Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31300715_1.fastq.gz | Fastqsanger.gz | |||
| SRR31300715_2.fastq.gz | Fastqsanger.gz | |||
| SRR31300716_1.fastq.gz | Fastqsanger.gz | |||
| SRR31300716_2.fastq.gz | Fastqsanger.gz | |||
| SRR31300717_1.fastq.gz | Fastqsanger.gz |
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Project description:A long form (tRNase ZL) of tRNA 3' processing endoribonuclease (tRNase Z, or 3' tRNase) can cleave any target RNA at any desired site under the direction of artificial small guide RNA (sgRNA). We discovered in human kidney 293 cell extracts various new small noncoding RNAs (ncRNAs) including 5'-half-tRNAs and 28S rRNA fragments, co-immunoprecipitated with tRNase ZL, and demonstrated that two of these ncRNAs work as sgRNAs for tRNase ZL in vivo as well as in vitro. In order to find genuine mRNA targets of tRNase ZL guided by ncRNAs, we performed DNA microarray analysis for mRNAs from the 293 cells transfected with the tRNase ZL expression plasmid, and found that PPM1F and DYNC1H1 mRNAs are its genuine targets. Experiment Overall Design: In order to find genuine mRNA targets of tRNase ZL guided by ncRNAs, we performed DNA microarray analysis for mRNAs from the 293 cells transfected with the tRNase ZL expression plasmid.
2009-06-23 | E-GEOD-12524 | biostudies-arrayexpress
Project description:A long form (tRNase ZL) of tRNA 3' processing endoribonuclease (tRNase Z, or 3' tRNase) can cleave any target RNA at any desired site under the direction of artificial small guide RNA (sgRNA). We discovered in human kidney 293 cell extracts various new small noncoding RNAs (ncRNAs) including 5'-half-tRNAs and 28S rRNA fragments, co-immunoprecipitated with tRNase ZL, and demonstrated that two of these ncRNAs work as sgRNAs for tRNase ZL in vivo as well as in vitro. In order to find genuine mRNA targets of tRNase ZL guided by ncRNAs, we performed DNA microarray analysis for mRNAs from the 293 cells transfected with the tRNase ZL expression plasmid, and found that PPM1F and DYNC1H1 mRNAs are its genuine targets.
2009-06-15 | GSE12524 | GEO
Project description:tRNase ZL-utilizing efficacious gene silencing (TRUE gene silencing) is an RNA-mediated gene expression control technology that has therapeutic potential. This technology is based on the properties of tRNase ZL that it can cleave any target RNA at any desired site under the direction of an appropriate artificial small guide RNA (sgRNA) and that cytosolic tRNase ZL can modulate gene expression by cleaving mRNA under the direction of cellular 5′-half-tRNA or microRNA as sgRNA. In order to estimate a number of potential therapeutic heptamer-type sgRNAs for hematological malignancies, we constructed an sgRNA library composed of 156 heptamer-type sgRNAs, and examined how the sgRNAs affect viability of leukemia and myeloma cells. And we found that 20 of the 156 sgRNAs can efficiently induce apoptosis in at least one of the cancer cell lines. Furthermore, we demonstrated that 4 of the 20 effective sgRNAs can reduce growth rates of HL60 cells in mouse xenograft models. DNA microarray analysis for changes in an mRNA profile by these four heptamer-type sgRNAs suggested at least one candidate target mRNA that contains a potential tRNase ZL target site for each sgRNA.
2014-06-30 | GSE49578 | GEO
Project description:tRNase ZL-utilizing efficacious gene silencing (TRUE gene silencing) is an RNA-mediated gene expression control technology that has therapeutic potential. This technology is based on the properties of tRNase ZL that it can cleave any target RNA at any desired site under the direction of an appropriate artificial small guide RNA (sgRNA) and that cytosolic tRNase ZL can modulate gene expression by cleaving mRNA under the direction of cellular 5M-bM-^@M-2-half-tRNA or microRNA as sgRNA. In order to estimate a number of potential therapeutic heptamer-type sgRNAs for hematological malignancies, we constructed an sgRNA library composed of 156 heptamer-type sgRNAs, and examined how the sgRNAs affect viability of leukemia and myeloma cells. And we found that 20 of the 156 sgRNAs can efficiently induce apoptosis in at least one of the cancer cell lines. Furthermore, we demonstrated that 4 of the 20 effective sgRNAs can reduce growth rates of HL60 cells in mouse xenograft models. DNA microarray analysis for changes in an mRNA profile by these four heptamer-type sgRNAs suggested at least one candidate target mRNA that contains a potential tRNase ZL target site for each sgRNA. Changes in gene expression in HL60 cells were measured after 18-hour incubation in the absence or presence of one of five different heptamer-type sgRNAs. *Heptamer sequences requested but not provided by submitter
2014-06-30 | E-GEOD-49578 | biostudies-arrayexpress
Project description:Facial features identify individuals, but the mechanisms shaping the human face remain elusive. Orofacial clefting (OFC), the most common craniofacial abnormality, results from failed fusion of the facial prominences, partly caused by persistence of the cephalic epithelium. Using mouse models to guide our studies, here we uncover the identity, behaviors, and molecular blueprints of a novel craniofacial epithelial population, Zippering Lambda (ZL), similarly characterized by cell cycle arrest in mouse and human embryos. Remarkably, in Pbx1/2 and p63 mutant mice with OFC cell cycle is unleashed in ZL epithelium. Intersecting ZL-enriched genes with human OFC whole-genome sequencing datasets identifies ZFHX3 variants in affected individuals and cephalic epithelial Zfhx3 deletion results in murine OFC. Our findings further demonstrate that ZFHX3 and PBX1 synergistically regulate cell cycle inhibitor genes acting within a complex in embryonic faces. Collectively, we deconstruct new mechanisms that pattern the face, connecting cell cycle arrest to developmental tissue fusion.
2025-06-11 | GSE299536 | GEO
Project description:Facial features identify individuals, but the mechanisms shaping the human face remain elusive. Orofacial clefting (OFC), the most common craniofacial abnormality, results from failed fusion of the facial prominences, partly caused by persistence of the cephalic epithelium. Using mouse models to guide our studies, here we uncover the identity, behaviors, and molecular blueprints of a novel craniofacial epithelial population, Zippering Lambda (ZL), similarly characterized by cell cycle arrest in mouse and human embryos. Remarkably, in Pbx1/2 and p63 mutant mice with OFC cell cycle is unleashed in ZL epithelium. Intersecting ZL-enriched genes with human OFC whole-genome sequencing datasets identifies ZFHX3 variants in affected individuals and cephalic epithelial Zfhx3 deletion results in murine OFC. Our findings further demonstrate that ZFHX3 and PBX1 synergistically regulate cell cycle inhibitor genes acting within a complex in embryonic faces. Collectively, we deconstruct new mechanisms that pattern the face, connecting cell cycle arrest to developmental tissue fusion.
2025-05-28 | GSE298136 | GEO
Project description:Covalent chemistry coupled with activity-based protein profiling (ABPP) offers a versatile way to discover ligands for pro-teins in native biological systems. Here, we describe a set of stereo- and regio-chemically defined spirocycle acrylamides and the analysis of these electrophilic ‘stereoprobes’ in human cancer cells by cysteine-directed ABPP. Despite showing attenuat-ed reactivity compared to structurally related azetidine acrylamide stereoprobes, the spirocycle acrylamides preferentially liganded specific cysteines on diverse protein classes. One compound ZL-12A stereoselectively promoted the degradation of the TFIIH helicase ERCC3. Interestingly, ZL-12A reacts with the same cysteine (C342) in ERCC3 as the natural product triptolide, which did not lead to ERCC3 degradation, but instead caused collateral loss of RNA polymerases. ZL-12A and triptolide cross-antagonized one another’s protein degradation profiles. Finally, we show that the anti-hypertension drug spi-ronolactone — previously found to promote ERCC3 degradation through an enigmatic mechanism — also reacts with ERCC3_C342. Our findings thus describe monofunctional degraders of ERCC3 and highlight how covalent ligands target-ing the same cysteine can produce strikingly different functional outcomes.
2025-11-06 | PXD050872 | Pride
Project description:Covalent chemistry coupled with activity-based protein profiling (ABPP) offers a versatile way to discover ligands for proteins in native biological systems. Here, we describe a set of stereo- and regio-chemically defined spirocycle acrylamides and their analysis in human cancer cells by cysteine-directed ABPP. Despite showing attenuated reactivity compared to structurally related azetidine acrylamides, the spirocycle acrylamides preferentially liganded specific cysteines on diverse protein classes. One compound ZL-12A stereoselectively promoted the degradation of the TFIIH helicase ERCC3. Interestingly, ZL-12A reacts with the same cysteine (C342) in ERCC3 as the natural product triptolide, which did not lead to ERCC3 degradation but instead caused collateral loss of RNA polymerases. ZL-12A and triptolide cross-antagonized one another’s protein degradation profiles. Finally, we show that the anti-hypertension drug spironolactone — previously found to promote ERCC3 degradation through an enigmatic mechanism — also reacts with ERCC3_C342. Our findings thus describe monofunctional degraders of ERCC3 and highlight how covalent ligands targeting the same cysteine can produce strikingly different functional outcomes.
2025-11-06 | PXD046356 | Pride
Project description:We performed a 16S sequencing analysis on Cervical Swab of women undergoing Assisted Reproductive Technologies
2023-11-17 | E-MTAB-11151 | biostudies-arrayexpress