Search results : 11267
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
Pandon Genome
Pandon genome
Taxonomy: Corydoras panda   Project data type: Whole genome sequencing
Submitter: yang fan    Date released: 2017-04-16
Accession: PRJCA000389
Resource: Project
1
13
Taxonomy: Homo sapiens   Project data type: Whole genome sequencing
Submitter: yang fan    Date released: 2017-04-11
Accession: PRJCA000418
Resource: Project
1
1
Taxonomy: Homo sapiens x Mus musculus hybrid cell line   Project data type: Whole genome sequencing
Submitter: yang fan    Date released: 2017-04-11
Accession: PRJCA000417
Resource: Project
A Comparative Transcriptomic Analysis of Uveal Melanoma and Normal Uveal Melanocyte
Uveal melanoma is the most common primary intraocular tumor in adults in western countries. It is associated with very severe visual morbidity and may lead to distant metastases even after successful treatment of the primary tumor. In order to gain better insight into molecular mechanisms related to tumorigenesis and metastasis of uveal melanoma, we used next-generation sequencing technology (SOLiD, Life Technologies) to acquire global transcriptome alteration between posterior uveal melanoma cells and normal uveal melanocyte.We have identified a large number of potentially interesting genes for biological investigation of uveal melanoma. The expression profiling also provides useful resources for other functional genomic and transcriptome studies.
Taxonomy: Homo sapiens   Project data type: Transcriptome or Gene expression
Submitter: gl wang    Date released: 2017-04-11
Accession: PRJCA000416
Resource: Project
Comprehensive simulation of metagenomic sequencing data with non-uniform sampling distribution
We developed a non-uniform Metagenomic sequencing Simulation system (nuMetaSim) that is capable of mimicking various factors in real metagenomic sequencing to reflect multiple properties of real data with customizable parameter settings. We generated 9 comprehensive metagenomic datasets with different composition complexity from of 203 bacterial genomes and 2 archaeal genomes related with human intestine system. The data can serve as benchmarks for comparing performance of different methods at different situations, and the software package allows users to generate simulation data that can better reflect the specific properties in their scenarios.
Taxonomy: bacterial mixed DNA library   Project data type: Metagenome
Submitter: Shansong Liu    Date released: 2017-04-06
Accession: PRJCA000415
Resource: Project
ascsdfg
ascsdfgascsdfgascsdfgascsdfg
Taxonomy: Ascarina marquesensis   Project data type: Whole genome sequencing
Submitter: zhang kaihua    Date released: 2017-04-01
Accession: PRJCA000434
Resource: Project
Target sequencing for Chinese autism cases
Target sequencing for over 200 autism risk genes in >1600 Chinese autism cases.
Taxonomy: Homo sapiens   Project data type: Targeted Locus (Loci)
Submitter: tianyun wang    Date released: 2017-03-28
Accession: PRJCA000408
Resource: Project
Genetic load in cancer cells
Our results suggest that the cancer cells must maintain a delicate balance to keep heterogeneity and to curb the relentlessly increased passenger mutations.
Taxonomy: Homo sapiens   Project data type: Whole genome sequencing
Submitter: Yawei Li    Date released: 2017-03-27
Accession: PRJCA000406
Resource: Project
Targeted sequencing and functional analysis reveal a potentially shared pathogenesis in autism spectrum disorders
Autism spectrum disorder (ASD) represents a set of complex neurodevelopmental disorders with large degrees of heritability and heterogeneity. We sequenced 136 microcephaly or macrocephaly (Mic-Mac)-related genes and 158 possible ASD-risk genes in 536 Chinese ASD probands and detected 22 damaging de novo mutations (DNMs) in 20 genes, including CHD8 and SCN2A, with recurrent events. Nine of the 20 genes were previously reported toreportedly harbour DNMs in ASD patients from other populations, and while 11 genes of them were first identified here for the first timein present study. We combined genetic variations of the 294 sequenced genes from publicly available whole-exome or whole-genome sequencing studies (4,167 probands plus 1,786 controls) with our Chinese population (536 cases plus 1,457 controls) to optimize the power of candidate-gene prioritization. As a result, we prioritized 67 ASD-candidate genes that exhibited significantly higher probabilities of haploinsufficiency and genic intolerance, and significantly interacted and co-expressed with each another, as well as other known ASD-risk genes. Probands with DNMs or rare inherited mutations in the 67 candidate genes exhibited significantly lower intelligence quotients, supporting their strong functional impact. Additionally, we prioritized 39 ASD-related Mic-Mac-risk genes, and showed their that interactioned and co-expressed expression with each other, as well other known Mic-Mac- or ASD-risk genes, and formedin a functional network that converged on chromatin remodelling, synapse transmission, and cell cycle progression. Genes within the three functional subnetworks exhibited distinct and recognizable spatiotemporal-expression patterns in human brains and laminar-expression profiles in the developing neocortex, highlighting their important roles in brain development.
Taxonomy: Homo sapiens   Project data type: Variation
Submitter: Jinchen Li    Date released: 2017-03-25
Accession: PRJCA000393
Resource: Project
o2n-seq
o2n-seq, an ultrasensitive and high-efficiency NGS library preparation method for discovering de novo, low-frequency mutations.
Taxonomy: Escherichia coli   Project data type: Whole genome sequencing
Submitter: Kaile Wang    Date released: 2017-03-24
Accession: PRJCA000397
Resource: Project
Total Records: 11267 Items of 1-20 Page size Page 1/564 << First < Prev Next > Last >> Jump To