Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21229053_1.fastq.gz | Fastqsanger.gz | |||
| SRR21229053_2.fastq.gz | Fastqsanger.gz | |||
| SRR21229054_1.fastq.gz | Fastqsanger.gz | |||
| SRR21229054_2.fastq.gz | Fastqsanger.gz | |||
| SRR21229055_1.fastq.gz | Fastqsanger.gz |
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Project description:We report that there are at least 236 known miRNAs expressed in safflower, of which 100 miRNAs with relatively high expression level exhibited evolutionary conservation across multiple plants. Comparison of their expression patterns among different tissues shows that a total of 116, 133 and 128 miRNAs are significantly differentially expressed between safflower seed/leaf, seed/petal and leaf/petal. Meanwhile, interestingly, the majority of the most significantly differentially expressed miRNAs between tissues are tissue-specific miRNAs. In addition, 15 putative novel miRNAs have been identified in safflower. The small RNA transcriptomes obtained in this study provide a basis for further investigation of the physiological roles of identified miRNAs in safflower.
2010-11-06 | GSE25165 | GEO
Project description:WGS of Lactobacilli isolated from Iranian Motal cheese
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Project description:We performed shallow whole genome sequencing (WGS) on circulating free (cf)DNA extracted from plasma or cerebrospinal fluid (CSF), and shallow WGS on the tissue DNA extracted from the biopsy in order to evaluate the correlation between the two biomaterials. After library construction and sequencing (Hiseq3000 or Ion Proton), copy number variations were called with WisecondorX.
2021-11-17 | E-MTAB-10548 | biostudies-arrayexpress
Project description:We report that there are at least 236 known miRNAs expressed in safflower, of which 100 miRNAs with relatively high expression level exhibited evolutionary conservation across multiple plants. Comparison of their expression patterns among different tissues shows that a total of 116, 133 and 128 miRNAs are significantly differentially expressed between safflower seed/leaf, seed/petal and leaf/petal. Meanwhile, interestingly, the majority of the most significantly differentially expressed miRNAs between tissues are tissue-specific miRNAs. In addition, 15 putative novel miRNAs have been identified in safflower. The small RNA transcriptomes obtained in this study provide a basis for further investigation of the physiological roles of identified miRNAs in safflower. Investigate the small RNA transcriptomes in 3 tissues
2010-11-06 | E-GEOD-25165 | biostudies-arrayexpress
Project description:Whole genome sequencing (WGS) of tongue cancer samples and cell line was performed to identify the fusion gene translocation breakpoint. WGS raw data was aligned to human reference genome (GRCh38.p12) using BWA-MEM (v0.7.17). The BAM files generated were further analysed using SvABA (v1.1.3) tool to identify translocation breakpoints. The translocation breakpoints were annotated using custom scripts, using the reference GENCODE GTF (v30). The fusion breakpoints identified in the SvABA analysis were additionally confirmed using MANTA tool (v1.6.0).
2024-02-17 | E-MTAB-12534 | biostudies-arrayexpress
Project description:RNA-Seq technology was used to investigate differences in the gene expression of pectoralis muscle tissue between two chicken breeds (Ross as commercial (rapidly growing) and Isfahani as Iranian local breed (slow-growing)).
2019-07-05 | GSE132299 | GEO
Project description:Background: Post-menopausal obesity is an established risk factor for breast cancer. Consumption of diets high in fat is known to be highly correlated with obesity. In this, we sought to evaluate the interaction(s) between high fat diet, weight gain and mammary carcinogenesis using an obese-resistant and obese-prone rat model with direct correlates to human disease. Methods: Female obese-prone (OP) and obese-resistant (OR) weanling rats were placed on either a low fat (10% kcal) or a high fat (39% kcal) n-6 polyunsaturated (PUFA) safflower diet for 30 days. At post natal day (PND) 50, global gene expression profiling was performed on microdissected mammary epithlelium from one cohort of rats and another cohort of rats were given a single oral gavage of either 7,12-dimethylbenz[a]anthracene (DMBA at 14 mg/kg) or vehicle. Rats were then maintained on the diets and body weights, food consumption and development of mammary lesions were monitored weekly. Results: The DMBA-treated OR rats on the 39% safflower diet had significantly greater incidence of ductal carcinoma-in-situ (DCIS) lesions and significantly greater DCIS multiplicity than DMBA-treated OR rats on the 10% safflower diet. These differences were not seen in the OP strain. Gene expression analysis of mammary ductal epithelium from OR rats on the high fat diet showed significant upregulation of proliferation-related genes compared to those consuming the low fat safflower diet. Again, these differences were not seen in the OP strain. Conclusion: Our findings indicate that consumption of high fat safflower diet enhances mammary carcinogenesis in an OR rat strain through increased proliferation of mammary epithelium at the time of exposure, but not in the OP rat strain. Thus, the diet-induced increase in sensitivity was strain-specific and independent of weight gain or obesity level.
2010-09-25 | GSE21150 | GEO
Project description:we used a combination of bottom-up (BU) and top-down (TD) proteomics approaches to identify and characterize venom protein compositions of Echis carinatus sochureki (ECS) from three different Iranian populations.
2021-01-29 | PXD021183 | Pride
Project description:In principle, whole-genome sequencing (WGS) of the human genome even at low coverage offers higher resolution for genomic copy number variation (CNV) detection compared to array-based technologies, which is currently the first-tier approach in clinical cytogenetics. There are, however, obstacles in replacing array-based CNV detection with that of low-coverage WGS such as cost, turnaround time, and lack of systematic performance comparisons. With technological advances in WGS in terms of library preparation, instrument platforms, and data analysis algorithms, obstacles imposed by cost and turnaround time are fading. However, a systematic performance comparison between array and low-coverage WGS-based CNV detection has yet to be performed. Here, we compared the CNV detection capabilities between WGS (short-insert, 3kb-, and 5kb-mate-pair libraries) at 1X, 3X, and 5X coverages and standardly used high-resolution arrays in the genome of 1000-Genomes-Project CEU genome NA12878. CNV detection was performed using standard analysis methods, and the results were then compared to a list of Gold Standard NA12878 CNVs distilled from the 1000-Genomes Project. Overall, low-coverage WGS is able to detect drastically more (approximately 5 fold more on average) Gold Standard CNVs compared to arrays and is accompanied with fewer CNV calls without secondary validation. Furthermore, we also show that WGS (at ≥1X coverage) is able to detect all seven validated deletions larger than 100 kb in the NA12878 genome whereas only one of such deletions is detected in most arrays. Finally, we show that the much larger 15 Mbp Cri-du-chat deletion can be clearly seen at even 1X coverage from short-insert WGS.
2018-06-26 | GSE105092 | GEO