Project description:Engineering mammalian cells to execute complex genetic programs remains a significant challenge in ‎synthetic biology. Synthetic gene circuits typically implement sophisticated programs through cascaded ‎computational layers, but these architectures require numerous orthogonal parts, increase genetic ‎payload, and deplete cellular resources, which limits functionality and scalability.‎‏ ‏We developed a modular design ‎framework to engineer scalable gene circuits that execute complex functions within fewer ‎computational layers. The platform integrates a toolkit to generate orthogonal trans-splicing-based ‎AND gates, native-synthetic hybrid promoters for tunable regulation, and synthetic microRNAs that ‎implement inhibitory logic. Using this approach, we engineered a three-input combinatorial logic gate, ‎a half adder, a full adder, and a dynamic 3-to-1 multiplexer with a dedicated Selector Overload Status ‎output, activated only when both selector inputs are activated. By minimizing computational layers while maintaining function, this strategy addresses scalability barriers in gene circuit engineering and expands opportunities for clinically relevant programmable therapies, biotechnology, and fundamental biology.‎

2026-03-29 | GSE316863 | GEO

Selection for ligand-independent EGFR activation

Project description:Selection of activating EGFR mutations from randomly mutated EGFR libraries

| PRJEB49811 | ENA

Population genome variations revealed by diversifying selection in chickens

Project description:We describe a total 269.15 Gb of chicken RNA-seq sequences generated from the 48 libraries

2019-08-08 | GSE85318 | GEO

Identifying crossover locations in an Arabidopsis thaliana Col x Di-G F2 population using genotyping by sequencing

Project description:Genomic DNA from 239 Col x Di-G F2 individuals was extracted using CTAB and used to generate sequencing libraries as described (Rowan et al; Yelina et al), with the following modifications. DNA was extracted from 3 rosette leaves of 5 week old plants and 150 ng of DNA used as input for each library. DNA shearing was carried out for 20 minutes at 37°C with 0.4U of DNA Shearase (Zymo research). Each set of 96 libraries was sequenced on one lane of an Illumina NextSeq500 instrument (300-cycle Mid Output run). The barcoded adapter sequences were trimmed and bases with quality lower than 19 were filtered using Cutadapt. Sequencing data was analysed to identify crossovers as previously reported, using the TIGER pipeline.

2024-08-19 | E-MTAB-14382 | biostudies-arrayexpress

Identifying crossover locations in an Arabidopsis thaliana pSPO11-mJ3 Col x Ler F2 population using genotyping by sequencing

Project description:Genomic DNA from 96 pSPO11-mJ3(G155R) Col x Ler F2 individuals was extracted using CTAB and used to generate sequencing libraries as described (Rowan et al; Yelina et al), with the following modifications. DNA was extracted from 3 rosette leaves of 5 week old plants and 150 ng of DNA used as input for each library. DNA shearing was carried out for 20 minutes at 37°C with 0.4U of DNA Shearase (Zymo research). The barcoded adapters used for library construction are listed in Rowan et al. Each set of 96 libraries was sequenced on one lane of an Illumina NextSeq500 instrument (300-cycle Mid Output run). Sequencing data was analysed to identify crossovers as previously reported, using the TIGER pipeline. These data can be compared to a set of wild type control libraries available at E-MTAB-10168.

2023-11-30 | E-MTAB-13413 | biostudies-arrayexpress

Identifying crossover locations in an Arabidopsis thaliana meiMIGS-HSP70 Col x Ler F2 population using genotyping by sequencing

Project description:Genomic DNA from 96 meiMIGS-HSP70 Col x Ler F2 individuals was extracted using CTAB and used to generate sequencing libraries as described (Rowan et al; Yelina et al), with the following modifications. DNA was extracted from 3 rosette leaves of 5 week old plants and 150 ng of DNA used as input for each library. DNA shearing was carried out for 20 minutes at 37°C with 0.4U of DNA Shearase (Zymo research). The barcoded adapters used for library construction are listed in Rowan et al. Each set of 96 libraries was sequenced on one lane of an Illumina NextSeq500 instrument (300-cycle Mid Output run). Sequencing data was analysed to identify crossovers as previously reported, using the TIGER pipeline. These data can be compared to a set of wild type control libraries available at E-MTAB-10168.

2023-11-30 | E-MTAB-13415 | biostudies-arrayexpress

Identifying crossover locations in an Arabidopsis thaliana recq4ab Col x recq4a Ler F2 population using genotyping by sequencing

Project description:Genomic DNA from 96 recq4ab Col x recq4a Ler F2 individuals was extracted using CTAB and used to generate sequencing libraries as described (Rowan et al; Yelina et al), with the following modifications. DNA was extracted from 3 rosette leaves of 5 week old plants and 150 ng of DNA used as input for each library. DNA shearing was carried out for 20 minutes at 37°C with 0.4U of DNA Shearase (Zymo research). The barcoded adapters used for library construction are listed in Rowan et al. Each set of 96 libraries was sequenced on one lane of an Illumina NextSeq500 instrument (300-cycle Mid Output run). Sequencing data was analysed to identify crossovers as previously reported, using the TIGER pipeline. These data can be compared to a set of wild type control libraries available at E-MTAB-10168.

2023-03-14 | E-MTAB-12726 | biostudies-arrayexpress

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