All (1556)
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Samples (1231)
Experiments (151)
Runs (156)
Search results for human : 1556
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
Source: 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
Source: 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
Source: 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
Source: 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
Source: 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
Source: 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
Source: 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
Source: Project
PAR-CLIP-seq of m6A readers
PAR-CLIP sequencing for YTHDF1 and YTHDF3 in human HeLa cells
Taxonomy: Homo sapiens   Project data type: Transcriptome or Gene expression
Submitter: sun baofa    Date released: 2017-01-06
Accession: PRJCA000273
Source: Project
Characterization of MV to identify senescence in human MSC
The senescence in human mesenchymal stem cells (MSCs) contributes to organism aging and the development of a variety of diseases, and severely impairs therapeutic properties of MSCs as a promising cell therapy. The studies searching for efficient biomarkers that practically represent cellular senescence have attracted many attentions; however, no single marker currently provides an accurate and practically cell-free representation of cellular senescence. Here, we studied characteristics of MSC-derived microvesicles (MSC-MVs) regarding their capacities of resembling the senescence in their parental MSCs. We found that senescent late passage (LP) MSCs secreted higher levels of MSC-MVs with smaller size than did early passage (EP) MSCs, and the level of CD105+ MSC-MVs decreased with the senescence in the parental MSCs. In addition, substantially weaker ability to promote the osteogenesis in MSCs was found in LP than EP MSC-MVs. Next, our comparative analysis of RNA sequencing showed the same trend of decreasing number of highly-expressed miRNAs with passages in both MSCs and MSC-MVs, and that most of the highly-expressed genes in LP MSCs and MSC-MVs are both involved in the regulation of senescence-related diseases, such as Alzheimer's disease. Furthermore, based on the obtained miRNA, transcription factor (TF) and genes regulatory network of MSC senescence and the dataset from GEO databases, we confirmed the expression of miR-146a-5p in MSC-MVs resembled the senescent state of their parental MSCs. Our findings give support to MSC-MVs as a key factor in the senescence-associated secretory phenotype of MSCs and demonstrate that their integrated characteristics can dynamically resemble the MSC senescence state, representing a potential biomarker in precise identifying and real-time monitoring of MSC senescence in vitro and even in vivo.
Taxonomy: Umbilicaria americana   Project data type: RNA sequencing and small RNA sequencing
Submitter: liu teng    Date released: 2016-12-25
Accession: PRJCA000325
Source: Project
Mechanism of multi-gene interactions underlying the genetic adaptation to high altitude hypoxia in Tibetan populations
The Tibetan Plateau is the highest mountainous area in the world, an ideal "laboratory" for studying the molecular mechanism of how living organisms adapt to the environmental extreme of high altitude hypoxia. Tibetans, as the indigenous population living in the Tibetan Plateau region have been well-adapted to the high-altitude environment due to longtime natural selection, making them an ideal population for studying adaptation to high-altitude hypoxia in humans. This project aims to dissect the sequence variations and their functions of the 18 candidate genes, selected based on our previous genome-wide analyses in Tibetans, and they are likely involved in hypoxic adaptation. We intend to reveal the strength and timing of natural selection acting on these candidate genes in Tibetans. Combining the approaches of large-sample-size genetic association analysis, gene expression profiling of placenta tissue (an important oxygen-exchange organ), induced hypoxia experiment using endothelial cells and transgenic analysis, we sought to understand "how humans and other organisms have improved their physiological functions through interactions among multiple genes in the genome and developed the ability for high-altitude hypoxia adaptation". The results of this project will shed light on the molecular mechanism of adaptation to high-altitude hypoxia in humans, and will provide valuable genetic data for drug design in order to prevent and cure the high-altitude related diseases, which is crucial not only for basic research , but also for future medical applications.
Taxonomy: Homo sapiens   Project data type: Transcriptome or Gene expression
Submitter: Yaoxi He    Date released: 2016-11-04
Accession: PRJCA000269
Source: Project
Mechanism of multi-gene interactions underlying the genetic adaptation to high altitude hypoxia in Tibetan populations
The Tibetan Plateau is the highest mountainous area in the world, an ideal "laboratory" for studying the molecular mechanism of how living organisms adapt to the environmental extreme of high altitude hypoxia. Tibetans, as the indigenous population living in the Tibetan Plateau region have been well-adapted to the high-altitude environment due to longtime natural selection, making them an ideal population for studying adaptation to high-altitude hypoxia in humans. This project aims to dissect the sequence variations and their functions of the 18 candidate genes, selected based on our previous genome-wide analyses in Tibetans, and they are likely involved in hypoxic adaptation. We intend to reveal the strength and timing of natural selection acting on these candidate genes in Tibetans. Combining the approaches of large-sample-size genetic association analysis, gene expression profiling of placenta tissue (an important oxygen-exchange organ), induced hypoxia experiment using endothelial cells and transgenic analysis, we sought to understand "how humans and other organisms have improved their physiological functions through interactions among multiple genes in the genome and developed the ability for high-altitude hypoxia adaptation". The results of this project will shed light on the molecular mechanism of adaptation to high-altitude hypoxia in humans, and will provide valuable genetic data for drug design in order to prevent and cure the high-altitude related diseases, which is crucial not only for basic research , but also for future medical applications.
Taxonomy: Mus musculus   Project data type: Transcriptome or Gene expression
Submitter: Yaoxi He    Date released: 2016-11-04
Accession: PRJCA000268
Source: Project
16s rRNA sequencing of microbial diversity on human conjuctiva
This study compares conjunctival microbial communities in two types of contact lens wearers with those in non-contact lens wearers.
Taxonomy: Homo sapiens   Project data type: Metagenome
Submitter: Zhang Hai Kun    Date released: 2016-05-23
Accession: PRJCA000237
Source: Project
human iPSC exome
compare three methods for generating human iPSCs based on exome sequencing
Taxonomy: Homo sapiens   Project data type: Exome
Submitter: Yadong Yang    Date released: 2016-05-05
Accession: PRJCA000229
Source: Project
Human mitochondrial genome sequence project
Sequenced mitochondrial genome for different tissue of human in order to find the hetero genotype
Taxonomy: Homo sapiens   Project data type: Whole genome sequencing
Submitter: Meng Yang    Date released: 2016-03-25
Accession: PRJCA000216
Source: Project
Erythroid differentiation
To explore the mechanisms controlling erythroid differentiation and development, we analyzed the genomewide transcription dynamics occurring during the differentiation of human embryonic stem cells (HESCs) into the erythroid lineage and development of embryonic to adult erythropoiesis using high throughput sequencing technology. HESCs and erythroid cells at three developmental stages: ESER (embryonic), FLER (fetal), and PBER (adult) were analyzed. Our findings revealed that the number of expressed genes decreased during differentiation, whereas the total expression intensity increased. At each of the three transitions (HESCs–ESERs, ESERs– FLERs, and FLERs–PBERs), many differentially expressed genes were observed, which were involved in maintaining pluripotency, early erythroid specification, rapid cell growth, and cell–cell adhesion and interaction. We also discovered dynamic networks and their central nodes in each transition. Our study provides a fundamental basis for further investigation of erythroid differentiation and development, and has implications in using ESERs for transfusion product in clinical settings.
Taxonomy: Homo sapiens   Project data type: Transcriptome or Gene expression
Submitter: Yadong Yang    Date released: 2016-03-18
Accession: PRJCA000210
Source: Project
Linkage analysis on microtia
Genome-wide linkage analysis on a microtia pedigree
Taxonomy: Homo sapiens   Project data type: Phenotype or Genotype
Submitter: Yong-Biao Zhang    Date released: 2016-02-06
Accession: PRJCA000150
Source: Project
RNA-seq of tree shrew tumors
Tree Shrew Glioblastoma Model Recapitulates Features of Human Glioblastoma
Taxonomy: Tupaia belangeri   Project data type: Transcriptome or Gene expression
Submitter: Junjun Hao    Date released: 2015-12-16
Accession: PRJCA000125
Source: Project
aaa
Sample name: aaa
Taxonomy: Homo sapiens    Sample type: human
Submitter: li cp   Date released: 2017-06-06
Accession: SAMC013144
Source: Sample
TJA-034
Sample name: TJA-034
Taxonomy: Homo sapiens    Sample type: human
Submitter: Yunzhi Huang   Date released: 2017-05-31
Accession: SAMC012656
Source: Sample
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