Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

TRF and tiRNA profiles in lung adenocarcinoma.

ABSTRACT: We investigate tRF and tiRNA profiles in lung adenocarcinoma and adjacent tissues using a NextSeq system. Total RNA was extracted from tissues and pretreated to remove the RNA modifications. In patients with lung adenocarcinoma, 338 types of tRFs and tiRNAs were detected via sequencing, 284 of which were not previously reported. Compared with the adjacent tissues, 17 types of tRFs and tiRNAs comprising 34 subtypes were found to be abnormally expressed in lung adenocarcinoma tissues, 20 of which were upregulated and 14 of which were downregulated. Finally, we show that tRF and tiRNA profiles in lung adenocarcinoma and adjacent tissues and identify several dysregulated tRFs and tiRNAs.

ORGANISM(S): Homo sapiens

PROVIDER: GSE168270 | GEO | 2021/05/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

tRF&tiRNA sequencing of human PTC tissues and corresponding paracancer tissues

Project description:Purpose: To study the expression and potential significance of tRF and tiRNA in PTC (Papillary thyroid carcinoma) by sequencing tRF and tiRNA in PTC tissues and corresponding paracancer tissues of thyroid cancer patients. Methods: Four pairs of PTC tissues and paracancer tissues were collected. Small RNA sequencing was performed on Illumina NexSeq instrument. Results: If P ≤ 0.05, fold change > 1.5 as the cutoff, there were 27 up-regulated tRFs & tiRNAs and 20 down-regulated tRFs & tiRNAs. Conclusions: Among the differentially expressed tRFs & tiRNAs, tiRNA-1:34-Lys-CTT-2 and tRF-1:30-Gly-CCC-3 may be the potential novel regulatory factors.

2022-02-26 | GSE197438 | GEO

tRF & tiRNA sequencing of breast cancer tissue samples and matched non-tumor adjacent tissues

Project description:Purposes: To investigate the biological function of tRF in breast cancer by tRF and tiRNA sequencing Methods: Breast cancer tissue samples and matched non-tumor adjacent tissues were obtained from five patients. Small RNA sequencing was performed on Illumina NexSeq instrument Results: If P ≤ 0.05, fold change ≥ 2 as the cut off, there were 3 up-regulated tRFs & tiRNAs and 13 down-regulated tRFs & tiRNAs. Conclusions:There were 3 up-regulated tRFs & tiRNAs and 13 down-regulated tRFs & tiRNAs in breast cancer tissue samples and matching adjacent tissue samples

2022-01-01 | GSE192737 | GEO

tRF & tiRNA sequencing of intestinal biopsies from IBS-D patients

Project description:Purposes: To investigate the epigenetic mechanism of IBS-D(Irritable Bowel Syndrome with Diarrhea) by tRF & tiRNA sequencing in intestinal biopsies of IBS-D patients and healthy volunteers Methods: Five IBS-D and five healthy volunteers were screened, and biopsies were taken under colonoscopy. Small RNA sequencing was performed on Illumina NexSeq instrument Results:If P < 0.05, fold change > 1.5 as the cutoff, there were 14 up-regulated tRFs & tiRNAs and 14 down-regulated tRFs & tiRNAs. Conclusions:There were 14 up-regulated tRFs & tiRNAs and 14 down-regulated tRFs & tiRNAs in intestinal tissues of IBS-D .

2023-11-04 | GSE166405 | GEO

Differences in the tRF & tiRNA Profiles of Sperm after Neonatal Sevoflurane Exposure

Project description:The ncRNAs derived from transfer RNAs (tRNAs), such as tRFs (tRNA-derived fragments) and tiRNAs (tRNA halves), play crucial roles in sperm development, maturation, and function, ultimately affecting the health of offspring. To further elucidate the changes in sperm tRF & tiRNA profiles induced by neonatal sevoflurane exposure, we collected sperm from the caudal epididymis of rats and isolated total RNA for tRF & tiRNA sequencing.

2024-07-05 | GSE271145 | GEO

tRNA-Derived Fragments Expression Profile and Their Potential Roles in Lung Adenocarcinoma Tissues

Project description:Transfer RNA-derived fragments (tRFs) and transfer RNA halves (tiRNAs) have been shown to play crucial roles in gene regulation. This study targets to reveal the expression profile of tRFs and tiRNAs and their possible biological roles in lung adenocarcinoma (LUAD). Five paired clinical lung adenocarcinoma tissues (LAT) and adjacent normal lung tissues (ANLT) were selected to conduct the expression of tRFs and tiRNAs. The sequencing results showed that 109 tRFs and tiRNAs were differentially expressed between LAT and ANLT, out of which 60 were upregulated and 49 were downregulated. Compared with ANLT, lower expression levels of three tRF-1s (tRF-Ser-TGA-010, tRF-Arg-CCT-018 and tRF-Val-CAC-017) in LAT were verified by quantitative real-time polymerase chain reaction. Subsequently, the putative target genes of tRF-1s were analyzed by computational prediction and the top ten significant results of GO and KEGG pathway enrichment analysis were presented. These signaling pathways are involved in the carcinogenesis of LUAD. This study has showed a landscape of tRFs and tiRNAs expression proﬁles in LUAD. Three newly found diﬀerentially expressed down-regulated tRF-1s may be involved in the pathogenesis of LUAD and might serve as potential diagnostic biomarkers.

2022-01-19 | GSE165918 | GEO

Expression of tRF & tiRNA in cholangiocarcinoma by RNA sequencing

Project description:The rapid development of high-throughput sequencing is conducive to the discovery of many new theories. The purpose of this study is to explore the differentially expressed of tRF & tiRNA in cholangiocarcinoma by high-throughput sequencing technology. We collected cholangiocarcinoma and adjacent normal tissues from three patients. After RNA extraction and RNA library preparation, we determined the raw data of tRF & tiRNA in cholangiocarcinoma and adjacent normal tissues by high-throughput RNA sequencing. Raw data were generated after sequencing,image analysis,basecalling and quality filtering on lllumina sequencer.Firstly,Q30 was used to perform quality control.The adaptor sequences were trimmed and the adaptor-trimmed-reads(>=16nt) were left by cut adapt software(v1.9.3).Then,the raw counts of each tRF&tiRNA(MINTbasev2.0) was calculated for all samples,defined as the raw expression level soft.The results showed that a total of 20102 tsRNA were detected in the two groups, 9616tsRNA were upregulated and 10486 were downregulated. There were 535 differentially expressed tsRNA in cholangiocarcinoma after edger standardization, of which 241 were upregulated and 294 were downregulated (| log2 (foldchange) | = 1andpvalue < 0.05). This study shows that high-throughput sequencing technology is helpful for us to determine the expression of tRF & tiRNA in cholangiocarcinoma, and to screen out differentially expressed tRF & tiRNA, and further to explore the factors that affect the progress of cholangiocarcinoma.

2021-10-31 | GSE147017 | GEO

tRF and tiRNA profiles in lung adenocarcinoma.

Project description:tRF and tiRNA profiles in lung adenocarcinoma.

| PRJNA706712 | ENA

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

The differential expression of tRF&tiRNA in eutopic and ectopic endometrial tissue of patients with ovarian endometriosis.

Project description:Endometriosis is a chronic gynecological disease that afflicts millions of women of reproductive age and has traditionally been diagnosed by laparoscopic surgery. This diagnostic barrier delays identification and treatment by years, resulting in prolonged pain and disease progression. Development of a noninvasive diagnostic test could significantly improve timely disease detection. We characterized eutopic and ectopic endometrium from five patients with ovarian endometriosis using tRF&tiRNA sequencing. We identified 294 tsRNAs by RNA microarray technique in eutopic and ectopic endometrium. Under the criteria of |log2FoldChange >2.0| and p-value < 0.05, 11 tRFs/tiRNAs were reported to be dysregulated in ectopic endometrial tissue compared with eutopic endometrial tissue, of which eight were up-regulated, and three were down-regulated.

2023-10-30 | GSE246202 | GEO

Altered Expression Profiles of tRNA-derived fragments in relapsed/refractory multiple myeloma

Project description:tRNA related fragments(tRF) and tRNA halves(tiRNA) are novel class of short non-coding RNA derived from tRNAs. Using RNA sequencing, we evaluated the tRFs/tiRNAs expression profiles in relapsed/refractory multiple myeloma and multiple myeloma patients. Bioinformatics analyses indicated that tRFs/tiRNAs may be involved in the progression and drug-resistance of multiple myeloma.

2021-05-19 | GSE171003 | GEO

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