Similar Datasets
Project description:To screen miRNAs for potential NDRG2 regulation, we performed micronome profiling in 3 pairs of SACC samples and the corresponding normal salivary glands. The sequencing analysis generated approximately 1,000,000 clean reads per sample. All reads were mapped to annotated miRNAs in the miRBase database (version 22), whereas approximately 45% of the clean reads were mapped to mature miRNAs in the database. After applying a stringent filtering criterion to compare the results from SACC tumor tissue and the adjacent normal salivary glands (log2 fold change >1, FDR<0.05), we identified 176 dysregulated miRNAs.
2018-12-25 | GSE117275 | GEO
Project description:To understand the role of RBM10 in the apoptosis of vascular smooth muscle cells (VSMC), we quantified the whole genome transcriptomes of VSMC that were treated by Rbm10 adenovirus (n=3) or control (n=3) for 24 h using RNA-seq. In total, we obtained over 60 million clean reads from each library after trimming adaptor sequences, low quality reads and multiple mapped reads. The clean reads were mapped to 58337 genes annotated in the human reference genome.
2021-11-07 | GSE188258 | GEO
Project description:The CUT&Tag and high-throughput sequencing technologies were used in this experiment. Results showed that 54857512-63235094 clean reads were obtained in this study.
2020-12-05 | GSE162661 | GEO
Project description:Purpose: Cucumber (Cucumis sativus L.) is an economically important vegetable crop worldwide, and cucumber fruit spine density has an important impact on the commercial value. However, little is known about the regulatory mechanism for the fruit spine formation.In this study, the transcriptome analyses of ovaries and pericarps from numerous-spine parent and few-spine parent were conducted to identify the gene regulatory networks involved in the formation and development of numerous fruit spines in cucumber. Methods: Cucumber mRNA profiles of ovaries and pericarps from numerous-spine parent and few-spine parent were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. Then, clean data (clean reads) were obtained by removing reads containing adapters, reads containing poly-N sequences and low-quality reads from the raw data. Simultaneously, the Q20, Q30 and GC contents of the clean data were calculated. All of the downstream analyses were based on the high-quality clean data. Clean paired-end reads were mapped to the reference genome using TopHat v2.0.12 (Trapnell et al. 2012). Then, the FPKM (fragments per kilobase of transcript sequence per million base pairs sequenced) value of each gene was calculated to estimate gene expression levels (Trapnell et al. 2010). Genes with an adjusted P-value < 0.05 identified by DESeq were assigned as differentially expressed genes(DEGs). Results: We generated 42.96-57.53 million raw reads from each library, and 39.85-54.02 million clean reads were obtained after the removal of low-quality reads and adapter sequences. Among the clean reads, 79.03-80.94% were mapped to the gene database . Based on the KEGG database, pathway enrichment analysis was performed to identify significantly enriched metabolic pathways or signal transduction pathways in DEGs. Plant hormone signal transduction was significantly enriched in up-regulated genes in both F_6DBF compared with M_6DBF and F_0DAA compared with M_0DAA. Conclusions: Based on the transcriptome analysis, we excavated possible biological regulatory networks involved in the formation and development of numerous fruit spines in cucumber. This work will promote the exploration of molecular mechanisms that regulate cucumber fruit spine density.
2018-01-27 | GSE109615 | GEO
Project description:De-multiplexing the unique identifiers discovered data consisted of 28,808,716 clean reads from fruit samples at 40 DAF, 27,941,132 reads from 65 DAF, and 25,457,565 reads from fruit sample at 90 DAF.
2016-01-27 | GSE77218 | GEO
Project description:We established three new rhesus embryonic stem cells lines and conducted their microRNA profilings by Solexa sequencing. Sequencing of small RNA libraries yielded 12.66 million, 13.12 million and 11.57 million raw reads from IVF1.2, IVF3.2 and IVF3.3, respectively. After filtering, we obtained 10.89 million (IVF1.2), 10.60 million (IVF3.2) and 9.26 million (IVF3.3) clean reads (18-30nt).
2011-06-20 | GSE27886 | GEO
Project description:Summary taken from our paper “Aspergillus terreus Sectorization: A Morphological Phenomenon Shedding Light on Amphotericin B Resistance Mechanism”: WT and ATSec strains were grown in AMM broth for 30 h at 30 °C. Afterwards, the cultures were subjected to either DMSO (control) or 1 µg/ml AmB treatment for 1 h/4 h. Triplicates of each combination of these factors were made, resulting in a total of 24 samples. RNA was extracted with a Promega GmbH kit (Madison, Wisconsin, USA) following the manufacturer’s instructions. The RNA-seq experiment was conducted by BGI, generating a total of around 20 million 100bp paired-end reads with the DNBSEQ platform. BGI employed SOAPnuke (51) to remove rRNA, adaptor-containing sequences, low quality reads, and reads with high unknown nucleotide content, producing "clean reads" datasets that were used in the analysis. On average, clean read datasets contain 45.1 Mb of reads, while the raw read datasets contain 48.7 Mb. For clean reads, the mean Q20 value is 98.3%, and the mean Q30 value is 92.5%.
2024-09-25 | GSE277670 | GEO
Project description:Purpose: We aimed to dissect response of Perennial_ryegrass to drought, heat and cold stresses and identify stress responsive genes in Perennial_ryegrass. Methods: The sequencing libraries was constructed using NEBNext® UltraTM RNA Library Prep Kit for Illumina®, sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated. Clean data (clean reads) were obtained after removing reads containing poly-N or adapter, and low quality reads from raw data. Transcriptome assembly was accomplished based on the left.fq.gz and right.fq.gz using Trinity. Gene function was annotated based on the following databases: NR (NCBI non-redundant protein sequences), Pfam (Protein family), KOG/COG/eggNOG (Clusters of Orthologous Groups of proteins), Swiss-Prot (A manually annotated and reviewed protein sequence database), KEGG (Kyoto Encyclopedia of Genes and Genomes) and GO (Gene Ontology). Differential expression analysis of two groups was performed using the DESeq R package (1.10.1). Genes with an adjusted P-value<0.05 and fold change>2 found by DESeq were assigned as differentially expressed. Results:In total, four samples with two biological replicates per genotype/treatment combination were used for RNA sequencing analysis. At least 5 G clean bases were generated for each sample.After sequencing quality control, a total 137822219 clean reads and 41.05 G clean bases were generated. The Q30 base percentage of each sample was higher than 91.0% (Table S1). A total of 32840 unigenes were obtained after transcriptome assembly. Comparative analysis identified genes modulated by drought, heat and cold stresses
2020-11-08 | GSE141654 | GEO