Search results : 17475
Recent Polyploidization Events in Three Saccharum Founding Species
Sugarcane (Saccharum spp.) contributes 70% of worldwide sugar production and is becoming increasingly important as a first generation biofuel crop. The complexity of the autopolyploid Saccharum genome hindered the progress of genome research and crop improvement. To understand the genome structure and organization of the Saccharum genome, RNAseq was used to sequence the transcriptomes of 59 individuals in a segregating F1 population derived from S. officinarum LA Purple (2n = 80, x = 10) and S. robustum Molokai5829 (2n = 80, x = 10), yielding a total of 1.9 billion reads. 11,157 and 8,998 single nucleotide polymorphisms (SNPs) markers were generated for LA Purple and Mol 5829, respectively, resulting in two high density linkage maps consisting of 83 linkage groups (LGs) for S. officinarum and 105 LGs for S. robstum. The majority of markers in each LG of S. officinarum and S. robustum could be aligned to single sorghum chromosome, indicating that these two Saccharum species share a similar chromosome structure with sorghum. Interchromosomal translocations were found to be common in the LGs, 14.1% (654) and 8.7% (268) of marker loci were detected to be interchromosomal translocations in sorghum-S. officinarum and sorghum-S. robustum, respectively. Moreover, only 10 (12%) and 25 (24%) LGs were all homologs of a single Sorghum chromosome, and intrachromosomal rearrangements were detected in all LGs of LA Purple and Mol 5829. At least 43 interchromosomal rearrangements detected in Saccharum-sorghum, were shared with S. officinarum and S. robustum, indicating that polyploidization occurred after their speciation event. RNAseq data from S. spontaneum were analyzed to estimate the divergence time of these two Saccharum species. The speciation event separating S. officinarum and S. robustum occured about 377 thousand years ago, and the two rounds of whole genome duplication events occured less than 377 thousand years ago. The common ancestor of S. officinarum and S. robustum diverged from S. spontaneum about 770 thousand years ago. Polyploidization events were less than 377,000 years in S. officinarum and S. robustum, and less than 770,000 years in S. spontaneum. Our results provide a clear sequence of the two speciation events separating the three founding species of the genus Saccharum, and prove that S. officinarum is a legitimate species in its own right, and not a selection from S. robustum during the domestication process in the past 10,000 years.
Taxonomy: Saccharum officinarum   Project data type: Transcriptome or Gene expression
Submitter: Qing Zhang    Date released: 2017-06-21
Accession: PRJCA000477
Resource: Project
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Taxonomy: Ailuropoda melanoleuca   Project data type: Whole genome sequencing
Submitter: a c b    Date released: 2017-06-19
Accession: PRJCA000473
Resource: Project
m6A modulates haematopoietic stem and progenitor cell specification
With data of MeRIP-seq, miCLIP-seq, RNA-seq and RIP-seq in zebrafish embryos at 28 hpf, we aim to uncover the indispensable function of m6A modification in the fate determination of HSPCs during vertebrate embryogenesis.
Taxonomy: Danio rerio   Project data type: Transcriptome or Gene expression
Submitter: sun baofa    Date released: 2017-06-08
Accession: PRJCA000469
Resource: Project
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Taxonomy: Homo sapiens   Project data type: Whole genome sequencing
Submitter: li cp    Date released: 2017-06-06
Accession: PRJCA000468
Resource: Project
Gastrointestinal microbial ecosystem restoration
Ecological restoration of antibiotics disturbed gastrointestinal microbial ecosystem with microbiota transplant
Taxonomy: gut metagenome   Project data type: Whole genome sequencing
Submitter: Hui Yan    Date released: 2017-06-03
Accession: PRJCA000455
Resource: Project
Population Genomics of Pakistan
Due to harboring high genetic and cultural diversity of populations, Central Asia is one key area for understanding the recent evolutionary history of humans. In this project, our aims include: (1) to resequence genome sequences with high sequencing depth for Central Asian populations Pakistan; (2) to discern the genomic diversity, populations structure and demographic history of Pakistan; (3) to investigate the genetic mechanisms for local adaptations in Pakistan.
Taxonomy: Homo sapiens   Project data type: Whole genome sequencing
Submitter: Min-Sheng Peng    Date released: 2017-06-01
Accession: PRJCA000456
Resource: Project
Population Genomics of Balti
Due to harboring high genetic and cultural diversity of populations, Central Asia is one key area for understanding the recent evolutionary history of humans. In this project, our aims include: (1) to resequence genome sequences with high sequencing depth for Central Asian populations Balti; (2) to discern the genomic diversity, populations structure and demographic history of Balti; (3) to investigate the genetic mechanisms for local adaptations in Balti.
Taxonomy: Homo sapiens   Project data type: Whole genome sequencing
Submitter: Min-Sheng Peng    Date released: 2017-06-01
Accession: PRJCA000457
Resource: Project
Population Genomics of Kyrgyz
Due to harboring high genetic and cultural diversity of populations, Central Asia is one key area for understanding the recent evolutionary history of humans. In this project, our aims include: (1) to resequence genome sequences with high sequencing depth for Central Asian populations Kyrgyz; (2) to discern the genomic diversity, populations structure and demographic history of Kyrgyz; (3) to investigate the genetic mechanisms for local adaptations in Kyrgyz.
Taxonomy: Homo sapiens   Project data type: Whole genome sequencing
Submitter: Min-Sheng Peng    Date released: 2017-06-01
Accession: PRJCA000458
Resource: Project
Resequencing on a modified MAGIC population of maize
A modified MAGIC population consist of 1404 individuals derived from twenty-four elite lines that have been widely applied in Chinese breeding programs has been developed, and all progenies and founders have been sequenced at low coverage (1x and 11x, respectively). DNA libraries were sequenced with Illumina HiSeq 2500 with 125-bp paired-end reads using V4 reagents, generating almost 2000x genome coverage.
Taxonomy: Zea mays   Project data type: Whole genome sequencing
Submitter: Jingyun Luo    Date released: 2017-06-01
Accession: PRJCA000346
Resource: Project
Y chromosome sequences of C3-F8894
Y-chromosome sequences of ten C3-F8894 samples, including eight samples with DYS448 deletion.
Taxonomy: Homo sapiens   Project data type: Whole genome sequencing
Submitter: Yunzhi Huang    Date released: 2017-05-31
Accession: PRJCA000419
Resource: Project
Rangier tarandus Genome sequencing
Here, we firstly reported a comparable high-quality genome of reindeer in China, which improves us to understand these biological appearance.The draft genome could serve as a valuable resource for research of the evolution and semi-domesticated of reindeer
Taxonomy: Rangifer tarandus   Project data type: Whole genome sequencing
Submitter: lin ze shan    Date released: 2017-05-20
Accession: PRJCA000451
Resource: Project
whole-genome sequencing
An unusual de novo mutation pattern as revealed by genome sequencing analyses of a Han family quartet from China
Taxonomy: Homo sapiens   Project data type: Whole genome sequencing
Submitter: lei xiaoyun    Date released: 2017-05-15
Accession: PRJCA000446
Resource: Project
Expression profiling of SCC15 cells treated by PAM
To reveal the signaling pathways, PAM was utilized to treat oral cancer cell SCC15 at an early time. Gene expression profiles were evaluated using RNA-seq to reveal the global response of PAM stimulation. QRT-PCR was carried out to validate the expression levels of selected genes. More than 6G clean data per sample were obtained in PAM-treated cancer cells. A total of 934 differentially expressed genes (DEGs) were identified and GO analysis implicated deeply involvement of signal transduction process.
Taxonomy: Homo sapiens   Project data type: Transcriptome or Gene expression
Submitter: Lei Shi    Date released: 2017-05-11
Accession: PRJCA000445
Resource: Project
Shuhui498 rice genome sequencing and assembly
Sequencing and de novo assembly of a near complete indica rice genome
Taxonomy: Oryza sativa   Project data type: Whole genome sequencing
Submitter: yan li    Date released: 2017-05-08
Accession: PRJCA000313
Resource: Project
MTBC
Comparative genomic analysis of Mycobacterium tuberculosis complex (MTBC)
Taxonomy: Mycobacterium tuberculosis complex bacterium   Project data type: Whole genome sequencing
Submitter: Xinmiao Jia    Date released: 2017-05-01
Accession: PRJCA000307
Resource: Project
RNA m5C sequencing in human HeLa cells and mouse tissues
By m5C sequencing in human HeLa cells and mouse tissues, we aimed to uncover RNA distributive features in whole mRNA transcriptomes and its tissue-specific and dynamic features across mammalian transcriptomes.
Taxonomy: Homo sapiens   Project data type: Epigenomics
Submitter: sun baofa    Date released: 2017-04-30
Accession: PRJCA000315
Resource: Project
Hypoxia-activated signaling pathways contribute to scleral myofibroblast differentiation and myopia development
Scleral fibroblasts/myofibroblast play important roles in extracellular matrix remodeling during myopia development. However, it is with uncertainty how myopia-induced vision bluring from retina triggers sclera ECM remodeling and whether or not changes in myofibroblast function underlie myopia progression. In this study, we identified gene expression changes associated with increase in myofibroblast population during myopia development. The proportion of myofibroblast-like cells (A2) increased in T eyes, suggesting a phenotypic shift towards A2 cells mediated by enhanced differentiation of fibroblasts (A1) into myofibroblasts. The myofibroblasts differentiated during myopia express lower levels of collagen. This shift was mimicked by exposing fibroblasts to two different in vitro hypoxic models. Pathway analysis revealed that the major functional differences between these two subpopulations arise from activation of eIF2 signaling, mTOR signaling and hypoxia signaling in cardiovascular system which were further validated in myopia animal models. Our results indicate that myopia development induces differentiation of myofibroblasts that may be affected by scleral hypoxic condition. It provides strategies to control myopia progression at an early stage via regulating scleral microenvironment.
Taxonomy: Mus musculus   Project data type: Transcriptome or Gene expression
Submitter: Lili Deng    Date released: 2017-04-24
Accession: PRJCA000432
Resource: Project
A549 cell transcriptome response to infection with H7N9 influenza virus. (human)
mRNA-Seq analysis was used to profile the cellular transcriptome of A549 cells at multiple time points in response to infection with influenza H7N9 (A/Anhui/1/2013).
Taxonomy: Homo sapiens   Project data type: Transcriptome or Gene expression
Submitter: Yingying Cao    Date released: 2017-04-19
Accession: PRJCA000428
Resource: Project
A Comprehensive Mouse Transcriptomic BodyMap by RNA-seq
The mouse has been widely used as a model organism for studying human diseases and for evaluating drug safety and efficacy. Many diseases and drug effects exhibit tissue specificity that may be reflected by tissue-specific gene-expression profiles. Here we construct a comprehensive mouse transcriptomic BodyMap across 17 tissues of six-weeks old C57BL/6JJcl mice using RNA-seq. We find different expression patterns between protein-coding and non-coding genes. Liver expressed the least complex transcriptomes, that is, the smallest number of genes detected in liver across all 17 tissues, whereas testis and ovary harbor more complex transcriptomes than other tissues. We report a comprehensive list of tissue-specific genes across 17 tissues, along with a list of 4,781 housekeeping genes in mouse. In addition, we propose a list of 27 consistently and highly expressed genes that can be used as reference controls in expression-profiling analysis. Our study provides a unique resource of mouse gene-expression profiles, which is helpful for further biomedical research.
Taxonomy: Mus musculus   Project data type: Transcriptome or Gene expression
Submitter: leming shi    Date released: 2017-04-19
Accession: PRJCA000427
Resource: Project
salinity stress responsive miRNAs in wild emmer wheat
To obtain more information on miRNAs in wild emmer, we systematically investigated and characterized the salinity-responsive miRNAs in wild emmer using deep sequencing technology.
Taxonomy: Triticum dicoccoides   Project data type: Transcriptome or Gene expression
Submitter: Kewei Feng    Date released: 2017-04-19
Accession: PRJCA000426
Resource: Project
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