Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Circular RNA Cdr1as inhibits proliferation and delays injury-induced regeneration of the intestinal epithelium

ABSTRACT: The data analysis includes five parts for the small RNA biotypes: miRNA, tsRNA (i.e. tRF & tiRNA), pre-miRNA, tRNA and snoRNA.

ORGANISM(S): Mus musculus

PROVIDER: GSE250489 | GEO | 2024/01/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

Human tRF & tiRNA sequencing in serum of sarcoidosis

Project description:Transfer-RNA-Derived Small RNA (tsRNA) is a novel class of short non-coding RNA including stress-induced tRNA fragments (tiRNA) and tRNA-derived fragments (tRF). Using RNA sequencing, we evaluated the tsRNA expression profiles in the serum of sarcoidosis (n = 3) compared with healthy control group (n = 3). Bioinformatics analyses indicated that tsRNAs were the important regulators and potential new biomarkers of sarcoidosis.

2022-03-15 | GSE198490 | GEO

Altered Expression Profiles of Transfer-RNA-Derived Small RNAs Reveal the Regulating Functions in Rat Brain After Intracerebral Hemorrhage (ICH) and the Potential Therapeutic Targets of Buyang Huanwu Decoction in ICH

Project description:Transfer-RNA-Derived Small RNA (tsRNA) is s a novel class of short non-coding RNA including stress-induced tRNA fragments (tiRNA) and tRNA-derived fragments (tRF). Using RNA sequencing, we evaluated the tsRNA expression profiles in the brain of intracerebral hemorrhage (ICH) and sham rats at days 21. Meanwhile, tsRNA levels in ICH treated with the Traditional Chinese Medicine named Buyang Huanwu Decoction (BYHWD) were detected. Bioinformatics analyses indicated that tsRNAs were the important regulators in ICH and potential new therapeutic targets of BYHWD.

2018-04-26 | GSE109697 | GEO

Expression profiles of tRNA-derived small RNAs and their potential roles in primary nasopharyngeal carcinoma

Project description:Transfer-RNA-Derived Small RNA (tsRNA) is a novel class of short non-coding RNA including stress-induced tRNA fragments (tiRNA) and tRNA-derived fragments (tRF). Using RNA sequencing, we evaluated the tsRNA expression profiles in the fresh nasopharyngeal carcinoma tissue specimens (n = 4) and mucosal tissue specimens (n = 4) in patients’ primary nasopharyngeal carcinoma (P-NPC) and nasopharyngitis. Bioinformatics analyses indicated that tsRNAs were the important regulators and potential new biomarkers of P-NPC.

2022-01-11 | GSE159746 | GEO

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 expression profile of RPE-choroid-sclera complex in the laser-induced choroidal neovascularization mouse model

Project description:To investigate the tRF/tiRNA expression pattern in the development of choroidal neovascularization, we built a laser-induced choroidal neovascularization mouse model and performed the tRF/tiRNA sequencing on RPE-choroid-sclera complexes at different time points after model establishment, while the tissues from mice without treatment were used as control group.

2022-08-05 | GSE210099 | GEO

Differential Expression Spectrum of tRNA-Derived small RNAs in Idiopathic Pulmonary Arterial Hypertension

Project description:Microarray detected 816 statistically differentially expressed tsRNAs, of which 243 tsRNAs were upregulated and 573 were downregulated. Eight validated tsRNAs in the results of Real Time-PCR were consistent with the small RNA microarray: four upregulations (tRF3a-AspGTC-9, 5'tiRNA-31-GluCTC-16, i-tRF-31:54-Val-CAC-1 and tRF3b-TyrGTA-4) and four downregulation (5'tiRNA-33-LysTTT-4, i-tRF-8:32-Val-AAC-2, i-tRF-2:30-His-GTG-1, and i-tRF-15:31-Lys-CTT-1).

2023-06-30 | GSE228750 | GEO

High-throughput tRF&tiRNA realtime PCR Array for 10 paired gastric cancer tissues and matched noncancerous tissues

Project description:Total RNA was isolated from ten pairs of matched gastric cancer tissues and non-cancerous tissues. RNAs were then pretreated with rtStar™ tRF&tiRNA Pretreatment Kit (Cat# AS-FS-005, Arraystar) and reverse-transcribed with rtStar™ First-Strand cDNA Synthesis Kit. The synthesed cDNA was used for realtime PCR to detect the differential expression of 353 tRF&tiRNA.

2020-12-30 | GSE163988 | 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

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

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