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Items: 1 to 20 of 63

1.

A deep mutational scanning platform to characterize the fitness landscape of anti-CRISPR proteins

(Submitter supplied) Deep mutational scanning is a powerful method for exploring the mutational fitness landscape of proteins. Its adaptation to anti-CRISPR proteins, which are natural CRISPR-Cas inhibitors and key players in the co-evolution of microbes and phages, facilitates their characterization and optimization. Here, we developed a robust anti-CRISPR deep mutational scanning pipeline in Escherichia coli that combines synthetic gene circuits based on CRISPR interference with flow cytometry coupled sequencing and mathematical modeling. more...
Organism:
Escherichia coli DH5[alpha]
Type:
Other
Platform:
GPL28103
28 Samples
Download data: CSV
Series
Accession:
GSE254101
ID:
200254101
2.

Functional characterization of enhancer activity during a long terminal repeat's evolution

(Submitter supplied) Many transposable elements (TEs) contain transcription factor binding sites and are implicated as potential regulatory elements. However, TEs are rarely functionally tested for regulatory activity, which in turn limits our understanding of how TE regulatory activity has evolved. We systematically tested the human LTR18A subfamily for regulatory activity using massively parallel reporter assay (MPRA) and found AP-1 and C/EBP-related binding motifs as drivers of enhancer activity. more...
Organism:
Escherichia coli DH5[alpha]; Homo sapiens
Type:
Other
Platforms:
GPL28104 GPL18573
11 Samples
Download data: TXT
Series
Accession:
GSE201068
ID:
200201068
3.

Genomic environments scale the activities of diverse core promoters

(Submitter supplied) One model for how cells integrate cis-regulatory information is that housekeeping and developmental core promoters respond specifically to certain types of enhancers or chromatin features at different chromosomal locations. We tested this model using a genome-integrated massively parallel reporter assay (MPRA) to measure the activity of hundreds of diverse core promoters at four genomic locations While genomic locations had large effects on expression, the relative strengths of core promoters were preserved across locations regardless of promoter class, suggesting that their intrinsic activities are scaled at different genomic locations. more...
Organism:
Escherichia coli DH5[alpha]; Homo sapiens
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL18573 GPL28104
38 Samples
Download data: BED, TXT
Series
Accession:
GSE173678
ID:
200173678
4.

Genome-wide Functional Characterization of ​Escherichia coli Promoters and Sequence Elements Encoding Their Regulation

(Submitter supplied) Using a novel multiplexed reporter assay, we characterize promoter activity of hundreds of thousands of DNA sequences spanning the entire E. coli genome. We use this powerful assay to identify promoters throughout the E. coli genome and systematically dissect their regulatory motifs which encode promoter activity using a series of experiments.
Organism:
Escherichia coli DH5[alpha]; Escherichia coli str. K-12 substr. MG1655
Type:
Other; Expression profiling by high throughput sequencing
4 related Platforms
60 Samples
Download data: TXT
Series
Accession:
GSE144621
ID:
200144621
5.

Quantifying variation within the bacterial species E. coli

(Submitter supplied) Escherichia coli strains are widely used in academic and applied research as well as in biotechnology for production of various compounds. Despite its status as a model organism, strain-specific differences and their underlying contributing factors are still not well characterized. These differences have a major impact on cell physiology and for the applied purposes of synthetic biology, metabolic engineering, and process design. more...
Organism:
Escherichia coli; Escherichia coli BL21; Escherichia coli W; Escherichia coli C; Escherichia coli str. K-12 substr. MG1655; Escherichia coli DH5[alpha]; Escherichia coli str. K-12 substr. W3110
Type:
Expression profiling by high throughput sequencing
7 related Platforms
14 Samples
Download data: CSV
Series
Accession:
GSE78756
ID:
200078756
6.

Development and evaluation of a 60-mer oligonucleotide microarray for profiling of biodegradation and bacterial 16S rRNA genes in diverse contaminated ecosystems

(Submitter supplied) We have developed a 60-mer oligonucleotide multibacterial microarray for detection and expression profiling of biodegradative genes and bacterial diversity (16S rRNA gene) in different habitats contaminated with varieties of hazardous chemicals. The genes selected were involved in biodegradation and biotransformation of various groups of compounds viz. nitroaromatic compounds (148 genes), chloroaromatic compounds (75 genes), monoaromatic compounds (373 genes), polyaromatic hydrocarbons (174 genes), pesticides/ herbicides (34 genes), alkanes/aliphatics (185 genes) and heavy metals (68 genes), which covered a total number of 133 chemicals. more...
Organism:
Rhodococcus jostii RHA1; Bordetella sp. IITR-02; Escherichia coli K-12; Sphingomonas sp. NM05; soil metagenome; synthetic construct; Escherichia coli DH5[alpha]; Escherichia coli BL21; freshwater sediment metagenome
Type:
Genome variation profiling by array
Platform:
GPL10926
17 Samples
Download data: TXT
Series
Accession:
GSE24353
ID:
200024353
7.

E.coli DH5alpha cells: reuterin-treated vs. untreated control cells

(Submitter supplied) Transcriptional profiling of E. coli DH5alpha cells comparing control untreated cells with cells exposed to sublethal concentrations of reuterin (3-hydroxypropionaldehyde).
Organism:
Escherichia coli; Escherichia coli DH5[alpha]
Type:
Expression profiling by array
Platform:
GPL7445
5 Samples
Download data: GPR
Series
Accession:
GSE19760
ID:
200019760
8.

Illumina NextSeq 500 (Escherichia coli DH5[alpha])

Organism:
Escherichia coli DH5[alpha]
3 Series
11 Samples
Download data
Platform
Accession:
GPL28104
ID:
100028104
9.

Illumina MiSeq (Escherichia coli DH5[alpha])

Organism:
Escherichia coli DH5[alpha]
2 Series
30 Samples
Download data
Platform
Accession:
GPL28103
ID:
100028103
10.

Illumina HiSeq 2000 (Escherichia coli DH5[alpha])

Organism:
Escherichia coli DH5[alpha]
1 Series
2 Samples
Download data
Platform
Accession:
GPL21534
ID:
100021534
11.

AcrIIA5 pre-sort single-mutant library replicate 2 [AcrDMS_v2_26-2]

Organism:
Escherichia coli DH5[alpha]
Source name:
DH5-alpha, genotpye: E. coli DH5a fhuA2Δ(argF-lacZ)U169 phoA glnV44 Φ80Δ(lacZ)M15 gyrA96 recA1 relA1 endA1 thi-1 hsdR17
Platform:
GPL28103
Series:
GSE254101
Download data
Sample
Accession:
GSM8033335
ID:
308033335
12.

AcrIIA4 pre-sort single-mutant library replicate 2 [AcrDMS_v2_25-2]

Organism:
Escherichia coli DH5[alpha]
Source name:
DH5-alpha, genotpye: E. coli DH5a fhuA2Δ(argF-lacZ)U169 phoA glnV44 Φ80Δ(lacZ)M15 gyrA96 recA1 relA1 endA1 thi-1 hsdR17
Platform:
GPL28103
Series:
GSE254101
Download data
Sample
Accession:
GSM8033334
ID:
308033334
13.

AcrIIA5 pre-sort single-mutant library replicate 1 [AcrDMS_v2_26]

Organism:
Escherichia coli DH5[alpha]
Source name:
DH5-alpha, genotpye: E. coli DH5a fhuA2Δ(argF-lacZ)U169 phoA glnV44 Φ80Δ(lacZ)M15 gyrA96 recA1 relA1 endA1 thi-1 hsdR17
Platform:
GPL28103
Series:
GSE254101
Download data
Sample
Accession:
GSM8033333
ID:
308033333
14.

AcrIIA4 pre-sort single-mutant library replicate 1 [AcrDMS_v2_25]

Organism:
Escherichia coli DH5[alpha]
Source name:
DH5-alpha, genotpye: E. coli DH5a fhuA2Δ(argF-lacZ)U169 phoA glnV44 Φ80Δ(lacZ)M15 gyrA96 recA1 relA1 endA1 thi-1 hsdR17
Platform:
GPL28103
Series:
GSE254101
Download data
Sample
Accession:
GSM8033332
ID:
308033332
15.

AcrIIA5 single-mutant library fraction 4 replicate 3 [AcrDMS_v2_24]

Organism:
Escherichia coli DH5[alpha]
Source name:
DH5-alpha, genotpye: E. coli DH5a fhuA2Δ(argF-lacZ)U169 phoA glnV44 Φ80Δ(lacZ)M15 gyrA96 recA1 relA1 endA1 thi-1 hsdR17
Platform:
GPL28103
Series:
GSE254101
Download data
Sample
Accession:
GSM8033331
ID:
308033331
16.

AcrIIA5 single-mutant library fraction 3 replicate 3 [AcrDMS_v2_23]

Organism:
Escherichia coli DH5[alpha]
Source name:
DH5-alpha, genotpye: E. coli DH5a fhuA2Δ(argF-lacZ)U169 phoA glnV44 Φ80Δ(lacZ)M15 gyrA96 recA1 relA1 endA1 thi-1 hsdR17
Platform:
GPL28103
Series:
GSE254101
Download data
Sample
Accession:
GSM8033330
ID:
308033330
17.

AcrIIA5 single-mutant library fraction 2 replicate 3 [AcrDMS_v2_22]

Organism:
Escherichia coli DH5[alpha]
Source name:
DH5-alpha, genotpye: E. coli DH5a fhuA2Δ(argF-lacZ)U169 phoA glnV44 Φ80Δ(lacZ)M15 gyrA96 recA1 relA1 endA1 thi-1 hsdR17
Platform:
GPL28103
Series:
GSE254101
Download data
Sample
Accession:
GSM8033329
ID:
308033329
18.

AcrIIA5 single-mutant library fraction 1 replicate 3 [AcrDMS_v2_21]

Organism:
Escherichia coli DH5[alpha]
Source name:
DH5-alpha, genotpye: E. coli DH5a fhuA2Δ(argF-lacZ)U169 phoA glnV44 Φ80Δ(lacZ)M15 gyrA96 recA1 relA1 endA1 thi-1 hsdR17
Platform:
GPL28103
Series:
GSE254101
Download data
Sample
Accession:
GSM8033328
ID:
308033328
19.

AcrIIA4 single-mutant library fraction 4 replicate 3 [AcrDMS_v2_20]

Organism:
Escherichia coli DH5[alpha]
Source name:
DH5-alpha, genotpye: E. coli DH5a fhuA2Δ(argF-lacZ)U169 phoA glnV44 Φ80Δ(lacZ)M15 gyrA96 recA1 relA1 endA1 thi-1 hsdR17
Platform:
GPL28103
Series:
GSE254101
Download data
Sample
Accession:
GSM8033327
ID:
308033327
20.

AcrIIA4 single-mutant library fraction 3 replicate 3 [AcrDMS_v2_19]

Organism:
Escherichia coli DH5[alpha]
Source name:
DH5-alpha, genotpye: E. coli DH5a fhuA2Δ(argF-lacZ)U169 phoA glnV44 Φ80Δ(lacZ)M15 gyrA96 recA1 relA1 endA1 thi-1 hsdR17
Platform:
GPL28103
Series:
GSE254101
Download data
Sample
Accession:
GSM8033326
ID:
308033326
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db=gds|term=txid668369[Organism:noexp]|query=1|qty=16|blobid=MCID_666ab120a997087fbe18c84e|ismultiple=true|min_list=5|max_list=20|def_tree=20|def_list=|def_view=|url=/Taxonomy/backend/subset.cgi?|trace_url=/stat?
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