GEO DataSets

(Submitter supplied) Adeno-associated viral vectors (AAV) are a leading delivery system for gene therapy in animal models and humans. With several FDA-approved AAV gene therapies on the market, issues related to vector manufacturing have become increasingly important. In this study, we focused on potentially toxic DNA contaminants that can arise from AAV proviral plasmids, the raw materials required for manufacturing recombinant AAV in eukaryotic cells. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL34723

2 Samples

Download data: CSV

(Submitter supplied) Adeno-associated viral vectors (AAV) are a leading delivery system for gene therapy in animal models and humans. With several FDA-approved AAV gene therapies on the market, issues related to vector manufacturing have become increasingly important. In this study, we focused on potentially toxic DNA contaminants that can arise from AAV proviral plasmids, the raw materials required for manufacturing recombinant AAV in eukaryotic cells. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL28978

19 Samples

Download data: CSV

(Submitter supplied) Gene variants resulting in insertions or deletions of amino acid residues (indels) have important consequences for evolution and are often linked to disease, yet compared to missense variants the effects of indels are poorly understood and ineptly predicted. To approach this issue, we developed a sensitive protein folding sensor based on complementation of uracil auxotrophy in yeast by circular permutated orotate phosphoribosyltransferase (CPOP). more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL27609

73 Samples

Download data: CSV

(Submitter supplied) The rhizosphere is a small region surrounding plant roots that is enriched in biochemicals from root exudates and populated with fungi, nematode, and bacteria. Interaction of rhizosphere organisms with plants is mainly promoted by exudates from the roots. Root exudates contain biochemicals that come from primary and secondary metabolisms of plants. These biochemicals attract microbes, which influence plant nutrition. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL21616

1 Sample

Download data: TAR, XLSX

(Submitter supplied) BRAF inhibitors are widely employed in the treatment of melanoma with the BRAF V600E mutation. However, the development of resistance greatly compromises their therapeutic efficacy. Here, we elucidate the role of polyamine biosynthesis and its regulatory mechanisms in promoting BRAF inhibitor resistance. Leveraging CRISPR-Cas9 screens, we identify AMD1 (S-adenosylmethionine decarboxylase 1), a critical enzyme for polyamine biosynthesis, as a druggable target whose inhibition reverses vemurafenib resistance. more...

Organism:

synthetic construct; Homo sapiens

Type:

Other

Platforms:

GPL19604 GPL16791

6 Samples

Download data: TXT

(Submitter supplied) 115 dB SPL of noise exposure for 2 hours causes high threshold shift at day 1 and recovers rapidly at day 3. Microarray was performed to identify up or down-regulated genes during rapid recovery of hearing.

Organism:

Rattus norvegicus; synthetic construct

Type:

Non-coding RNA profiling by array

Platform:

GPL19117

64 Samples

Download data: CEL

(Submitter supplied) Small molecule compounds that inducespark the mRNA-selective translation repression, are attracting interesthave arisen due to their potential for expansion ofin druggable space expansion. However, only limited examples have been reported to datewere found. Here we showed that pateamine A (PatA) represses translation in an mRNA-selective manner by clamping eIF4A, a DEAD-box RNA-binding protein, on GNG motifs. more...

Organism:

synthetic construct; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL20301 GPL21616 GPL26697

36 Samples

Download data: CSV, TXT

(Submitter supplied) Sequence-specific DNA-binding proteins (DBPs) play critical roles in biology and biotechnology, and there has been considerable interest in the engineering of DBPs with new or altered specificities for genome editing and other applications. While there has been some success in reprogramming naturally occurring DBPs using selection methods, the computational design of new DBPs that recognize arbitrary target sites remains an outstanding challenge. more...

Organism:

Homo sapiens; synthetic construct

Type:

Other

Platform:

GPL23935

12 Samples

Download data: TXT

(Submitter supplied) Identifying the DNA-binding specificities of transcription factors (TF) is central to understanding gene networks that regulate growth and development. Such knowledge is lacking in oomycetes, a group of microbes that includes many important plant and animal pathogens. Here we describe the use of protein-binding oligonucleotide microarrays (PBMs) to define the DNA-binding preferences of 14 families of TFs from the oomycete Phytophthora infestans, which causes late blight of potato and tomato. more...

Organism:

synthetic construct; Phytophthora infestans

Type:

Other

Platform:

GPL11260

146 Samples

Download data: TXT

(Submitter supplied) To understand the expression patterns of miRNAs expression during acute in vitro infection of human neutrophils by L. infantum we performed a microarray.

Organism:

synthetic construct; Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL21572

10 Samples

Download data: CEL

(Submitter supplied) Intracellular pH (pHi) dynamics regulates diverse cell processes such as proliferation, dysplasia, and differentiation, often mediated by the protonation state of a functionally critical histidine residue in endogenous pH sensing proteins. How pHi dynamics can directly regulate gene expression and whether transcription factors can function as pH sensors has received limited attention. We tested the prediction that transcription factors with a histidine in their DNA binding domain (DBD) that forms hydrogen bonds with nucleotides can have pH-regulated activity, which is relevant to more than 85 transcription factors in distinct families, including FOX, KLF, SOX and MITF/Myc. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL26967

9 Samples

Download data: XLSX

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

Organism:

Homo sapiens; unidentified plasmid

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

5 related Platforms

139 Samples

Download data: BW, PSI, TAB

(Submitter supplied) Although CRISPR-Cas technology has revolutionized functional genomics, the systematic exploration of the role of individual exons for critical cellular phenotypes is lagging, limiting our understanding of genome regulation. To overcome this constraint, we have optimized and applied massively parallel exon deletion and splice site mutation screens in human cell lines identifying thousands of exons required for cell fitness. more...

Organism:

Homo sapiens; unidentified plasmid

Type:

Other

5 related Platforms

85 Samples

Download data: TXT

(Submitter supplied) Spatial transcriptomics (ST) methods have been developed to unlock molecular mechanisms underlying tissue development, homeostasis, or disease. However, there is a need for easy-to-use, high-resolution, cost-efficient, and 3D-scalable methods. Here, we report Open-ST, a sequencing-based, open-source experimental and computational resource to address these challenges and to study the molecular organization of tissues in 3D. more...

Organism:

Homo sapiens; Mus musculus; synthetic construct

Type:

Other

4 related Platforms

27 Samples

Download data: CSV, H5AD, TAR

(Submitter supplied) To systematcially explore targets that can regulated tumor's response to immune checkpoint therapy, we performed an in vivo targeted CRISPR knockout screen in a mouse model of bladder cancer. Cas9-expressing MB49 cells were transfected with two sub-libraries to make two cell pools. We first validated full representation of sgRNA composition in cell pools by comparing to that in the plasmid pools. For in vivo screen, we first compared PBS or anti-PD-1 treated tumors to original cell pools to get condition specific change, then compared anti-PD-1 treated tumors to PBS treated tumors to identify genes that may regulate anti-PD-1 response.

Organism:

synthetic construct; Mus musculus

Type:

Other

Platforms:

GPL19424 GPL19057

20 Samples

Download data: CSV

(Submitter supplied) Transporters mediate and control the flux of molecules across compartmental membranes. The human genome encodes 1500 genes with transport functions, of which the solute carriers (SLCs) form the largest superfamily with more than 450 members. Over 250 different SLCs are expressed in a typical human cell, many exhibiting overlapping expression patterns and substrate specificities. The collective role of these often seemingly redundant transporters in defining cellular outcomes, such as cell survival, remains unclear. more...

Organism:

Homo sapiens; synthetic construct

Type:

Other

4 related Platforms

129 Samples

Download data: TXT

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

Organism:

Mus musculus; synthetic construct

Type:

Other

Platforms:

GPL17021 GPL19604

39 Samples

Download data

(Submitter supplied) Massively parallel reporter assays (MPRA) are widely used to discover functional enhancers but have largely been limited to transfected cell models, which are confounded by vector-induced innate immune responses and lack the physiologically relevant cellular and endogenous hormonal context and chromatin environment of complex mammalian tissues. Here, we combine hydrodynamic injection with a modified STARR-seq-based MPRA to determine condition-specific enhancer activity in mouse liver at scale. more...

Organism:

Mus musculus; synthetic construct

Type:

Other

Platforms:

GPL17021 GPL19604

15 Samples

Download data: TXT, XLSX

(Submitter supplied) Massively parallel reporter assays are widely used to discover functional enhancers but have largely been limited to transfected cell models, which are confounded by vector-induced innate immune responses and lack the physiologically relevant cellular and endogenous hormonal context and chromatin environment of complex mammalian tissues. Here, we combine hydrodynamic injection with a modified STARR-seq-based MPRA to determine condition-specific enhancer activity in mouse liver at scale. more...

Organism:

synthetic construct; Mus musculus

Type:

Other

Platforms:

GPL19604 GPL17021

12 Samples

Download data: TXT, XLSX

(Submitter supplied) An important and largely unsolved problem in synthetic biology is how to target gene expression to specific cell types. Here, we apply iterative deep learning to design synthetic enhancers with strong differential activity between two human cell lines. We initially train models on published datasets of enhancer activity and chromatin accessibility and use them to guide the design of synthetic enhancers that maximize predicted specificity. more...

Organism:

synthetic construct; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL27609 GPL21697

16 Samples

Download data: CSV