Data supporting a saturation mutagenesis assay for Tat-driven transcription with the GigaAssay

Benjamin, Ronald; Giacoletto, Christopher J.; FitzHugh, Zachary T.; Eames, Danielle; Buczek, Lindsay; Wu, Xiaogang; Newsome, Jacklyn; Han, Mira V.; Pearson, Tony; Wei, Zhi; Banerjee, Atoshi; Brown, Lancer; Valente, Liz J.; Shen, Shirley; Deng, Hong−Wen; Schiller, Martin

doi:10.1016/j.dib.2022.108641

Cited by 2 publications

(4 citation statements)

References 10 publications

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“…The GigaAssay was used for two experiments on Tat examining the transcriptional activities of all possible single amino acid substitutions in two different cell lines. [ 31 , 32 ] For each mutant, the activities were measured in ~ 100 separate single cells and the measured activities had a ~ 95% accuracy measured by three independent approaches. All experimental methods and the bioinformatics pipeline details are in these previous reports.…”

Section: Resultsmentioning

confidence: 99%

“…All experimental methods were as previously described using the Tat cDNA (accession number: AAK08486.1). [ 31 , 32 ]…”

Section: Methodsmentioning

confidence: 99%

“…Data analysis was completed using the raw data from the HIV-1 Tat GigaAssay. Transcriptional activities were calculated as previously reported [ 31 , 32 ]; however, we used additional measures of UMI barcode filtration. The read data were from 17 samples including the plasmid library, selected cell libraries, and flow-sorted pools for each of two cell lines.…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Most synonymous allelic variants in HIV tat are not silent

Giacoletto¹,

Benjamin²,

Deng³

et al. 2023

Genomics

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Section: Resultsmentioning

confidence: 99%

“…All experimental methods were as previously described using the Tat cDNA (accession number: AAK08486.1). [ 31 , 32 ]…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Most synonymous allelic variants in HIV tat are not silent

Giacoletto¹,

Benjamin²,

Deng³

et al. 2023

Genomics

Self Cite

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“…Flow cytometry, high content screening, and the GigaAssay all meet the throughput qualification (n > 1,000 samples), and have accuracies >90%, thus are close to becoming HAT assays. [17,23,[48][49][50][51][52] Flow cytometry is a high throughput approach that separates cell based on a fluorescent signal in which 10,000s of single cells can be measured and sorted rapidly. However, even under optimal conditions the best achievable accuracies are ∼92%.…”

Section: Discussionmentioning

confidence: 99%

The history and conceptual framework of assays and screens

Giacoletto

Schiller

2023

BioEssays

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Since the 16th century, assays and screens have been essential for scientific investigation. However, most methods could be significantly improved, especially in accuracy, scalability, and often lack adequate comparisons to negative controls. There is a lack of consistency in distinguishing assays, in which accuracy is the main goal, from screens, in which scalability is prioritized over accuracy. We dissected and modernized the original definitions of assays and screens based upon recent developments and the conceptual framework of the original definitions. All methods have three components: design/measurement, performance, and interpretation. We propose a model of method development in which reproducible observations become new methods, initially assessed by sensitivity. Further development can proceed along a path to either screens or assays. The screen path focuses on scalability first, but can later prioritize analysis of negatives. Alternatively, the assay path first compares results to negative controls, assessing specificity and accuracy, later adding scalability. Both pathways converge on a high-accuracy and throughput (HAT) assay, like next generation sequencing, which we suggest should be the ultimate goal of all testing methods. Our model will help scientists better select among available methods, as well as improve existing methods, expanding their impact on science.

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Data supporting a saturation mutagenesis assay for Tat-driven transcription with the GigaAssay

Cited by 2 publications

References 10 publications

Most synonymous allelic variants in HIV tat are not silent

Most synonymous allelic variants in HIV tat are not silent

The history and conceptual framework of assays and screens

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