Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30416200_1.fastq.gz | Fastqsanger.gz | |||
| SRR30416200_2.fastq.gz | Fastqsanger.gz | |||
| SRR30416201_1.fastq.gz | Fastqsanger.gz | |||
| SRR30416201_2.fastq.gz | Fastqsanger.gz | |||
| SRR30416202_1.fastq.gz | Fastqsanger.gz |
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Project description:Radiopharmaceutical imaging and targeted radionuclide therapy rely on endogenous molecular targets which are frequently heterogeneous, absent, or lost during cancer progression. We developed SMART, a Stiffness-responsive Mesenchymal stem cell (MSC)-Assisted Relayed tumor-Targeting platform that converts elevated matrix stiffness, a conserved biophysical feature of tumors, into localized expression of synthetic radiopharmaceutical targets. Engineered MSCs sensing stiff tumor microenvironments induced tumor-restricted expression of prostate-specific membrane antigen (PSMA), enabling 68Ga-PSMA-617 positron emission tomography (PET) imaging and 177Lu-AB-PSMA-617 therapy across diverse tumor models. SMART-enabled PET improved detection sensitivity relative to 18F-fluorodeoxyglucose PET, including in brain, lung, and bone metastases. The platform is modular, extendable to targets such as somatostatin receptor 2, and compatible with induced pluripotent stem cell (iPSC)-derived MSCs. SMART therefore decouples radiotheranostic performance from endogenous biomarker status and establishes a generalizable strategy for targeting biophysical hallmarks of cancer.
2026-07-14 | GSE337702 | GEO
Project description:We developed Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) for de novo detection of global chromatin interactions, and comprehensively mapped the chromatin interaction network bound by estrogen receptor α (ERα) in the human genome. We performed 454 and Illumina sequencing analyses. Keywords: Epigenetics Using 454, we examined 3 libraries: IHM001 (Estrogen Receptor ChIA-PET), IHM043 (Estrogen Receptor ChIP-PET) and IHM062 (IgG ChIA-PET) Using Illumina, we examined 4 libraries: IHM001 (Estrogen Receptor ChIA-PET replicate 1, Paired End Sequencing), IHH015 (Estrogen Receptor ChIA-PET replicate 2, Paired End Sequencing), H3K4me3 ChIP-Seq and RNA polymerase II ChIP-Seq
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Project description:We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to https://www.encodeproject.org/about/data-use-policy Chromatin interactions identified by ChIA-PET for 4 different histone modifications (H3K4me1, H3K4me2, H3K4me3, H3K27ac), RAD21 and RNAPII in the K562 cell line, two biological replicates each. Additionally, chromatin interactions were identified by ChIA-PET in the GM12878 cell line for RAD21.
2014-08-21 | E-GEOD-59395 | biostudies-arrayexpress
Project description:HEK293T/17 cells were genetically edited by SMART editing to assess the effectiveness of SMART editing. There are 4 target genes: CXCR4, Lmnb1, Nrl and NRXN3. Cultured cells were first synchronized at the G2/M phase. Then, cells were transfected with Cas9 RNP along with SMART or traditional templates. After culture for two to three days, cells were harvested, and genomic DNA was extracted. The targeted loci were amplified by PCR and sequenced on an Illumina MiSeq.
2025-04-21 | E-MTAB-14909 | biostudies-arrayexpress
Project description:To get further insights on the micro-nanoplastic (MNP) effects on plants, the aim of this study was to: 1) shed light on the transcriptome changes provoked by two different polyethylene terephthalate (PET) MNPs in plant roots; 2) determine their effects on key plant growth parameters in hydroponically-cultivated Arabidopsis thaliana. MNPs of transparent (Tr-PET) and blue (Bl-PET) material caused a significant reduction in root length, while only Bl-PET significantly reduced rosette area. Plant fresh and dry weight did not change, even though various OJIP-test parameters decreased in the presence of MNPs. RNA-seq data showed that Bl-PET and, especially, Tr-PET affected gene expression in comparison to controls. Tr-PET induced starch degradation and isoprenoids, while glycolysis, trehalose metabolism and fermentation were generally repressed. Tr-PET upregulated genes involved in signaling of xenobiotics, whereas Bl-PET scarcely affected root transcriptomic profile, activating few gene categories for abiotic stresses. Regarding hormones, genes involved in ABA response were repressed, while brassinosteroid-related genes were differentially regulated by Tr-PET. Both MNPs, but especially Tr-PET, upregulated major latex protein-related genes. These results allowed to gain insight into the effects of MNP contamination in plant metabolism, identifying targets for biotechnological strategies to enhance plant tolerance and phytoremediation of these xenobiotic agents.
2024-12-31 | E-MTAB-13532 | biostudies-arrayexpress
Project description:High-order rice chromatin contains numerous interactions among DNA, RNA and protein to regulate critical biological processes in various aspects of rice life. We developed an effective method for mapping histone-mediated chromatin associated RNA-DNA interactions, followed by paired-end-tag sequencing (ChRD-PET) in rice. With H3K4me3 ChRD-PET, H3 ChRD-PET and RNase H treated H3K4me3 ChRD-PET, we present a highly comprehensive map of RNA and chromatin interactions around promoters in rice MH63. Through integrating ChIA-PET (published data), ChRD-PET and ssDRIP-seq data analysis, we demonstrated the function of RNAs-chromatin interactions in different level. We also conducted ATAC-seq and integrative analysis uncovered the relationship of epigenetic modifications and ChRD-PET interactions. Our findings firstly revealed the map and features of RNAs-chromatin interactions in rice.
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Project description:Polyethylene terephthalate (PET) is one of the most commonly used plastics, utilized in synthetic fibers, water containers, and food packaging. From the 1990s onwards, the demand for PET, and therefore its production, increased exponentially. This increased usage of PET has resulted in a staggering accumulation of undegraded plastic waste. Nearly 80% of the 6300 million tons of plastic waste that had been generated as of 2015 were accumulated in landfills or the natural environment. Moreover, the production of PET relies heavily on non‐renewable fossil fuels, exacerbating environmental concerns over its widespread use. In alignment with principles of environmental sustainability, the biotechnological upcycling of PET has recently emerged as a compelling solution. Since the discovery of PETase, a hydrolase capable of depolymerizing this polyester, enzymatic plastic breakdown is increasingly considered as a promising solution for managing PET waste. This enzyme and its improved derivatives, such as Fast‐PETase, enable the breakdown of PET into bis(2‐41 hydroxyethyl) terephthalate (BHET) and mono(2‐hydroxyethyl) terephthalate (MHET). Subsequently, the enzyme MHETase is responsible for further degradation of MHET into ethylene glycol and terephthalic acid. The metabolic capability of microorganisms to utilize these monomers of PET for growth has been explored in various biotechnological applications, especially in the context of bioremediation and bioconversion processes aimed at transforming plastic waste into useful products using genetically engineered bacteria.
2025-05-23 | PXD060720 | Pride
Project description:Newborn neurons enter an extended maturation stage, during which they acquire excitability characteristics crucial for development of presynaptic and postsynaptic connectivity. In contrast to earlier specification programs, little is known aboutthe regulatory mechanisms that control neuronal maturation. The Pet-1 ETS (E26 transformation-specific) factor is continuously expressed in serotonin (5-HT) neurons and initially acts in postmitotic precursors to control acquisition of 5-HT transmitter identity. Using a combination of RNA sequencing, electrophysiology, and conditional targeting approaches, we determined gene expression patterns in maturing flow-sorted 5-HT neurons and the temporal requirements for Pet-1 in shaping these patterns for functional maturation of mouse 5-HT neurons. We report a profound disruption of postmitotic expression trajectories in Pet-1 / neurons, which prevented postnatal maturation of 5-HT neuron passive and active intrinsic membrane properties, G-protein signaling, and synaptic responses to glutamatergic, lysophosphatidic, and adrenergic agonists. Unexpectedly, conditional targeting revealed a postnatal stage-specific switch in Pet-1 targets from 5-HT synthesis genes to transmitter receptor genes required for afferent modulation of 5-HT neuron excitability. 5-HT1a autoreceptor expression depended transiently on Pet-1, thus revealing an early postnatal sensitive period for control of 5-HT excitability genes. Chromatin immunoprecipitation followed by sequencing revealed that Pet-1 regulates 5-HT neuron maturation through direct gene activation and repression. Moreover, Pet-1 directly regulates the 5-HT neuron maturation factor Engrailed 1, which suggests Pet-1 orchestrates maturationthrough secondary postmitotic regulatoryfactors. The early postnatal switch in Pet-1targets uncovers a distinct neonatal stage-specific function for Pet-1, during which it promotes maturation of 5-HT neuron excitability. 5-HT neuron mRNA profiles of E11.5, E15.5, and postnatal (P1-P3) wild type (WT) and Pet-1-/- mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. Myc-tagged Pet-1 ChIP-seq was performed on E12.5 to E14.5 hindbrains and sequencing using NextSeq 500.
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