Human tRF & tiRNA sequencing in serum of sarcoidosis
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ABSTRACT:
PROVIDER: PRJNA815634 | ENA |
REPOSITORIES: ENA
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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
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
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
Project description:We first analyzed tsRNA signatures in SLE serum and identified that tRF-His-GTG-1 was significantly upregulated in SLE serum. The combination of tRF-His-GTG-1 and anti-dsDNA could serve as biomarkers for diagnosing SLE with a high AUC of 0.95 (95% CI=0.92-0.99), sensitivity (83.72%) and specificity (94.19%). Importantly, the non-invasive serum tRF-His-GTG-1 could also be used to distinguish SLE with LN or SLE without LN with AUC of 0.81 (95% CI, 0.73–0.88) and performance (sensitivity 66.27%, specificity 96.15%). Moreover, the serum tsRNA is mainly secreted via exosome and directly target signaling molecules that play crucial roles in regulating the immune system.
2021-11-09 | GSE179950 | GEO
Project description:We digested and extracted tissue exosomes from fresh ectopic endometrial tissue and control endometrial tissue, and analyzed the expression of tRF&tiRNA in the two groups of exosomes through high-throughput sequencing
2021-10-07 | GSE185273 | GEO
Project description: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.
2021-05-19 | GSE168270 | GEO
Project description:Human tRF & tiRNA sequencing of SLE and LN patients
| PRJNA745976 | ENA
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
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
Project description:tRF and tiRNA profiles in lung adenocarcinoma.
| PRJNA706712 | ENA