SC Lab: Instrument Data Flow | 3', 5', Multiome

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Make sure library values are being synced to the entity so that Seq Lab will have the information it needs.

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Two main areas of focus

• Quibit and Agilent protocol
• Library Construction (GEX and Feature)

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libraries_v_cdna_aliquot.md

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Things I'm noticing:

• Requested Number of Reads (M) is not part of cDNA entity
• Client Assessed Concentration (ng/µl) but not Assessed Concentration (ng/µl)

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• Instrument Data

  Qubit / Agilent

• [x] Column name changes to align with entity values

  Qubit (ng/\xB5l) -> Assessed Concentration (ng/µl) Final Yield ng (35 \xB5l) -> Final Yield ng (35 µl) Size (bp) -> Average Library Size (bp) Remaining Volume (\xB5l) -> Remaining Volume (µl)

• [x] Make sure entity is being updated

  protocol action to sync Assessed Concentration , Remaining Volume and Average Library Size (bp) in qubit protocol protocol action to sync Assessed Concentration and Remaining Volume in Agilent HS protocol

• [x] Make sure correctly cited and used in dilution
• [x] Dilution values based on calculations synced

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• Billing Information

  Workday Cost Center not showing up work being done on #410

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• Index Selection syncing to entity

  Being handled by Lee

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onChange functions to modify:

• [x] sclab_qubit_calc_total_yield(api, row)
• [x] sclab_agilent_calc_total_yield(api, row)

  Now also sets Assessed Concentration (ng/µl) in hidden column to update entity value

• [x] sc_dilution_calc(api, row, columnName, newValue);
• [ ] onrender_sc_hide_illumina_entity_fields(api);

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Remaining Volume (µl) is kinda its own set of concerns

• Qubit protocols -> Remaining Volume - 2µl
• Agilent HS -> Remaining Volume - 1µl
• Aliquot node -> Volume - 5 or 10 µl most of the time
• Dilution node -> variable, based on concentration = {{ float(entity_value('Remaining Volume (µl)')) - float(cell('DNA (µl)')) }}
• Dilution remaining volume is dna volume and EB volume {{ float(cell('DNA (µl)')) + float(cell('EB (µl)')) }}

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• Calculation for the dilution concentration? Concentration (ng/μL)=Molarity (M)×Molecular Weight (g/mol)× 1000 μL/L / 1000000 ng/g

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In qubit/agilent protocols:

who do these values belong to? Aliquot or Library?

• Assessed Concentration - Both
• Average Library Size - Library -> make a link to sync in sample protocol
• Remaining Volume - Aliquot? -> sync within protocol

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• Added Make Dilutions button in SC Lab: Set Up Dilutions
• Setting Assessed Concentration (ng/µl) and Remaining Volume (µl) to the incoming Library
• Setting the dilution's Concentration, Remaining Volume and Molarity into column for referencing in SC Lab: Create Dilutions

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⚡ git merge gtac/feat-399-1
Updating 9fb315bc..ec3d51e6
Fast-forward
 content/protocols/sc_3_prime_agilent_hs_protocol.yml         | 48 +++++++++++++++++++++++++++++++++----------
 content/protocols/sc_3_prime_qubit_and_agilent_protocol.yml  | 45 ++++++++++++++++------------------------
 content/protocols/sc_5_prime_agilent_hs_protocol.yml         | 64 ++++++++++++++++++++++++++++++++++++++-------------------
 content/protocols/sc_5_prime_qubit_and_agilent_protocol.yml  | 91 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++---------------------
 content/protocols/sc_agilent_hs_protocol.yml                 | 43 ++++++++++++++++++++++++++++++--------
 content/protocols/sc_aliquot_protocol.yml                    |  1 -
 content/protocols/sc_aliquot_setup_protocol.yml              |  6 +++---
 content/protocols/sc_create_dilutions_protocol.yml           |  1 +
 content/protocols/sc_multiome_agilent_hs_protocol.yml        | 55 ++++++++++++++++++++++++++++++++++++-------------
 content/protocols/sc_multiome_qubit_and_agilent_protocol.yml | 99 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++----------------------
 content/protocols/sc_setup_dilutions_protocol.yml            | 78 ++++++++++++++++++++++++++++++++++++---------------------------------
 content/workflows/sc_3P_cdna.yml                             | 16 +++++++++------
 content/workflows/sc_3P_feature_lc.yml                       | 13 +++++++++---
 content/workflows/sc_3P_gex_lc.yml                           | 14 +++++++++----
 content/workflows/sc_aliquot_workflow.yml                    |  9 ++++++--
 content/workflows/sc_dilutions_workflow.yml                  |  9 ++++----
 extensions/client/invokables.js                              | 95 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-------------------
 17 files changed, 477 insertions(+), 210 deletions(-)

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5 Prime and Multiome cDNA, Aliquot and Library construction nodes will have to be updated with methods used in 3 prime once they are tested. This work will be continued on another branch.