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Series GSE244153 Query DataSets for GSE244153
Status Public on Oct 02, 2023
Title RNA sequence (RNA-seq) profiling of SynIX strain
Organism Saccharomyces cerevisiae BY4741
Experiment type Expression profiling by high throughput sequencing
Summary We describe the complete synthesis, assembly, debugging and characterization of a synthetic 404,963 bp yeast chromosome, synIX. Combined chromosome construction methods were used to synthesize the left arm of synIX (synIXL) and retrofit previously described synIXR. During synIX strain characterization, we identified and resolved a bug related to EST3, a gene involved in telomerase function, producing a synIX strain with near wild-type fitness. To facilitate future synthetic chromosome consolidation and increase flexibility of chromosome transfer between distinct strains we combined chromoduction, a method to transfer a whole chromosome between two strains, with conditional centromere destabilization to substitute a chromosome of interest for its native counterpart. We found that both synIX transfer via chromoduction and wild-type IX destabilization were efficient methods. We observed that wild-type II tended to co-transfer with synIX and was co-destabilized with wild-type IX, suggesting a potential gene dosage compensation relationship between these two chromosomes.
Overall design To assess the effects of synthetic genome design on gene expression levels, we performed mRNA sequencing of SynIX strain yLHM1601 against wildtype strain BY4741 at 30C and 37C.
Contributor(s) McCulloch LH, Boeke JD
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BioProject PRJNA900304
Submission date Sep 27, 2023
Last update date Oct 02, 2023
Contact name Jitong Cai
Organization name NYU Langone Health
Department NYU Langone Health
Lab Jef Boeke
Street address 435 E 30th street
City New York
State/province NY
ZIP/Postal code 10016
Country USA
Platforms (1)
GPL20138 Illumina NextSeq 500 (Saccharomyces cerevisiae BY4741)
Samples (12)
GSM7807893 SynIX RNA-seq at 30C replicate 1
GSM7807894 SynIX RNA-seq at 30C replicate 2
GSM7807895 SynIX RNA-seq at 30C replicate 3

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Supplementary file Size Download File type/resource
GSE244153_RAW.tar 1.1 Mb (http)(custom) TAR (of TSV)
GSE244153_dge-ylhm1601-vs-wt_30C.csv.gz 266.5 Kb (ftp)(http) CSV
GSE244153_dge-ylhm1601-vs-wt_37C.csv.gz 266.7 Kb (ftp)(http) CSV
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