Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chimeric tRNAs and antifungal

ABSTRACT: In this study we tested the hypothesis that generalized codon ambiguity could be beneficial to evolution of resistance against amphotericin B. For this, we have evolved C. albicans strains that incorporate serine at CTA , CTC, CTT (Leucine), ATC (Isoleucine), GCC (Alanine), GGA (Glycine), AAG (Lysine), ACC (Threonine) and TAC (Tyrosine) codons in the presence amphotericin B and characterized them at the genome level. We identified a number of genomic features and key genes that shed new light onto how chimeric tRNAs affects acquisition of resistance to amphotericin B.

PROVIDER: PRJEB12264 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR1198130_1.fastq.gz	Fastqsanger.gz
	ERR1198130_2.fastq.gz	Fastqsanger.gz
	ERR1198140_1.fastq.gz	Fastqsanger.gz
	ERR1198140_2.fastq.gz	Fastqsanger.gz
	ERR1198131_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 38

Similar Datasets

5’ half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos [small RNA-Seq, ssDRIP-seq]

Project description:5’tRFls are small tRNA fragments derived from 5’ half of mature tRNAs. However, it is unknown whether 5’tRFls could feed back to regulate tRNA biogenesis. Here we show that 5’tRFlGly/GCC and 5’tRFlGlu/CTC function to promote transcription of corresponding tRNA genes and are essential for vertebrate early embryogenesis. During zebrafish embryogenesis, dynamics of 5’tRFlGly/GCC and 5’tRFlGlu/CTC levels correlates with that of tRNAGly/GCC and tRNAGlu/CTC levels. Morpholino-mediated knockdown of 5’tRFlGly/GCC or 5’tRFlGlu/CTC down-regulates tRNAGly/GCC or tRNAGlu/CTC levels respectively, and causes embryonic lethality that is efficiently rescued by co-injection of properly refolded corresponding tRNA. In zebrafish embryos, tRNA:DNA and 5’tRFl:DNA hybrids commonly exist on the template strand of tRNA genes. Mechanistically, unstable 5’tRFl:DNA hybrid may prevent the formation of transcriptionally inhibitory stable tRNA:DNA hybrids on the same tRNA loci so as to facilitate tRNA genes transcription. The uncovered mechanism may be implicated in other physiological and pathological processes.

2021-08-25 | GSE147253 | GEO

5’ half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos [tRNA-seq]

2021-08-25 | GSE181683 | GEO

Function and relevance of sushi domain-containing protein 2 (SUSD2) in circulating tumor cells of metastatic estrogen receptor positive breast cancer

Project description:Albeit responding well to therapy, estrogen receptor positive breast cancers frequently become subsequently resistant. This leads to distant metastasis and release of circulating tumor cells (CTCs) into the blood stream and ends with the death of the patient. Here we analyzed the proteome of CTC-ITB-01 by mass spectrometry and quantified 7954 different proteins using MCF-7 as a reference proteome. The data were deposited in a database for public access. CTC-ITB-01 is a CTC cell line derived from a patient with metastatic and estrogen receptor alpha (ER-alpha) positive breast cancer. We found remarkable high levels of the protein sushi domain-containing protein 2 (SUSD2) in CTC-ITB-01. Presence of SUSD2 in CTC of patients with breast cancer was confirmed by CellSearch (9/23 CTC positive cases). Ectonucleotide pyrophosphatase /phosphodiesterase family member 1 (ENPP1) was detected in CTC-ITB-01 and confirmed in CTC of breast cancer patients (n=3). ENPP1 can mediate immune evasion of tumor cells. Overexpression of SUSD2 in MCF-7 revealed upregulation of ER-alpha, 78 kDa glucose-regulated protein (GRP78) downregulation of programmed cell death protein 4 (PDCD4). GRP78 mediates resistance to chemotherapy, whereas loss of PDCD4 is involved in drug resistance and malignant transformation. Database search revealed significantly reduced overall survival in luminal breast cancer for low PDCD4 levels (n=348; p=0.0323). In conclusion, high levels of SUSD2 may confer improved cytoprotection of metastatic breast cancer cells and their CTC travelers to distant organs in the blood.

2025-02-04 | PXD047444 | Pride

tsRNAs Are Potential Biomarkers of Acute Rejection in Vascularized Composite Allotransplantation

Project description:Purpose: to explore the function and mechanism of acute rejection in vascularized composite allotransplantation Method: tRF & tiRNA profiles of acute rejection in vascularized composite allotransplantation were generated by deep sequencing, using Illumina NextSeq 500. qRT–PCR validation was performed using SYBR Green assays. Results:Sequencing was used to screen expression profiles and predict target genes. Compared with the control group, there were significant differences in the expression levels of 16 tRFs & tiRNAs, including 5 up-regulated target genes and 11 down-regulated target genes. Bioinformatics analysis and RT-qPCR revealed potential up regulation of tRFs & tiRNAs(tiRNA-1-33-Gly-GCC-1, tiRNA-1-34-Glu-CTC-1, tRF-1-32-Gly-GCC-2-M2) and down regulation of tRFs & tiRNAs (tRF-59:75-Gln-CTG-2-M2, tRF-59:76-Val-AAC-1-M2). Conclusion: In conclusion, it is speculated that tiRNA-1-34-Glu-CTC-1 plays an important role in VCA induced acute rejection by regulating CACNA1D gene in MAPK signaling pathway. This provides a new insight into the mechanism and therapeutic targets of acute rejection.

2022-07-20 | GSE190008 | GEO

Expression data from 17-AAG resistance cell line

Project description:Develop the 17-AAG resistance human lung cancer cell line and used microarrays to observe the gene alternnation

2017-01-11 | GSE93384 | GEO

Transcriptome Analysis of the Zebrafish Mind Bomb Mutant

Project description:To identify the genes differentially expressed in the zebrafish mibta52b mutant, genome-wide transcriptome analysis was performed using Serial Analysis of Gene Expression (SAGE). 335 transcripts were identified whose expressions were significantly altered in the mibta52b mutant as compared with the wild-type. After mRNA isolation using oligo(dT)25 beads (Dynal Biotech ASA, Oslo, Norway), cDNA synthesis was carried out using anchored oligo(dT) primers to reduce truncated cDNA through internal poly(A) priming (Nam et al., 2002). SAGE analysis was carried out as described (Velculescu et al., 1995) but was modified slightly according to Lee et al (Lee et al., 2007). We performed a low-cycle PCR (14 cycles) using the GeneAmp PCR System 2400 (Applied Biosystem, Foster City, CA) to amplify 3’cDNA in order to generate a sufficient amount of templates for SAGE analysis. The sense primer used was a SAGE primer 1 (5’-GGA TTT GCT GGT GCA GTA CA-3’) or SAGE primer 2 (5’-CTG CTC GAA TTC AAG CTT CT-3’); the antisense primer used was 5’-biotin- ACT ATC TAG AGC GGC CGC TT-3’, which was located in the 3’ end of all cDNAs generated from the anchored oligo(dT) primers. BsmFI-released fragments containing SAGE tags, were gel purified before being used for ditag formation and concatenation to provide high-quality tags for SAGE analysis. SAGE tag sequences were collected with Big-Dye sequencing and an ABI3730 sequencer, and tag sequences were extracted with SAGE 300 software. A total of 92,970 SAGE tags were collected from the two libraries.

2008-10-08 | E-GEOD-13050 | biostudies-arrayexpress

Expression data from human colonic cancer cell line SW480 and its acquired 17-AAG resistance cell line SW480-R

Project description:Heat shock protein 90 (HSP90) is a molecular chaperone required for the stability and function of many proteins. The chaperoning of oncoproteins by HSP90 enhances survival, growth and invasive potential of cancer cells. HSP90 inhibitors are promising new anticancer agents, in which the benzoquinone ansamycin 17-allylamino-17-demethoxygeldanamycin (17-AAG) is currently in clinical evaluation. However, the implications of acquired resistance to this class of drug remain largely unexplored. In the present study, we have generated isogenic human colonic cancer cell line SW480 that is resistant to 17-AAG by continued culturing in the compound. We used microarrays to detail the global programme of gene expression underlying the acquired resistance to 17-AAG in SW480 and SW480-R cell lines.

2015-03-14 | GSE66867 | GEO

Epigenomic reprogramming of therapy-resistant circulating tumor cells in colon cancer

Project description:Therapy resistance is a major limitation for treatment efficacy in colorectal cancer. Circulating tumor cells (CTCs) and epigenetic modifications, such as DNA methylation, are involved in the development of acquired resistance during treatment. The aim of this work was to characterize the DNA methylation landscape of colon CTCs during cancer progression and the development of therapy resistance. We analyzed nine permanent colon CTC-derived cell lines, which were collected at baseline (CTC-MCC-41) and during treatment and cancer progression (CTC-MCC-41.4 and CTC-MCC-41.5 [A-G]) from peripheral blood samples of a patient with metastatic colon cancer. The DNA methylome of these nine CTC lines was analyzed by EPIC arrays.

2023-12-13 | GSE239549 | GEO

miR-210 expression is strongly hypoxia-induced in anaplastic thyroid cancer cell SW1736

Project description:Anaplastic thyroid carcinoma (ATC) is a rare but deadly form of thyroid cancer. Hypoxia is frequent in aggressive solid tumors like ATC and can promote resistance to therapy via the hypoxia-inducible factor (HIF) pathway. miR-210 has been previously identified as a direct target of hypoxia-inducible factor 1 (HIF-1) and is upregulated in many solid tumors. Here we show that miR-210 expression is upregulated in ATC cell line SW136 in hypoxia relative to normoxia. Identifying and targeting hypoxic cells is an attractive approach to detecting and treating ATC.

2022-09-08 | GSE212703 | GEO

Amino acid substituents as a response to amino acid restriction

Project description:Correct charging of tRNAs with their corresponding amino acid is crucial for accurate translation of the genetic code into proteins. However, a growing body of evidence shows that unicellular organisms (bacteria and yeast) can sacrifice translational fidelity to preserve protein synthesis under deprivation of specific essential amino acids.1 Several weeks ago, Pataskar and colleagues described the first instance of codon reassignments caused by amino acid restriction in mammalian cells. Specifically, when human cancer cells were deprived of tryptophan (W), tRNATrp was misacylated with the structurally similar amino acid phenylalanine (F) by tryptophanyl-tRNA synthetase (WARS1), resulting in W>F substitutions in synthesized proteins.2 The authors show that W>F substitutions do preserve translation, but generally result in dysfunctional proteins and that presentation of W>F peptides stimulates T cell-mediated killing. Together this would impair survival of cancer cells that incorporate W>F substitutions in their proteome.2 In the context of growing interest in amino acid depletion diets and related disorders,2 we wondered whether amino acid substitutions are restricted to pathological states like cancer or may represent a more generalized mechanism to maintain translation despite unfavorable circumstances. It is known that ARSs can misactivate tRNAs with structurally similar amino acids3, but editing activity ensures extreme specificity under physiological conditions.4,5 Given the structural similarities between isoleucine and valine, we speculated that isoleucyl-tRNA synthetase (IARS1) would misacylate tRNAIle with valine under isoleucine restriction, leading to I>V substitutions in the proteome. Not only did these substitutions occur in healthy primary human cells, but they also preserved translation and promoted cell viability upon nutritional stress.

2024-11-26 | PXD033426 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data