Echo-MS Detection of Molecules from an Enzymatic Reaction (Cell Free)
-
-**URL:** https://cloud.ginkgo.bio/protocols/echo-ms-cfps-detection
-**Status:** Beta
-**Price:** $44/sample
-**Turnaround:** up to 13 days
-
-## Overview
-
-Fastest path from a protein sequence to a functional, quantitative readout on enzyme activity. Using a proprietary reconstituted E. coli transcription-translation (CFPS) system, Ginkgo expresses your enzyme of interest in 4-16 hours. A substrate or product is then added directly to the well and substrate conversion is measured by acoustic ejection mass spectrometry (Echo-MS), delivering a go/no-go signal without protein purification. Enzyme expression and Echo-MS are performed using the baseline Cell Free Protein Synthesis Master Mix.
-
-To run this protocol, the relevant analyte/method must first be onboarded (see [echo-ms-method-onboarding.md](echo-ms-method-onboarding.md)).
-
-## Input
-
-- **DNA Input:** Enzyme construct(s)
-- Reaction substrate/product and reaction conditions (provided with the order)
-
-## Output
-
-- **Method summary**
-- **Peak table** (substrate depletion and/or product formation)
-
-## Automated Workflow
-
-### Phase 1 - CFPS Expression
-
-1. Express enzyme in CFPS master mix (4-16 h)
-
-### Phase 2 - Enzymatic Reaction
-
-1. Dispense molecule, buffers, reagents (Agilent Bravo 96)
-2. Incubate under reaction conditions (Inheco)
-
-### Phase 3 - Echo-MS Detection
-
-1. Acoustic ejection mass spectrometry readout of substrate/product
-
-## Ordering
-
-- **Number of Samples:** configurable ($44/sample)
-- **File Upload:** CSV, Excel, FASTA, TXT, PDF, ZIP
-- **Additional Details:** free-text field for special requirements
-
-## Use Cases
-
-- Go/no-go enzyme activity screening without purification
-- Detecting substrate depletion / product formation for biocatalysis
-- High-throughput functional triage of enzyme variants

package/skills/ginkgo-cloud-lab/references/echo-ms-method-onboarding.md

@@ -1,56 +0,0 @@
-# Echo-MS Method Onboarding
-
-**URL:** https://cloud.ginkgo.bio/protocols/echo-ms-method-onboarding
-**Status:** Ginkgo Certified
-**Price:** $799/molecule
-**Turnaround:** up to 3 weeks
-
-## Overview
-
-Echo-MS is an open-access, high-throughput mass spectrometry platform that eliminates the chromatography step. An acoustic liquid handler (Labcyte/Beckman Echo) ejects nanoliter droplets directly from a source plate into an open-port sampling interface connected to a mass spectrometer. Without a column to equilibrate, cycle times drop to 1-5 seconds per sample, enabling analysis of a full 384-well plate in ~2 hours (with replicates). Best suited for relative quantitation, screening, and titer assays where throughput matters more than chromatographic resolution.
-
-This protocol onboards your analyte for future experiments: MS conditions (spray voltage, curtain gas, ion source settings) and ejection parameters (volume, interval, carrier solvent) are optimized, and a simple sample-prep protocol is established. Onboard a method here before running [echo-ms-cfps-detection.md](echo-ms-cfps-detection.md).
-
-## Input
-
-(Download Template)
-
-- Molecule CAS ID
-- Expected reaction and conversion amount
-- Expected concentrations of substrates
-- Reaction conditions (time sensitivities, buffers, pure/lysate)
-
-## Output
-
-For each molecule of interest:
-
-- Echo-MS method and calibration curve in the Cell Free Protein Expression Matrix
-- LOD + LOQ in the Cell Free Protein Expression Matrix
-- Validation run and report
-- Recommended next steps (e.g., sample-prep optimization) if method development was not successful
-
-## Automated Workflow
-
-### Phase 1 - In Silico Triage & Procurement
-
-1. Intake and triage (Nebula Core)
-2. Standard procurement (Nebula Core)
-
-### Phase 2 - Method Development with CFPS Matrix
-
-1. Establish standard solutions (Nebula Core)
-2. Optimize MRM transitions (SciEx TripleQuad 6500+ / EchoMS)
-3. Optimize EchoMS parameters (SciEx TripleQuad 6500+ / EchoMS)
-4. Matrix validation (SciEx TripleQuad 6500+ / EchoMS)
-
-## Ordering
-
-- **Number of Molecules:** configurable ($799/molecule)
-- **File Upload:** CSV, Excel, FASTA, TXT, PDF, ZIP
-- **Additional Details:** free-text field for special requirements
-
-## Use Cases
-
-- Onboarding a small molecule/analyte for high-throughput Echo-MS screening
-- Establishing calibration curves, LOD/LOQ in the CFPS matrix
-- Prerequisite for Echo-MS enzymatic detection runs

package/skills/ginkgo-cloud-lab/references/ecoli-expression-purification-quantification.md

@@ -1,49 +0,0 @@
-# E. coli Protein Expression, Purification, and Quantification
-
-**URL:** https://cloud.ginkgo.bio/protocols/ecoli-expression-purification-quantification
-**Status:** Ginkgo Certified
-**Price:** $209/sample
-**Turnaround:** up to 3 weeks
-**Throughput:** Up to 96 constructs in parallel
-
-## Overview
-
-Fully automated, end-to-end service that takes DNA constructs from heat shock transformation through bacterial expression, cell lysis, magnetic His-tag (IMAC) bead purification, quantitative yield measurement by A280 absorbance, and LabChip-based purity and size assessment - all in a single unattended workflow. Instruments include the Agilent Bravo 96/384, BioTek MultiFlo, Inheco and Cytomat incubators, a Spark plate reader, and the Revvity LabChip.
-
-## Input
-
-- **Protein designs:** AA or DNA sequence submitted in CSV format
-- **His-tag orientation:** N-terminal or C-terminal fusion; linker sequence (default GGGS if unspecified)
-- **Known expression notes:** Disulfide bonds, cofactor requirements, toxicity concerns, or PTM needs
-
-## Output
-
-- **Yield Quantification:** A280 per well, converted to protein concentration (mg/mL) via the protein's molar extinction coefficient
-- **Expression Confirmation:** Fluorescence signal relative to controls
-- **Purity & Size Assessment:** LabChip-based purity percentage and apparent molecular weight per construct, with virtual gel images
-- **OD culture growth data** reported per construct
-- **Assay Quality Metrics:** Per-run quality summary with plate-level controls
-- QC-flagged PDF results report plus downloadable raw CSV files
-
-## Automated Workflow
-
-Five phases coordinated across automated instruments:
-
-1. **Transformation with LB recovery** (heat shock)
-2. **Culture growth and harvest**
-3. **Cell lysis**
-4. **Magnetic bead IMAC purification with A280 yield readout** (BioTek MultiFlo, Agilent Bravo 96, Bioshake, Spark)
-5. **LabChip purity / size assessment** (Revvity LabChip)
-
-## Ordering
-
-- **Number of Proteins:** configurable
-- **Number of Replicates:** configurable
-- **File Upload:** CSV, Excel, FASTA, TXT, PDF, ZIP
-- **Additional Details:** free-text field for special requirements
-
-## Use Cases
-
-- Bacterial expression with purified yield plus purity/size profiling in one run
-- Characterizing up to 96 constructs before scale-up
-- Producing and QC-ing His-tagged protein for downstream work

package/skills/ginkgo-cloud-lab/references/ecoli-minibinder-expression-histag-a280.md

@@ -1,62 +0,0 @@
-# E. coli Minibinder Expression with His-tag Purification and Yield via A280
-
-**URL:** https://cloud.ginkgo.bio/protocols/ecoli-minibinder-expression-histag-a280
-**Status:** Ginkgo Certified
-**Price:** $199/sample
-**Turnaround:** up to 3 weeks
-**Throughput:** Up to 96 constructs in parallel
-
-## Overview
-
-Fully automated, end-to-end service that takes designed minibinder candidates from heat shock transformation through bacterial expression, cell lysis, magnetic His-tag (IMAC) bead purification, and quantitative yield measurement by A280 absorbance - built to screen binder designs before scale-up. Instruments include the Agilent Bravo 96/384, BioTek MultiFlo, Inheco and Cytomat incubators, and a Spark plate reader.
-
-## Input
-
-- **DNA Input:** Minibinder designs (use the E. coli input template, `.xlsx`)
-- **His-tag orientation:** N-terminal or C-terminal fusion; linker sequence (default GGGS if unspecified)
-- **Known expression notes:** Disulfide bonds, cofactor requirements, toxicity concerns, or PTM needs
-
-## Output
-
-- **Yield Quantification:** A280 per well, converted to protein concentration (mg/mL) via the protein's molar extinction coefficient
-- **Expression Confirmation:** Fluorescence signal relative to controls
-- **OD culture growth data** reported per construct
-- **Assay Quality Metrics:** Per-run quality summary with plate-level controls
-- QC-flagged PDF results report plus downloadable raw CSV files
-
-## Automated Workflow
-
-Four phases coordinated across automated instruments:
-
-### Phase 1 - Transformation & Heat Shock Recovery
-
-1. Pre-chill ATC (Inheco ATC 384)
-2. Heat shock & cycle (Inheco ATC 384)
-3. Add LB recovery media (Agilent Bravo 384)
-4. Recovery incubation (Inheco)
-
-### Phase 2 - Culture Growth & Harvest
-
-### Phase 3 - Cell Lysis & Clarification
-
-### Phase 4 - His-tag Purification & A280 Yield
-
-1. Dispense PBS (BioTek MultiFlo)
-2. Load sample onto beads (Agilent Bravo 96)
-3. Binding incubation (Bioshake)
-4. Wash beads (Agilent Bravo 96)
-5. Elute protein (Agilent Bravo 96)
-6. Read A280 (Agilent Bravo 96 + Spark)
-
-## Ordering
-
-- **Number of Proteins:** configurable
-- **Number of Replicates:** configurable
-- **File Upload:** CSV, Excel, FASTA, TXT, PDF, ZIP
-- **Additional Details:** free-text field for special requirements
-
-## Use Cases
-
-- Screening designed minibinder/binder candidates in E. coli before scale-up
-- Parallel yield comparison across up to 96 binder designs
-- Producing His-tagged binders for downstream characterization

package/skills/ginkgo-cloud-lab/references/ecoli-protein-expression-hibit.md

@@ -1,44 +0,0 @@
-# E. coli Protein Expression with HiBiT Quantification
-
-**URL:** https://cloud.ginkgo.bio/protocols/ecoli-protein-expression-hibit
-**Status:** Ginkgo Certified
-**Price:** $79/sample
-**Turnaround:** up to 3 weeks
-**Throughput:** Up to 384 constructs per run
-
-## Overview
-
-Fully automated, end-to-end workflow for expressing and quantifying HiBiT-tagged proteins in E. coli. Heat shock transformation is followed by inoculation into lactose-based autoinduction media for target protein expression, then cell pelleting, detergent-based lysis, and HiBiT-based quantification. Results are reported as both raw and standard curve-normalized values, enabling quantitative comparison across up to 384 constructs per run.
-
-## Input
-
-- **DNA Input:** HiBiT-tagged constructs (use the E. coli input template)
-- **HiBiT tag orientation:** N-terminal or C-terminal fusion (default GGGS linker if unspecified)
-
-## Output
-
-- **OD600 growth confirmation:** Per-well absorbance readings confirming bacterial growth prior to pelleting
-- **HiBiT luminescence values:** Raw bcRLU per well from BMG PHERAstar luminescence read
-- **Normalized expression estimate:** Per-construct expression normalized to an on-plate HiBiT standard curve
-- **QC report:** PDF with per-construct results, process control outcomes, and pass/fail status; raw CSV available
-
-## Automated Workflow
-
-1. **Transformation** (heat shock)
-2. **Autoinduction expression** in lactose-based media
-3. **Cell pelleting**
-4. **Detergent-based lysis**
-5. **HiBiT detection & luminescence read** (BMG PHERAstar)
-
-## Ordering
-
-- **Number of Proteins:** configurable
-- **Number of Replicates:** configurable
-- **File Upload:** CSV, Excel, FASTA, TXT, PDF, ZIP
-- **Additional Details:** free-text field for special requirements
-
-## Use Cases
-
-- Very high-throughput expressibility screening in E. coli (up to 384 constructs)
-- Relative expression comparison across large construct sets
-- Early triage before His-tag purification tiers

package/skills/ginkgo-cloud-lab/references/ecoli-protein-expression-histag-a280.md

@@ -1,47 +0,0 @@
-# E. coli Protein Expression with His-tag Purification and Yield via A280
-
-**URL:** https://cloud.ginkgo.bio/protocols/ecoli-protein-expression-histag-a280
-**Status:** Ginkgo Certified
-**Price:** $199/sample
-**Turnaround:** up to 3 weeks
-**Throughput:** Up to 96 constructs in parallel
-
-## Overview
-
-Fully automated, end-to-end service that takes DNA constructs from heat shock transformation through bacterial expression, cell lysis, magnetic His-tag (IMAC) bead purification, and quantitative yield measurement by A280 absorbance - in a single unattended workflow. Instruments include the Agilent Bravo 96/384, BioTek MultiFlo, Inheco and Cytomat incubators, and a Spark plate reader.
-
-## Input
-
-- **Protein designs:** AA or DNA sequence submitted in CSV format
-- **His-tag orientation:** N-terminal or C-terminal fusion; linker sequence (default GGGS if unspecified)
-- **Known expression notes:** Disulfide bonds, cofactor requirements, toxicity concerns, or PTM needs
-
-## Output
-
-- **Yield Quantification:** A280 per well, converted to protein concentration (mg/mL) via the protein's molar extinction coefficient
-- **Expression Confirmation:** Fluorescence signal relative to controls
-- **OD culture growth data** reported per construct
-- **Assay Quality Metrics:** Per-run quality summary with plate-level controls
-- QC-flagged PDF results report plus downloadable raw CSV files
-
-## Automated Workflow
-
-Four phases coordinated across automated instruments:
-
-1. **Transformation with LB recovery** (heat shock; Inheco ATC, Agilent Bravo 384)
-2. **Culture growth and harvest**
-3. **Cell lysis and clarification**
-4. **Magnetic bead IMAC purification with A280 yield readout** (BioTek MultiFlo, Agilent Bravo 96, Bioshake, Spark)
-
-## Ordering
-
-- **Number of Proteins:** configurable
-- **Number of Replicates:** configurable
-- **File Upload:** CSV, Excel, FASTA, TXT, PDF, ZIP
-- **Additional Details:** free-text field for special requirements
-
-## Use Cases
-
-- Bacterial expression and purification of soluble proteins
-- Parallel screening of up to 96 constructs for yield
-- Producing His-tagged protein for downstream assays