AP-1 demo price record · 2026-10-08 · read from prices.csv cited at oligo-pool count 101-500; length 301-350 · pool-primers count 1-96 · R3539 · R3733 · R0629 · R0560 · 60242-2 count 1-24 · cuvettes count 1-50 · plasmid prep count 1-50cited by the bill
Thermo Fisher Scientific, Zero Blunt TOPO PCR Cloning Kit user guide · docs/research/synthesis-and-assembly.md cited at TOPO cloning reactioncited by Part carrier
Twist Bioscience, Twist Oligo Pools Amplification Protocol · DOC-4060 REV 1.0 · held under reference_docs/ · docs/research/oligo-pool-pcr-cycles.md cited at Before You Begin · Appendix Bcited by Cargo ordering and pool preparation, Cargo creation
Endura Competent Cells manual, Lucigen / Biosearch Technologies · MA133 26Feb2018 · plain curl · 2026-10-06 cited at p. 4-5cited by Cargo creation, Library assembly in rounds, Final cargo ligation
liulab-mbio, Figure sources for four designs · docs/research/figure-sources.md cited at section 1, Baker's three-primer PCR design · section 2, Cargo GGA ligation · section 3, DMX · section 4, iGGAcited by Cargo creation, Cargo validation: barcode ligation, Cargo validation: index PCR, Library assembly in rounds, Final cargo ligation
Long, Y. et al. 2025, LevSeq, Supporting Information · held under reference_docs/ · 2026-10-06 https://doi.org/10.1021/acssynbio.4c00625cited at step 1 · step 2 · step 3 · step 4 · thermal cycler tablecited by Cargo creation, Cargo validation: index PCR
New England Biolabs NEBioCalculator · script main-6f3020c533.js, capture 2026-08-28 · Wayback Machine · docs/research/primer-design-and-pcr.md cited at dsDNA molecular weightcited by Cargo creation, Library assembly in rounds, Final cargo ligation
New England Biolabs #E1602S/L NEBridge Golden Gate Assembly Kit (BsmBI-v2) instruction manual · version 3.0_6/26 · 2026-09-12 · docs/research/golden-gate-assembly.md https://www.neb.com/-/media/nebus/files/manuals/manuale1602.pdfcited at assembly protocolcited by Cargo creation
Qian et al. 2026, Supplementary Information · Nat. Commun. 10.1038/s41467-026-76740-9 · held under reference_docs/ · 2026-10-06 https://doi.org/10.1038/s41467-026-76740-9cited at Day 2 · Day 3 · Day 4.1cited by Cargo validation: barcode ligation, Cargo validation: index PCR
Lund, S. et al. (2024) Highly parallelized construction of DNA from low-cost oligonucleotide mixtures using Data-optimized Assembly Design and Golden Gate. ACS Synth. Biol. 13, 745-751 · docs/research/synthesis-and-assembly.md https://doi.org/10.1021/acssynbio.3c00694cited at colonies screened per genecited by Cargo validation: barcode ligation, Cargo validation: index PCR
New England Biolabs, Product Specification: Taq DNA Polymerase with ThermoPol Buffer · PS-M0267S/L/X/E v2.0, effective 12 Feb 2020 · plain curl · 2026-10-08 · docs/research/route-b-index-pcr.md https://www.neb.com/en/-/media/catalog/specifications/m/0/m0267s_l_x_e_v2.pdfcited at Concentrationcited by Cargo validation: index PCR
New England Biolabs #M0318 T7 DNA Ligase product page · r.jina.ai · 2026-10-06 https://www.neb.com/en/products/m0318-t7-dna-ligasecited at reaction conditions · note 4cited by Library assembly in rounds, Final cargo ligation
New England Biolabs product specification sheets · #R3733S/L, #R3539S/L, #R0629S/L, #R0560S/L · plain curl · 2026-10-06 · docs/research/bench-numbers.md cited at #R3539L, concentration · #R0629L, concentration · #R3733L, concentration · #R0560L, concentrationcited by Library assembly in rounds, Final cargo ligation
Takacsi-Nagy, O. et al. (2026) Synthetic transcription factors designed by domain recombination enhance CAR T cell antitumor function. Cell 189, 1-20 · STAR Methods, METHOD DETAILS pp. e4-e5 · docs/research/protein-library-assembly.md https://doi.org/10.1016/j.cell.2026.07.054cited at p. e4, digest · p. e5, recovery and outgrowth · p. e4, one-pot assemblycited by Library assembly in rounds, Final cargo ligation
Clarke, L. and Carbon, J. (1976) A colony bank containing synthetic ColE1 hybrid plasmids representative of the entire E. coli genome. Cell 9, 91-99 · docs/research/protein-library-assembly.md https://doi.org/10.1016/0092-8674(76)90055-6cited at the clones a library takescited by Library assembly in rounds
Joung, J. et al. (2017) Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Nat. Protoc. 12, 828-863 · docs/research/vector-qc-panel.md https://doi.org/10.1038/nprot.2017.016cited at library representationcited by Library assembly in rounds, Final cargo ligation
Imkeller, K. et al. (2020) gscreend: modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detection. Genome Biol. 21, 53 · docs/research/vector-qc-panel.md https://doi.org/10.1186/s13059-020-1939-1cited at Table 2cited by Library assembly in rounds
Van Nieuwerburgh, F. et al. (2011) Quantitative bias in Illumina TruSeq and a novel post amplification barcoding strategy for multiplexed DNA and small RNA deep sequencing. PLoS ONE 6, e26969 · docs/research/barcode-design.md https://doi.org/10.1371/journal.pone.0026969cited at barcode positioncited by Library assembly in rounds
Alon, S. et al. (2011) Barcoding bias in high-throughput multiplex sequencing of miRNA. Genome Res. 21, 1506-1511 · docs/research/barcode-design.md https://doi.org/10.1101/gr.121715.111cited at ligated against amplified barcodescited by Library assembly in rounds
docs/projects/igga.md, the iGGA method page. The 34-base internal stuffer is the method's own, and a round excises the 30-base core of it: the two figures are the same stuffer, counted whole and counted after the entry overhang it opens on. The external stuffers lay BsaI and PmeI at the offsets their own cut offsets ask for, so every overhang is read off the DNA rather than stated.https://liuhlab.github.io/liulab-mbio/projects/igga/cited by Library assembly in rounds