GEO DataSets

(Submitter supplied) Cellular transcription enables cells to adapt to various stimuli and maintain homeostasis. Transcription factors bind to transcription response elements (TREs) in gene promoters, initiating transcription. Synthetic promoters, derived from natural TREs, can be engineered to control exogenous gene expression using endogenous transcription machinery. This technology has found extensive use in biological research for applications including reporter gene assays, biomarker development, and programming synthetic circuits in living cells. more...

Organism:

Homo sapiens; Mesocricetus auratus; synthetic construct; Mus musculus

Type:

Expression profiling by high throughput sequencing

5 related Platforms

65 Samples

Download data: CSV

(Submitter supplied) REPLACE was engineered from an orthogonal alphaviral RNA replication system. It generates a large, continuously diversified library of replicative RNAs through a replicase-limited mode of replication and inducible mutagenesis. We analyzed the variation of RNA mutations induced by two nucleoside analogues over time and at different concentrations. This data was used to guide the construction of RNA mutant libraries.

Organism:

Mesocricetus auratus

Type:

Other

Platform:

GPL29575

48 Samples

Download data: CSV

(Submitter supplied) REPLACE was engineered from an orthogonal alphaviral RNA replication system. It generates a large, continuously diversified library of replicative RNAs through a replicase-limited mode of replication and inducible mutagenesis. We analyzed the mutation frequency at Day0 (IVT RNA), Day1, Day3, Day7, Day14, Day21 and DNA plasmid to estimate the RNA mutation rate. This data was used to guide the construction of RNA mutant libraries.

Organism:

Mesocricetus auratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29575

21 Samples

Download data: CSV

(Submitter supplied) Transcriptional regulators are fundamental elements in synthetic biology. We sought to use REPLACE to evolve synthetic transcriptional regulators. Through weeks of directed evolution experiments, we succesufuly modified the sensitivity of TetR and PadR to ligand molecules.

Organism:

Mesocricetus auratus

Type:

Other

Platform:

GPL29575

3 Samples

Download data: XLSX

(Submitter supplied) Drug resistance poses a significant clinical challenge, and comprehending the mechanisms underlying this resistance can facilitate the design of novel inhibitors and advance cancer treatment. The REPLACE system was employed to examine resistance mutations in MEK1 during the administration of 3 allosteric inhibitors (i.e., cobimetinib, trametinib, and selumetinib). These experiments represent a category of experiments that utilize REPLACE to achieve continuous evolution (or adaptation) by linking the activity of evolutionary targets with the survival of mammalian cells.

Organism:

Mesocricetus auratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29575

12 Samples

Download data: XLSX

(Submitter supplied) A dominant-negative gene therapy approach has been proposed and tested on proto-oncogene KRAS, wherein the oncogenic activity (and cell proliferation) of KRAS can be suppressed by introducing a dominant-negative KRAS allele (S17N). We employed REPLACE to conduct continuous evolution on KRAS (S17N) and examined its potential pathways for conferring resistance in this gene therapy methodology.

Organism:

Mesocricetus auratus

Type:

Other

Platform:

GPL29575

12 Samples

Download data: XLSX

(Submitter supplied) In the directed evolution experiments of EGFP or StayGold, the objective was to blue-shift the excitation light spectrum of GFP towards shorter wavelengths, resulting in an enhancement of fluorescence intensity upon 405 nm laser excitation. This facilitates the advancement of novel fluorescent proteins. These experiments represent a category of experiments that utilize REPLACE to achieve discontinuous directed evolution through FACS sorting (screening).

Organism:

Mesocricetus auratus

Type:

Other

Platform:

GPL29575

14 Samples

Download data: XLSX

(Submitter supplied) Drug resistance poses a significant clinical challenge, and comprehending the mechanisms underlying this resistance can facilitate the design of novel inhibitors and advance cancer treatment. The REPLACE system was employed to examine resistance mutations in MEK1 during the administration of 3 allosteric inhibitors. To explore the accumulation of mutations in various RNAs during the MEK1 evolution experiment, we established a barcoded library and conducted lineage tracing of replicative RNAs carrying MEK1 throughout the drug resistance evolution process.

Organism:

Mesocricetus auratus

Type:

Other

Platforms:

GPL29575 GPL33510

9 Samples

Download data: TXT, XLSX

(Submitter supplied) A dominant-negative gene therapy approach has been proposed and tested on proto-oncogene KRAS, wherein the oncogenic activity (and cell proliferation) of KRAS can be suppressed by introducing a dominant-negative KRAS allele (S17N). We employed REPLACE to conduct continuous evolution on KRAS (S17N) and examined its potential pathways for conferring resistance in this gene therapy methodology.To explore the accumulation of mutations in various RNAs during the KRAS (S17N) evolution experiment, we established a barcoded library and conducted lineage tracing of replicative RNAs carrying KRAS (S17N) throughout the evolution process.

Organism:

Mesocricetus auratus

Type:

Other

Platform:

GPL33510

13 Samples

Download data: TXT

(Submitter supplied) SARS-CoV-2 infection generates a systemic immune response mediated by type I interferons. Pernio is a rare cutaneous manifestation of disorders characterized by excessive IFN-I signaling. Pernio increased in incidence during the pandemic but lacks direct evidence of SARS-CoV-2. We characterized clinical pernio samples and mechanistic feasibility in a rodent model which phenocopies human SARS-CoV-2 infection. more...

Organism:

Mesocricetus auratus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL28997

38 Samples

Download data: SF

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mesocricetus auratus; Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL24676 GPL28997

17 Samples

Download data

(Submitter supplied) Cumulative research demonstrated that heart muscles in the dilated cardiomyopathy (DCM) patients are marked by down-regulated expression of α-myosin heavy chain (α-MHC) coding by MYH6 while it remains unknown whether this reduction contributes to DCM. In our work, we proved that the expression level of α-MHC was decreased in the heart of DCM patients compared to that of non-failure donors. We established two Myh6 down-expressed Syrian Hamster models: one with α-MHC deficiency across all systems, the other with α-MHC knockdown specifically in the heart by using adeno-associatedvirus (AAV). more...

Organism:

Mesocricetus auratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28997

8 Samples

Download data: TXT

(Submitter supplied) SARS-CoV-2 was the cause of the COVID-19 global pandemic that resulted in millions of deaths worldwide. SARS-CoV-2 infection is often accompanied by renal manifestations such as acute kidney injury and kidney fibrosis, however there is a lack of effective treatment options that also address renal involvement. In this study, golden hamsters were inoculated with Delta variant SARS- CoV-2, and given either vehicle or Andrographis paniculata (AP) standardized extract as treatment. more...

Organism:

Mesocricetus auratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34677

15 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mesocricetus auratus

Type:

Other; Expression profiling by high throughput sequencing

4 related Platforms

112 Samples

Download data: FA, GTF, MTX, TSV, TXT, XLSX

(Submitter supplied) Directed evolution in mammalian cells can facilitate the engineering of mammalian-compatible biomolecules and can enable synthetic evolvability for mammalian cells. We engineered an orthogonal alphaviral RNA replication system to evolve synthetic RNA-based devices, enabling RNA replicase-assisted continuous evolution (REPLACE) in live mammalian cells. Toinvestigatetheexpressionheterogeneityofself-replicatingRNAsinrepRNA-v4cells,weperformedsingle-cellRNA-seqanalysisusingthe10xGenomicssequencingmethod.Ouranalysisofthesingle-cellRNA-seqprofilingdatarevealedarelativelyuniformexpressionpatternofself-replicatingRNAswithinrepRNA-v4cells.

Organism:

Mesocricetus auratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28997

1 Sample

Download data: FA, GTF, MTX, TSV

(Submitter supplied) Directed evolution in mammalian cells can facilitate the engineering of mammalian-compatible biomolecules and can enable synthetic evolvability for mammalian cells. We engineered an orthogonal alphaviral RNA replication system to evolve synthetic RNA-based devices, enabling RNA replicase-assisted continuous evolution (REPLACE) in live mammalian cells. To determine the degradation rate of alphaviral RNA in BHK-21 cells, 10 µg of repRNA-v4 RNA was transfected into 4 million wildtype BHK-21 cells via electroporation. more...

Organism:

Mesocricetus auratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32830

6 Samples

Download data: TXT

(Submitter supplied) Directed evolution in mammalian cells can facilitate the engineering of mammalian-compatible biomolecules and can enable synthetic evolvability for mammalian cells. We engineered an orthogonal alphaviral RNA replication system to evolve synthetic RNA-based devices, enabling RNA replicase-assisted continuous evolution (REPLACE) in live mammalian cells. To investigate the process of mutation accumulation in REPLACE system, we constructed a repRNA-v4 plasmid library containing 64 barcodes. more...

Organism:

Mesocricetus auratus

Type:

Other

Platform:

GPL33510

5 Samples

Download data: FA, XLSX

(Submitter supplied) Directed evolution in mammalian cells can facilitate the engineering of mammalian-compatible biomolecules and can enable synthetic evolvability for mammalian cells. We engineered an orthogonal alphaviral RNA replication system to evolve synthetic RNA-based devices, enabling RNA replicase-assisted continuous evolution (REPLACE) in live mammalian cells. we employed REPLACE to drive the continuous intracellular evolution of the cancer-related protein MEK1 with the aim of conferring resistance to Cobimetinib. more...

Organism:

Mesocricetus auratus

Type:

Other

Platform:

GPL28997

2 Samples

Download data: XLSX

(Submitter supplied) Directed evolution in mammalian cells can facilitate the engineering of mammalian-compatible biomolecules and can enable synthetic evolvability for mammalian cells. We engineered an orthogonal alphaviral RNA replication system to evolve synthetic RNA-based devices, enabling RNA replicase-assisted continuous evolution (REPLACE) in live mammalian cells. Using REPLACE, we attempted continuous intracellular evolution of the negative dominant mutant KRAS (S17N). more...

Organism:

Mesocricetus auratus

Type:

Other

Platform:

GPL28997

8 Samples

Download data: XLSX

(Submitter supplied) Directed evolution in mammalian cells can facilitate the engineering of mammalian-compatible biomolecules and can enable synthetic evolvability for mammalian cells. We engineered an orthogonal alphaviral RNA replication system to evolve synthetic RNA-based devices, enabling RNA replicase-assisted continuous evolution (REPLACE) in live mammalian cells. RNA-seq of 3 different cells was performed to analyze the effect of introducing different versions of RNA replication systems (i.e., repRNA-v3 and repRNA-v4) into BHK-21 cells on endogenous gene expression. more...

Organism:

Mesocricetus auratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32830

6 Samples

Download data: TXT