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Degradome sequence data

ABSTRACT: To identity the targets of miRNAs, we bundled 12 samples from different developing satages into four mixture samples. These samples were used to cosntruct degradome libraries and preform degradome sequencing on Illumina Hi-seq 2000 analyzer. More than 44.98 millions clean reads were obtained and 33.52 million reads were mapped to the soybean cDNA. The mapped reads were used to identity miRNA targets by CleaveLand4 pipeline. 4 degradome mixed samples, no replicates, but every degradome data consists of two parts data. Please note that every degradome sample has two processed and two raw data files. To have enough data, additional sequencing was performed from each sample library. And each sample raw data was processed separately (tissue_name*degradome.txt) and also combined (all_degradome*.txt).

ORGANISM(S): Glycine max

SUBMITTER: Zhixi Tian

PROVIDER: E-GEOD-72903 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Global investigation of the co-evolution of MIRNA genes and microRNA targets during soybean domestication.

Liu Tengfei T Fang Chao C Ma Yanming Y Shen Yanting Y Li Congcong C Li Qing Q Wang Min M Liu Shulin S Zhang Jixiang J Zhou Zhengkui Z Yang Rui R Wang Zheng Z Tian Zhixi Z

The Plant journal : for cell and molecular biology 20160201 3

Although the selection of coding genes during plant domestication has been well studied, the evolution of MIRNA genes (MIRs) and the interaction between microRNAs (miRNAs) and their targets in this process are poorly understood. Here, we present a genome-wide survey of the selection of MIRs and miRNA targets during soybean domestication and improvement. Our results suggest that, overall, MIRs have higher evolutionary rates than miRNA targets. Nonetheless, they do demonstrate certain similar evol ...[more]

PMID: 26714457

Similar Datasets

degradome sequence data

Project description:To identity the targets of miRNAs, we bundled 12 samples from different developing satages into four mixture samples. These samples were used to cosntruct degradome libraries and preform degradome sequencing on Illumina Hi-seq 2000 analyzer. More than 44.98 millions clean reads were obtained and 33.52 million reads were mapped to the soybean cDNA. The mapped reads were used to identity miRNA targets by CleaveLand4 pipeline.

2017-05-01 | GSE72903 | GEO

Endogenous miRNA targets identified by sequencing of the Soybean degradome

Project description:To identify more targets in soybean, particularly specific targets of Cd-stress-responsive miRNAs, high-throughput degradome sequencing was used. In total, we obtained 8913111 raw reads from the library which was constructed from a mixture of four samples (HX3-CK, HX3-Cd-treatment, ZH24-CK and ZH24-Cd-treatment). After removing the reads without the CAGAG adaptor, 5430126 unique raw-reads were obtained. The unique sequences were aligned to the G. max genome database, and 6516276 reads were mapped to the genome. The mapped reads from the libraries represented 51481 annotated G. max genes.

2013-12-20 | GSE50063 | GEO

Endogenous miRNA targets identified by sequencing of the Soybean degradome

2013-12-20 | E-GEOD-50063 | biostudies-arrayexpress

RNA Sequencing analysis of transcriptomics to investigate the bile stress response in L. paracasei L9

Project description:Purpose: To understand the bile salts resistance mechanisms in L. paracasei L9 Methods: Samples from L9 cultured with or without bile salts were sequenced on an Illumina Hiseq platform. Three independent biological replicates were produced including 6 samples in total. Results: Raw data were firstly processed through in-house perl scripts to generate clean data, and then clean date were mapped to the reference genome, getting about 8-10 million total mapped reads per sample.

2018-01-17 | GSE108713 | GEO

RNA sequencing analysis of transcriptomics to study the growth of Lactobacillus salivarius Ren in raffinose

Project description:Purpose: To understand the metabolic mechanism of Lactobacillus salivarius Ren in raffinose Methods: Samples of Lactobacillus salivarius Ren grown in glucose and raffinose were sequenced on the Illumina Hiseq platform. Three independent biological replicates were generated, including a total of six samples. Results: Raw data were firstly processed through in-house perl scripts to generate clean data, and then clean date were mapped to the reference genome, getting about 8-10 million total mapped reads per sample.

2018-11-14 | GSE122483 | GEO

Specific modulation of HIV RNA splicing and upregulation of anti-inflammatory miR-124 by the new drug candidate ABX464

Project description:Purpose: To ensure that ABX464 acted specifically on HIV splicing and did not significantly or globally affect the splicing events of human genes, we used a high-throughput RNAseq approach. Many genome-wide expression studies of HIV infection are based on analyses of total peripheral blood mononuclear cells (PBMCs), which consist of over a dozen cell subsets, including T cells, B cells, NK cells and monocytes Methods: The CD4 T cells were uninfected or infected with the YU2 strain and were untreated or treated for 6 days with ABX464, followed by high-throughput RNAseq. Each raw dataset of the samples contained between 44 and 105 million single-end reads (50 bp), with an average of approximately 60 million raw reads per sample Results: Approximately 98% of the total raw reads were mapped to the human genome sequence (GRCh38), giving an average of 60 million human reads per sample for further analyses. The reads that were correctly mapped (approximately 98% of total input reads) to the gene and transcript locations (GTF annotation file) Conclusions: The MDS of our gene expression data showed, without any outliers, that the different donors segregated well and distributed into the DMSO (untreated) and ABX464 treatments that were infected or uninfected. The displayed variance was donor-dependent (clustered by donor) but treatment-independent (no data structure related to the different treatments), which suggests that the ABX464 molecule did not induce a major difference in CD4 T cell gene expression.

2018-06-22 | GSE116073 | GEO

Degradome analysis in Phalaenopsis aphrodite subsp. formosana

Project description:We performed one degradome sequencing for identification and characterization of novel microRNAs in Phalaenopsis aphrodite subsp. formosana. Plant tissues of leaves, stalk, and flower buds frozen in liquid nitrogen were ground to fine powder using a mortar and pestle, respectively. Total RNA extraction was freshly prepared using Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer's instructions. About 50 Î¼g of leaves with or without low temperature treatment, stalks and flower buds were taken separately and then mixed. The degradome library was constructed by the Genomics BioSci & Tech. Company following the manufactoring protocol. In brief, 200 Î¼g of total RNA was passed though polyA column using the Oligotex kit (Qiagen). The 5'-RNA adapter containing a Mme I recognition site was ligated by T4 RNA ligase and further reverse transcribed to amplify the templates. After digesting with Mme I then ligated to a 3'-double DNA adapter, the products were amplified by additional PCR cycles and gel-purified for Illumina sequencing. The files contain the raw data of degradome sequencing. Examination of one degradome of mixed tissues of Phalaenopsis orchid

2012-11-06 | E-GEOD-35739 | biostudies-arrayexpress

RNA-sequencing reveals transcriptional signature of pathological remodeling in the diaphragm of rats after myocardial infarction

Project description:Purpose: In the current study, we used RNA-Seq to determine the transcriptional changes and understand the genetic reprogramming of the diaphragm in the chronic phase post-myocardial infarction. Methods: Rat diaphragm mRNA profiles 16 weeks post Sham and Myocardial infarction (MI) surgeries were generated by deep sequencing using llumina NextSeq 500. The sequence reads that passed quality filters were analyzed at the transcript level with TopHat followed by Cufflinks. Results: After quality control and data filtering, on average, 33,972,308 raw reads per sample were obtained. For each sample, 88.49 % to 91.70 % reads were uniquely mapped to the rat reference genome. Median CV coverage uniformity was 0.45± 0.01. Distribution of mapped reads over DNA regions showed 48% of reads mapped to coding region, 20% of reads mapped to untranslated region (UTR), 12% of reads mapped to intron region, and 20% reads mapped to intergenic region. The resulting Sham and MI transcriptomes, created from generated transcriptomes of each individual sample in each group and merged transcriptomes within the same group, were used for differential gene expression analysis. A total of 112 differentially expressed genes (DEGs) were identified out of a total of 9664 genes with measured expression in MI and Sham groups. Among DEGs, 42 were upregulated and 70 were downregulated in the MI group. Hierarchical clustering heat map, pathway enrichment and gene ontology (GO) analyses, and analysis of DEGs in the framework skeletal muscle-specific biological networks were performed. Conclusions: Our study represents the first detailed analysis of diaphragm transcriptomes post-myocardial infarction generated by RNA-Seq technology.

2020-12-31 | GSE141859 | GEO

Comparative expression profiling of miRNA during anther development in genetic male sterile and wild type cotton [degradome]

Project description:In this study, in order to identify miRNA targets, a degradome library derived from anthers of the WT and GMS (Genetic Male Sterility) mutant representing three stages of development was constructed and sequenced, resulting in the generation of 24.6 million raw reads. After removal of low quality sequences and adapter sequences, 24.4 million clean reads were obtained and 98% were 20 or 21 nt in length as expected in that normally length distribution peak of degradome fragment is between 20 and 21 nt [Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ: Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol 2008, 18:758-762].

2013-07-28 | GSE43389 | GEO

WT colonic scRNA-seq experiment [re-analysis]

Project description:The GSE114044 data was re-mapped and re-analyzed. Duplicated sample records were created for the convenient retrieval of the complete raw data from SRA.

2020-08-24 | GSE146042 | GEO

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