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			BioProject







The Human Genome [video]
  
Characterizing the major structural variant alleles of the human genomeThe Human Genome Project, currently maintained by the Genome Reference Consortium (GRC)
we sequenced 15 samples, assembled reads aligning to the genome, and identified structural variants in all samples.The human reference assembly defines a standard upon which other whole genome studies are based.
Human Genome Structural Variation Project.Celera Genomics WGS human genome sequencing project
The sequence-based survey of human genome structural variation aims to characterize common structural variants that are larger than SNPsCelera Genomics was founded to sequence and assemble the human genome and pioneered the use of whole genome shotgun (WGS) sequencing strategy for large eukaryotic genomes.






Encyclopedia of DNA Elements (ENCODE) [video]
Production projects for the human ENCODE projectProduction ENCODE transcriptome data
The aim of the ENCODE project is to identify all functional elements in the human genome sequenceRNA profiling data sets generated by the Production ENCODE project.
Production ENCODE epigenomic dataProduction ENCODE functional genomics data.
DNA methylation, histone modification and chromatin accessibility data setsDNA-binding protein profiling and other functional genomic data sets






Electronic Medical Records and Genomics (eMERGE) [video]
eMERGE-I Genome Wide Association Studies of Network PhenotypeseMERGE Network Imputed GWAS for 41 Phenotypes
The goal of eMERGE is to conduct genome-wide association studies in approximately 19,000 individuals using EMR-derived phenotypes and DNA from linked Biorepositories.The goal of eMERGE is to conduct genome-wide association studies in approximately 55,000 individuals using EMR-derived phenotypes and DNA from linked Biorepositories.
eMERGE-I Genome Wide Association Studies of Network PhenotypeseMERGE Network Imputed GWAS for 41 Phenotypes
The goal of eMERGE is to conduct genome-wide association studies in approximately 19,000 individuals using EMR-derived phenotypes and DNA from linked Biorepositories.The goal of eMERGE is to conduct genome-wide association studies in approximately 55,000 individuals using EMR-derived phenotypes and DNA from linked Biorepositories.






Electronic Medical Records and Genomics (eMERGE)
eMERGE Genome Wide Association Study of Electrocardiographic QRS DurationeMERGE Genome Wide Association Studies of Cardiovascular Diseases and T2DM
The Vanderbilt EMR is a state of the art clinical and research tool (that includes >1.7 million records), and is associated with a DNA repository which has been in development for over 3 yearsIPM Biobank disease burden is reflective of health disparities with broad public health impact
eMERGE Genome Wide Association Study of Electrocardiographic QRS DurationeMERGE Genome Wide Association Studies of Cardiovascular Diseases and T2DM
The Vanderbilt EMR is a state of the art clinical and research tool (that includes >1.7 million records), and is associated with a DNA repository which has been in development for over 3 yearsIPM Biobank disease burden is reflective of health disparities with broad public health impact






Electronic Medical Records and Genomics (eMERGE)
eMERGE Genome Wide Association Studies of obesity (metabochip)eMERGE Genome Wide Association Studies of obesity
The Geisinger eMERGE Genome Wide Association Studies of Obesity (Metabochip) Project is a genetic study of a cohort of primarily Caucasian patients with extreme obesity who have undergone bariatric surgery.The Geisinger eMERGE Genome-Wide Association Studies of Obesity Project is a genetic study of a cohort of primarily Caucasian patients with extreme obesity who have undergone bariatric surgery.
eMERGE Genome Wide Association Studies of obesity (metabochip)eMERGE Genome Wide Association Studies of obesity
The Geisinger eMERGE Genome Wide Association Studies of Obesity (Metabochip) Project is a genetic study of a cohort of primarily Caucasian patients with extreme obesity who have undergone bariatric surgery.The Geisinger eMERGE Genome-Wide Association Studies of Obesity Project is a genetic study of a cohort of primarily Caucasian patients with extreme obesity who have undergone bariatric surgery.






Electronic Medical Records and Genomics (eMERGE)
eMERGE: A Multi-Center Pilot of Pharmacogenetic Sequencing in Clinical PracticeeMERGE: A Multi-Center Pilot of Pharmacogenetic Sequencing in Clinical Practice
eMERGE-PGx is a multi-site test of the concept that sequence information can be coupled to electronic medical records (EMRs) for use in healthcare.eMERGE-PGx is a multi-site test of the concept that sequence information can be coupled to electronic medical records (EMRs) for use in healthcare.






Clinical Sequencing Evidence-Generating Research (CSER) [video]
CSER: Clinical Sequencing in Cancer: Clinical, Ethical, and Technological StudiesCSER: The Use of Sequencing to Guide the Care of Cancer Patients
The Clinical Sequencing Exploratory Research (CSER) program supports multi-disciplinary projects that bring together clinicians, bioinformaticians, and ethicistsThe overall goal of the CanSeq U01 project is to study the impact of whole-exome sequencing (WES) on the clinical care of cancer patients and oncology provider practices.
CSER: Clinical Sequencing in Cancer: Clinical, Ethical, and Technological StudiesCSER: The Use of Sequencing to Guide the Care of Cancer Patients
The Clinical Sequencing Exploratory Research (CSER) program supports multi-disciplinary projects that bring together clinicians, bioinformaticians, and ethicistsThe overall goal of the CanSeq U01 project is to study the impact of whole-exome sequencing (WES) on the clinical care of cancer patients and oncology provider practices.






Clinical Sequencing Evidence-Generating Research (CSER)
CSER: NCGENES (North Carolina Clinical Genomics Evaluation by NextGen Exome SequencingCSER: NCGENES (North Carolina Clinical Genomics Evaluation by NextGen Exome Sequencing
This study is part of a larger consortium project investigating the validity and best use of next-generation sequencing (in particular, whole exome sequencing, or WES) in clinical care.This study is part of a larger consortium project investigating the validity and best use of next-generation sequencing (in particular, whole exome sequencing, or WES) in clinical care.
CSER: Clinical Implementation of Carrier Testing Using Next Generation Sequencing (NGS)CSER: Clinical Implementation of Carrier Testing Using Next Generation Sequencing (NGS)
We will investigate the clinical implementation of genome sequencing (GS) for carrier screening to aid reproductive decision-making in adults.We will investigate the clinical implementation of genome sequencing (GS) for carrier screening to aid reproductive decision-making in adults.






1000 Exomes
Adolescent Idiopathic Scoliosis 1000 Exomes StudyAdolescent Idiopathic Scoliosis 1000 Exomes Study
Accurate methods of predicting curve progression are needed to develop personalized prevention strategies for those at high riskAccurate methods of predicting curve progression are needed to develop personalized prevention strategies for those at high risk






1000 Genomes [video]
The 1000 Genomes Project1000 Genomes Project phase3
The purpose of the project is to support the discovery and understanding of genetic variants that influence human disease.The 1000 Genomes Project phase 3 contains the variants, genotypes, and integrated haplotypes for the complete set of 2504 samples from 26 populations.
1000 Genomes Platinum Calls for NA128781000 Genomes Project phase3 release V3+
These analyses contain the phased SNPs and indels in NA12878 that have been identified as accurateThis submission contains variant sites and phased genotypes for all autosomes






NHLBI TOPMed [video]
NHLBI TOPMed: Phase III variation dataTOPMed sequencing of 1000 Genomes samples
TOPMed project reports variation data aggregated across all participants from contributing studies which are part of NHLBI's Trans-Omics for Precision Medicine (TOPMed) Whole Genome Sequencing (WGS) Project.Five 1000 Genomes DNA samples are being sequenced repeatedly as quality control standards in the NHLBI Translational Opportunities for Precision Medicine (TOPMed) whole genome sequencing program.






NHLBI NextGen Consortium: iPSCORE
NextGen Consortium: The iPSCORE (iPSC Collection for Omic Research) ResourceNextGen Consortium: The iPSCORE (iPSC Collection for Omic Research) Resource - Whole Genome Sequence
The overarching purpose of the iPSCORE Resource is to provide a large collection of hiPSCs for use in studying the impact of genetic variation on molecular and physiological phenotypes.A total of 273 individuals have participated in the study for which 222 have had hiPSCs generated from fibroblasts
NextGen Consortium: The iPSCORE (iPSC Collection for Omic Research) ResourceNextGen Consortium: The iPSCORE (iPSC Collection for Omic Research) Resource - Whole Genome Sequence
The overarching purpose of the iPSCORE Resource is to provide a large collection of hiPSCs for use in studying the impact of genetic variation on molecular and physiological phenotypes.A total of 273 individuals have participated in the study for which 222 have had hiPSCs generated from fibroblasts






NHLBI NextGen Consortium: Pulmonary Hypertension & Platelet Aggregation
NextGen Consortium: iPSC Derived EC as Surrogates Using Pulmonary Hypertension as a Prototype DiseaseNextGen Consortium: Functional Genomics of Platelet Aggregation Using iPS and Derived Megakaryocytes
The transcriptome of pulmonary arterial endothelial cells from healthy lungs and from lungs of patients with idiopathic pulmonary arterial hypertension have been analyzedGWAS study of native platelet aggregation phenotypes and aggregation in response to low dose aspirin in 2200 subjects
NextGen Consortium: iPSC Derived EC as Surrogates Using Pulmonary Hypertension as a Prototype DiseaseNextGen Consortium: Functional Genomics of Platelet Aggregation Using iPS and Derived Megakaryocytes
The transcriptome of pulmonary arterial endothelial cells from healthy lungs and from lungs of patients with idiopathic pulmonary arterial hypertension have been analyzedGWAS study of native platelet aggregation phenotypes and aggregation in response to low dose aspirin in 2200 subjects






NHLBI NextGen Consortium: Lipids & Sickle Cell Globin
NextGen Consortium: Phenotyping Lipid traits in iPS derived hepatocytes Study (PhLiPS Study)NextGen Consortium: Globin Gene Expression in Sickle Cell Genotype-Specific iPS cells
The goal of the PhLiPS study is to create a library of induced pluripotent stem cell (iPSC) lines and iPSC-derived hepatocytes of diverse genotypes for use in metabolic profiling and interrogating lipid phenotypes.Determine the effects of the three known HbF major quantitative trait loci (QTL) on globin gene expression in disease-specific iPS cells during in vitro erythropoiesis... Search for novel HbF genetic modifiers
NextGen Consortium: Phenotyping Lipid traits in iPS derived hepatocytes Study (PhLiPS Study)NextGen Consortium: Globin Gene Expression in Sickle Cell Genotype-Specific iPS cells
The goal of the PhLiPS study is to create a library of induced pluripotent stem cell (iPSC) lines and iPSC-derived hepatocytes of diverse genotypes for use in metabolic profiling and interrogating lipid phenotypes.Determine the effects of the three known HbF major quantitative trait loci (QTL) on globin gene expression in disease-specific iPS cells during in vitro erythropoiesis... Search for novel HbF genetic modifiers






NHLBI NextGen Consortium: Insulin Resistance
NextGen Consortium: GENESiPS Study: Identifying the Gene Networks of Insulin ResistanceNextGen Consortium: GENESiPS Study: Identifying the Gene Networks of Insulin Resistance
SNP array data from individuals included in RNA-seq transcriptome profiling study of human induced pluripotent stem cellsSNP array data from individuals included in RNA-seq transcriptome profiling study of human induced pluripotent stem cells






Induced Pluripotent Stem Cells (iPSC): Generation [video]
Generation of Human Induced Pluripotent Stem Cells by Direct Delivery of Reprogramming ProteinsGeneration of human induced pluripotent stem cells from mesenchymal cells of gut mesentery by Oct4/Sox2/Nanog
Here we report the generation of stable human iPS cells from human fibroblasts by directly delivering defined reprogramming proteins.In the present study, we investigated whether genetically marked human mesenchymal cells of gut mesentery may give rise to iPS cells.
Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cellshuman induced pluripotent stem cell
Human fibroblast-derived, pluripotent cell lines are described that have normal karyotypes, express high levels of telomerase activity, and express both cell surface markers and genes that characterize human embryonic stem (ES) cells.Here, we demonstrate the generation of iPS cells from adult human dermal fibroblasts with the same four factors: Oct3/4, Sox2, Klf4, and c-Myc.






Induced Pluripotent Stem Cells (iPSC): Expression [video]
iPSC day 8aged iPSC Exome
We investigated the gene expression at day 8 of induced pluripotent stem cell reprogrammingTo study how ZSCAN10 makes recovery of genomic stability in induced pluripotent stem cells from aged donors.
RNA-Seq in PWS iPSC-derived neuronsGene expression profiles in human iPS cells cultured by four methods
Transcriptional analysis of PWS iPSC-derived neurons compared to unaffected controlsHepatocyte-like cells differentiated from human iPS cells are expected to be utilized in pharmaceutical research and regenerative medicine.






Directed Differentiation: iPSC to Ectoderm Lineage
Expression profiles of the four human major ectodermal lineagesDifferentiation of human neural progenitor cells
Here we report a chemically defined strategy to derive the entire human ectoderm from pluripotent stem cells.The present study used RNA sequencing to identify the transcriptional landscape of two human neural progenitor cell lines
Expression data from Neural Progenitor cells cultured on 2D flat surfaces and in 3D scaffoldsExpression analysis of neural progenitor cells derived from iPS cells generated from skin fibroblasts and umbilical cord mesenchymal cells
A genomic expression comparison was done among neural progenitor cells cultured on 2D substrates, 3D porous polystyrene scaffolds, and as 3D neural spheresInvestigation of whole genome gene expression level changes in neural progenitor cells derived from iPS cells generated from umbilical cord mesenchymal cells, compared to neural progenitor cells derived from iPS cells generated fromskin fibroblasts






Directed Differentiation: iPSC to Mesoderm Lineage [video]
Gene expression in erythroid cell differentiationTime-course expression: hiPSC differentiation toward cardiomyocytes
RNA was extracted from each sample of cells at a different stage of differentiation and subjected to microarray studies in duplicates.In this study, we used microarrays to detail the global gene program during cardiac differentiation
Human skeletal muscle differentiation time courseAdipocyte Differentiation
Primary human skeletal muscle cells were grown in proliferating mediumFor differentiation, preadipocytes were treated for 30 days with plating medium (without serum)






Directed Differentiation: iPSC to Endoderm Lineage
cAMP-induced differentiation of endometrial stromal cellsHuman podocyte differentiation
Timecourse of cAMP-induced decidualization of endometrial stromal cells.Microarray analysis of the molecular phenotype of the glomerular podocyte during temperature shift-induced differentiation
Gene expression analysis during differentiation of EPC to OECHuman bronchial epithelial cell differentiation time course
Gene expression profiles during the differentiation of EPCs into OECsMicroarray analysis was performed to identify transcriptional changes that occur during mucociliary differentiation of human primary bronchial epithelial cells






Directed Differentiation: iPSC to Endoderm Pancreatic Cells
5hmC dynamically correlated with enhancer's activities during hES-to-Pancreatic endoderm cell differentiation (Bisulfite-Seq)5hmC dynamically correlated with enhancer's activities during hES-to-Pancreatic endoderm cell differentiation (RNA-Seq)
We generated 5hmC, WGBS and RNAseq of the cells in 5 stages during hES-to-pancreatic endoderm cell differantiation, and investigated the 5hmC correlation with 4 histonesWe generated 5hmC, WGBS and RNAseq of the cells in 5 stages during hES-to-pancreatic endoderm cell differantiation, and investigated the 5hmC correlation with 4 histones
5hmC dynamically correlated with enhancer's activities during hES-to-Pancreatic endoderm cell differentiation (ATAC-Seq)5hmC dynamically correlated with enhancer's activities during hES-to-Pancreatic endoderm cell differentiation (CMS)
We generated 5hmC, WGBS and RNAseq of the cells in 5 stages during hES-to-pancreatic endoderm cell differantiation, and investigated the 5hmC correlation with 4 histonesWe generated 5hmC, WGBS and RNAseq of the cells in 5 stages during hES-to-pancreatic endoderm cell differantiation, and investigated the 5hmC correlation with 4 histones






Immortalized Human Cell Lines
Gene Expression Profiling of an Immortalized Human Neural Stem Cell Line HB1.F3Gene Expression Profile of the SV40-immortalized human corneal epithelial cells
Neural stem cells (NSC) with self-renewal and multipotent properties serve as an ideal cell source for transplantation to treat spinal cord injury, stroke, and neurodegenerative diseases.Microarray was used to study global gene expression of a cell culture model based on SV40-immortalized human corneal epithelial (iHCE) cells
Gene Expression Analysis of HPV-immortalized keratinocytesTranscription profiling time series of finite life span and immortal non-malignant human mammary epithelial cell lines
We isolated mRNA from three independent cultures each of Keratinocytes and HPV16-immortalized keratinocytesproliferating counterparts can be used to classify breast cancer patients into poor and good prognosis groups with high accuracy






Immortalized Human Cell Lines
Nascent RNA profiles from immortalized human cell linesRNA-sequencing in immortalized human mammary epithelial cells
GRO-Seq libraries were performed from immortalized human cell lines to study nascent RNA profiles including non-coding RNA expression and transcriptional pausing.RNA-sequencing libraries were generated from immortalized human mammary epithelial cells (HME)
RNA-seq of FSHD and control immortalised myoblasts IIExpression data from immortalized human lung small airway epithelial cells
FSHD Myoblasts were plated at 312,000 cells per 12 well plate in proliferation media and cultured for 48 hours or until 100% confluentTo elucidate the mechanism by which p53 loss enhances invasive and motile activities in human lung small airway epithelial cells (SAECs), we performed comprehensive expression profiling analyses between p53 knockdown and control cells






Immortalized Mesenchymal Stromal Cell Line
Generation and Characterization of an immortalized human mesenchymal stromal cell line modelGeneration and Characterization of an immortalized human mesenchymal stromal cell line model
[Affymetrix][Illumina adipocyte differentiation]
Generation and Characterization of an immortalized human mesenchymal stromal cell line modelGeneration and Characterization of an immortalized human mesenchymal stromal cell line model
[Illumina iMSC#3 and hMSC primary cultures][Illumina DNA methylation]






CRISPR/Cpf1 & CRISPR/Cas9 [video]
Base editing with a Cpf1–cytidine deaminase fusionHigh-fidelity base editing mediated by Cpf1-cytidine deaminase fusion
Examination of indels and base substitutions induced by the CRISPR/Cpf1 base editorsExamination of indels and base substitutions induced by the CRISPR/Cpf1 base editors
On the design of CRISPR-based single cell molecular screensUncovering mechanisms of early human lineage specification by CRISPR/Cas9-mediated genome editing [RNA-seq]
Shendure Lab, Genome Sciences, University of Washington (Owner)Here we use CRISPR?Cas9-mediated genome editing to investigate the function of the pluripotency transcription factor OCT4 during human embryogenesis.






CRISPR-Cas SunTag
DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A [BS-Seq]DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A [RNA-Seq]
Here, we demonstrate that dCas9-SunTag-DNMT3A dramatically increased CpG methylation at the HOXA5 locus in human embryonic kidney 293T cells (HEK293T).We demonstrate that dCas9-SunTag-DNMT3A dramatically increased CpG methylation at the HOXA5 locus in human embryonic kidney 293T cells (HEK293T).
DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A [WGBS]DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A [RRBS]
We demonstrate that dCas9-SunTag-DNMT3A dramatically increased CpG methylation at the HOXA5 locus in human embryonic kidney 293T cells (HEK293T).We demonstrate that dCas9-SunTag-DNMT3A dramatically increased CpG methylation at the HOXA5 locus in human embryonic kidney 293T cells (HEK293T).






CRISPR-SKIP
CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors [gDNA]CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors [off-targets]
We here present a versatile method termed CRISPR-SKIP that utilizes cytidine deaminase single-base editors to program de-novo exon skipping by mutating target DNA bases within splice acceptor sites.We here present a versatile method termed CRISPR-SKIP that utilizes cytidine deaminase single-base editors to program de-novo exon skipping by mutating target DNA bases within splice acceptor sites.
CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors [RNA-seq]
We here present a versatile method termed CRISPR-SKIP that utilizes cytidine deaminase single-base editors to program de-novo exon skipping by mutating target DNA bases within splice acceptor sites.






Blood and Skeletal Muscle Gene Signatures of Exercise
Blood and skeletal muscle gene signatures of exercise training in men (Muscle data set)Blood and skeletal muscle gene signatures of exercise training in men (PBMC data set)
Two groups of healthy untrained policemen recruits (G1, n=20, 26±4 yrs; G2, n= 21, 27±3 yrs) were selected.Two groups of healthy untrained policemen recruits (G1, n=20, 26±4 yrs; G2, n= 21, 27±3 yrs) were selected.
Blood and skeletal muscle gene signatures of exercise training in men (Total blood data set G1)Blood and skeletal muscle gene signatures of exercise training in men (Total blood data set G2)
Two groups of healthy untrained policemen recruits (G1, n=20, 26±4 yrs; G2, n= 21, 27±3 yrs) were selected.Two groups of healthy untrained policemen recruits (G1, n=20, 26±4 yrs; G2, n= 21, 27±3 yrs) were selected.






Normal Blood
Longitudinal study of gene expression in healthy individualsGene Expression Profiles of Pregnant and Non-pregnant Whole Blood
The gene expression profile of blood drawn from healthy individuals was studied over a period of six months, at five time points.Comparison of gene expression profiles in whole blood collected from pregnant and non-pregnant females.
Gene Expression Profiling of Whole Blood: Comparison of target preparation methodsGene Expression signatures in whole blood to predict vaccine responses
We compared four different methods for preparing microarray hybridization targets from human whole blood collected in PAXGene tubes.Gene expression arrays were performed on whole blood of vaccinees before (n=28) and one (n=18) or three days (n=10) after vaccination.






Normal Tissue
Normal Human Tissue Sequencing ProjectNormal Human Tissue Sequencing Project
The Normal Human Tissue Sequencing Project provides RNA expression and DNA methylation data from normal (non-diseased) human tissues.The Normal Human Tissue Sequencing Project provides RNA expression and DNA methylation data from normal (non-diseased) human tissues.
Atlas of RNA sequencing profiles of normal human tissuesGene expression profiles of 25 normal human tissues
Comprehensive analysis of molecular pathology requires a collection of reference samples representing normal tissues from healthy donors.We performed microarray experiments to identify genes specifically expressed in human tissues and investigated association of recombination rates with the tissue-specific genes.






Normal Tissue
GeneNote-Gene Normal tissue ExpressionmiRNA Microarray Profiling of Nine Different Normal Human Tissues
Normal human tissue expression profilingWe measured the expression of 470 human miRNAs in nine human tissues using Agilent DNA microarrays.
Hydroxymethyl DNA-IP of genomic DNA for many different normal human tissuesDNA methylation distinguishes pathologically normal human tissues
We profile this mark in several normal human tissues 5-hmC patterns are highly tissue specificWe analyzed 217 non-pathologic human tissues from 10 anatomic sites at 1413 autosomal CpG loci associated with 773 genes to investigate tissue-specific differences in DNA methylation, and to discern how aging and exposures contribute to normal variation in methylation.






Tumors & Adjacent Normal Tissue
Expression data from glioblastoma tissue and matched adjacent normal tissueGlobal gene expression profile in human glioma tissue & Adjacent normal tissue samples
A total of 3 GBM tissues and the matched adjacent normal brain tissues were obtained for RNA extractionDifferential gene expression was assesed of genes related to tumor associated macrophages in human gliomas
Predictive analysis of long non-coding RNA expression profiles in tumor and normal tissues from glioblastoma patientsDifferential expressed miRNAs between tumor tissues and adjecent normal tissues from a patient with glioblastoma
We compared lncRNA expression data in tumor tissues from 9 patients and 3 healthy tissuesA paired miRNAs tumor tissues & Adjacent tissues of a glioblastoma patient was used in this study.






Tumors & Adjacent Normal Tissue
Expression data from breast cancer tissues & Adjacent normal tissuesEpigenome analysis of tumor adjacent normal tissue from breast cancer patients
we examined gene expression profiles from paired breast normal/ tumor tissues, and coupled with Gene Ontology and public data base analysis.Samples included 70 tumor-adjacent normal breast tissue with invasive disease, 8 tissues from breast prophylactic patients, and 18 tissues from breast reduction patients.
mRNA-sequencing of breast cancer subtypes and normal tissueHigh-throughput RNA sequencing on circular RNA profiles of human triple-negative breast cancer & Adjacent normal tissues
mRNA profiles of 17 breast tumor samples of three different subtypes (TNBC, non-TNBC and HER2-positive) and normal human breast organoids (epithelium) samples (NBS) were sequenced using Illumina HiSeq.Circular RNAs profiles of three pairs of triple-negative breast cancer (TNBC) & Adjacent normal tissues were generated by RNA deep-sequencing, using HiSeq3000, Illumina.






Tumors & Adjacent Normal Tissue
Expression data from gastroesphageal cancers and adjascent normal tissueSmall RNA Solexa sequencing of colorectal tumor and adjancent normal tissues
Differences in gene expression were evaluated between tumor and normal tissue (N=8 patients), and between post-treatment and pretreatment specimens for bortezomib alone (N=2 patients) and bortezomib plus irinotecan (N=10 patients).Construction of small RNA libraries from size fractionated RNA was carried out by following Solexa protocol and the obtained libraries were sequenced by Illumina HiSeq 2000 sequencer.
Expression data from bladder tumors & Adjacent normal tissuesmiRNA expression differences between FFPE prostate cancer & Adjacent normal tissues using real-time quantitative PCR array analysis
miRNA profiling was performed on paired bladder cancer tissues and differentially expressed miRNAs were identified in BC & Adjacent noncancerous tissuesmRNA from 10 Prostate Cancer patients (5 Caucasian American and 5 African American) and their paired adjacent normal tissue were analysed






T Cell Transcription Profiling
Gene expression profile of 4/7 ICR modified T cells compared to control ΔIL4R T cellsGene expression profile of TBBR modified T cells compared to control ΔTGFbRII T cells
The objective of this experiment was to compare the transcriptional profile of 4/7 ICR (IL4R ectodomain fused to IL7R endodomain) vs control ΔIL4R (truncated version that lacks an endodomain) modified T cells.The objective of this experiment was to compare the transcriptional profile of TBBR (TGFbRII ectodomain fused to 41BB endodomain) vs control ΔTGFbRII (truncated version that lacks an endodomain) modified T cells.
Gene expression profile of CAR T cells compared to control ΔCAR T cellsGene expression profile of SmarT-cells compared to control T cells modified to express ΔCAR, ΔTGFbRII and ΔIL4R
The objective of this experiment was to compare the transcriptional profile of CAR (CD3z endodomain) vs control ΔCAR (truncated version that lacks an endodomain) modified T cells.The objective of this experiment was to compare the transcriptional profile of T cells modified to express CAR, TBBR and 4/7 ICR (i.e. SmarT-cells) against control T cells expressing the delta constructs (i.e. ΔCAR, ΔTGFbRII and ΔIL4R).






T Cell Antigen Screening & Immunotherapy [video]
High-throughput determination of the antigen specificities of T cell receptors in single cellsDefining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma
High-throughput linking of T cell receptor (TCR) sequences to their binding antigenswe performed an unbiased analysis on 16,291 CD45+ immune cells from 32 patients (48 samples) treated with checkpoint therapy
High-throughput determination of the antigen specificities of T cell receptors in single cellsDefining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma
High-throughput linking of T cell receptor (TCR) sequences to their binding antigenswe performed an unbiased analysis on 16,291 CD45+ immune cells from 32 patients (48 samples) treated with checkpoint therapy






HipSci Sequencing & Genotyping
HipSci whole exome sequencing data for healthy volunteersHipSci imputed whole exome sequencing data for healthy volunteers
whole exome sequencing using Agilent whole exome pulldown method on iPS cellsimputed whole exome sequencing using Agilent whole exome pulldown method on iPS cells
HipSci imputed genotyping array data for healthy volunteersHipSci genotyping array data for healthy volunteers
imputed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cellsGenotyping analysis using the Infinium HumanExome BeadChip on iPS cells






Ancient Genomes [video]
Georgian and Swiss ancient genomesLow Coverage Genomes of Ancient Indiviudals from British Columbia
Molecular population genetics (Owner)University of Illinois Urbana-Champaign (Owner)
Ancient Hungarian Genomes25 Ancient Human Exomes from Prince Rupert Harbour, BC
Trinity College Dublin (Owner)University of Illinois Urbana-Champaign (Owner)






Ancient Genomes
Ancient mitochondrial DNA sequencing of an ancient Phoenician from Tunisia.Population genetics context of ancient human genome sequence of an extinct Palaeo-Eskimo
University of Otago (Owner)Estonian Biocentre (Owner)
Ancient Mitogenomes of Phoenicians from Sardinia and LebanonAncient human genome sequence of an extinct Palaeo-Eskimo
University of Otago (Owner)Centre for GeoGenetics, Natural History Museum of Denmark (Owner)






Ancient Genomes
Ancient Ethiopian 'Mota' genomeAncient Mitogenome sequence data
Molecular population genetics (Owner)Pennsylvania State University (Owner)
Ancient Human Mitogenomes Mexico and Central AmericaWhole genome sequencing of ancient sample from Anzick site
University of Calgary (Owner)University of Copenhagen (Owner)






Extracellular RNA [video]
UCSF Center for Reproductive Health (CRH) Research BankUCSF Center for Reproductive Health (CRH) Research Bank
The purpose of this study is to provide a reference profile of small extracellular RNAs in body fluids.The purpose of this study is to provide a reference profile of small extracellular RNAs in body fluids.






Epigenomics
Epigenomic profilesNIH Epigenomics Roadmap Initiative
Chromosomal methylation profiles of normal and transformed cell linesEpigenetics is an emerging frontier of science that involves the study of changes in the regulation of gene activity and expression that are not dependent on gene sequence.
Homo sapiens epigenomics projectDistinct epigenomic landscapes of pluripotent and lineage-committed human cells
Source of DNA used for sequencing was ChIP samples from SH-SY5Y cells using anti-DJ-1 antibody and anti-rabbit IgG as a negative control.Human embryonic stem cells share identical genomic sequences with other lineage-committed cells yet possess the remarkable properties of self-renewal and pluripotency.






Epigenomics of Glioma
Characterizing the epigenome of glioma stem cells (RNA-Seq)Characterizing the epigenome of glioma stem cells (ChIP-Seq)
We isolated glioma stem cells from patient-derived xenografts and profiled their epigenomic featuresA core set of 12 glioma stem cell lines and 3 neural stem/progenitor cell lines were mapped
Characterizing the epigenome of glioma stem cells (Methylation BeadChip)Characterizing the epigenome of glioma stem cells (RRBS)
We isolated glioma stem cells from patient-derived xenografts and profiled their epigenomic featuresWe isolated glioma stem cells from patient-derived xenografts and profiled their epigenomic features






Ovarian Cancer [video]
Characterization of three Epithelial Ovarian Cancer cell lines resistant to cisplatin (mRNA).Expression analysis of platinum sensitive and resistant epithelial ovarian cancer patient samples.
GEP experiments were performed in 3 Epithelian Ovarian Cancer cell lines Platinum-resistant vs their parentalOverall design: 6 clinical samples of platinum sensitive and 6 samples of resistant.
Characterization of three Epithelial Ovarian Cancer cell lines resistant to cisplatin (microRNA).The profile of exosomal and cellular miRNA in ovarian cancer cell lines
microRNA experiments were performed in 3 Epithelian Ovarian Cancer cell lines Platinum-resistant vs their parentalTo check the profile of exosomal and cellular miRNA in ovarian cancer cell lines, total RNA were extracted from exosomes and cells






The Cancer Genome Atlas
TCGA - CCLE CollaborationTCGA - The Cancer Genome Atlas
The Cancer Cell Line Encyclopedia (CCLE) project is a collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer modelsThe Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing.
The Cancer Genome Atlas (TCGA) Consortium Integrated DNA Methylation Analysis
Aberrant hypermethylation of CpG dinucleotides located in CpG islands within the promoters of key cancer genes is an epigenetic abnormality associated with heritable transcriptional gene silencing and inactivation in cancer.






SMAD2/3 in Breast Cancer
SMAD2 binding regions in triple negative breast cancer cell line, Hs578TSMAD2 binding regions in estrogen receptor-positive breast cancer cell line, T47D
SMAD2 ChIP-seq analysis was performed in triple negative breast cancer after Activin A with/without Palbociclib treatmentSMAD2 ChIP-seq analysis was performed in estrogen receptor-positive breast cancer after Activin A with/without Palbociclib treatment
SMAD2/3 binding pattern in a breast epithelial cell line, MCF10A MII [ChIP-seq]SMAD2/3 binding pattern in triple-negative breast cancer cell lines, Hs578T and BT549 [ChIP-seq]
SMAD2/3 ChIP-seq analyses were performed in MCF10A MII cells at 2 different time points after TGFβ treatment.SMAD2/3 ChIP-seq analyses were performed in 2 different TNBCs at 2 different time points after TGFβ treatment.






Rheumatoid Arthritis
Comprehensive Epigenetic Landscape of Rheumatoid Arthritis FLSWhite blood cells from rheumatoid arthritis patients and matched healthy donors
We characterized the epigenetic landscape of rheumatoid arthritis fibroblast-like synoviocytes (FLS) compared with osteoarthritis FLS.The experiment was designed to assess gene expression differences between rheumatoid arthritis patient and healthy donor white blood cells.
Comprehensive Epigenetic Landscape of Rheumatoid Arthritis FLSSynovial fluid and blood neutrophils from rheumatoid arthritis patients and matched healthy controls
We characterized the epigenetic landscape of rheumatoid arthritis fibroblast-like synoviocytes (FLS) compared with osteoarthritis FLS.Synovial fluid and blood neutrophils from 7 rheumatoid arthritis patients and 5 matched healthy controls






PREVAIL
Time series gene expression in critically ill patients: PREVAIL study
Time series gene expression profiling of critically ill patients undergoing mechanical ventilation






Environmental Stress
PESBART: Effects of Physical Environment and Stress in Blacks in relation to Asthma severity and Response to TherapyPESBART: Effects of Physical Environment and Stress in Blacks in relation to Asthma severity and Response to Therapy
once-daily tiotropium (n = 532) or twice-daily LABAs (n = 538,) and were followed...once-daily tiotropium (n = 532) or twice-daily LABAs (n = 538,) and were followed...






Population Genome & Exome Sequencing: Indian
The South Asian genome: Whole Genome SequencingThe South Asian genome: Exome sequencing
The data contained within this project relates to the 40-50x coverage whole genome sequencing of 8 individuals.The data contained within this project relates to the whole-exome sequencing of 147 individuals.
The South Asian genome: Low Coverage Whole Genome Sequencing
The data contained within this project relates to the 4-5x coverage whole genome sequencing of 168 individuals.






Population Genome & Exome Sequencing: Indian
Whole genome sequencing of (ITU) Indian Telugu in the UK HapMap populationExome sequencing of (ITU) Indian Telugu in the UK HapMap population
1000 Genomes Project (Owner)1000 Genomes Project (Owner)
Whole genome sequencing of (ITU) Indian Telugu in the UK HapMap population. DNA for sequencing was extracted from whole bloodExome sequencing of (ITU) Indian Telugu in the UK HapMap population. DNA for sequencing was extracted from whole blood
1000 Genomes Project (Owner)1000 Genomes Project (Owner)






Population Genome & Exome Sequencing: Indian
Whole genome sequencing of (GIH) Gujarati (India) ancestry, in Houston, Texas US HapMap populationExome sequencing of (GIH) Gujarati India ancestry in Houston, Texas population
1000 Genomes Project (Owner)1000 Genomes Project (Owner)
Whole genome sequencing of (BEB) Bengali in Bangladesh HapMap populationExome sequencing of (BEB) Bengali in Bangladesh HapMap population
1000 Genomes Project (Owner)1000 Genomes Project (Owner)






Population Genome & Exome Sequencing: Indian
Whole genome sequencing of (RDH) Reddy in Hyderabad, India HapMap populationExome sequencing of (RDH) Reddy in Hyderabad, India HapMap population
1000 Genomes Project (Owner)1000 Genomes Project (Owner)
Whole genome sequencing of (PJL) Punjabi HapMap populationExome sequencing of (PJL) Punjabi HapMap population
1000 Genomes Project (Owner)1000 Genomes Project (Owner)






Population Genome & Exome Sequencing: Sri Lankan
Whole genome sequencing of (STU) Sri Lankan Tamil in the UK HapMap population. DNA for sequencing was extracted from whole bloodExome sequencing of (STU) Sri Lankan Tamil in the UK HapMap population. DNA for sequencing was extracted from whole blood
1000 Genomes Project (Owner)1000 Genomes Project (Owner)
Whole genome sequencing of (STU) Sri Lankan Tamil in the UK HapMap populationExome sequencing of (STU) Sri Lankan Tamil in the UK HapMap population
1000 Genomes Project (Owner)1000 Genomes Project (Owner)






Population Genome & Exome Sequencing: Chinese
Whole genome sequencing of (CHS) Southern Han Chinese population HapMap populationExome sequencing of (CHS) Southern Han Chinese population HapMap population
1000 Genomes Project (Owner)1000 Genomes Project (Owner)






Population Genome & Exome Sequencing: Vietnamese
Whole genome sequencing of (KHV) Kinh in Ho Chi minh City, Vietnam HapMap population from primary bloodExome sequencing of (KHV) Kinh in Ho Chi minh City, Vietnam HapMap population
1000 Genomes Project (Owner)1000 Genomes Project (Owner)
Whole genome sequencing of (KHV) Kinh in Ho Chi minh City, Vietnam. DNA for sequencing was extracted from whole bloodExome sequencing of (KHV) Kinh in Ho Chi minh City, Vietnam HapMap population. DNA for sequencing was extracted from whole blood
1000 Genomes Project (Owner)1000 Genomes Project (Owner)






Population Genome & Exome Sequencing: British
Whole genome sequencing of (GBR) British from England and Scotland HapMap populationExome sequencing of (GBR) British from England and Scotland HapMap population
1000 Genomes Project (Owner)1000 Genomes Project (Owner)






Population Genome & Exome Sequencing: Italian
Exome sequencing of (TSI) Toscani in Italia HapMap populationWhole genome sequencing of (TSI) Toscani in Italia HapMap population
1000 Genomes Project (Owner)1000 Genomes Project (Owner)






Population Genome & Exome Sequencing: Spanish
Whole genome sequencing of (IBS) Iberian populations in Spain HapMap populationExome sequencing of (IBS) Iberian populations in Spain HapMap population
1000 Genomes Project (Owner)1000 Genomes Project (Owner)






Population Genome & Exome Sequencing: Peruvian
Whole genome sequencing of (PEL) Peruvian in Lima, Peru HapMap population. DNA for sequencing was extracted from whole bloodExome sequencing of (PEL) Peruvian in Lima, Peru HapMap population. DNA for sequencing was extracted from whole blood
1000 Genomes Project (Owner)1000 Genomes Project (Owner)
Whole genome sequencing of (PEL) Peruvian in Lima, Peru HapMap populationExome sequencing of (PEL) Peruvian in Lima, Peru HapMap population
1000 Genomes Project (Owner)1000 Genomes Project (Owner)






Population Genome & Exome Sequencing: Puerto Rican
Whole genome sequencing of (PUR) Puerto Rican in Puerto Rico HapMap population DNA for sequencing was extracted from whole bloodExome sequencing of (PUR) Puerto Rican in Puerto Rico HapMap population. DNA for sequencing was extracted from whole blood
1000 Genomes Project (Owner)1000 Genomes Project (Owner)
Whole genome sequencing of (PUR) Puerto Rican in Puerto Rico HapMap populationExome sequencing of (PUR) Puerto Rican in Puerto Rico HapMap population
1000 Genomes Project (Owner)1000 Genomes Project (Owner)






Population Genome & Exome Sequencing: African Caribbean
Whole genome sequencing of (ACB) African Caribbean in Barbados HapMap population. DNA for sequencing was extracted from whole bloodExome sequencing of (ACB) African Caribbean in Barbados HapMap population. DNA for sequencing was extracted from whole blood
1000 Genomes Project (Owner)1000 Genomes Project (Owner)
Whole genome sequencing of (ACB) African Caribbean in Barbados HapMap populationExome sequencing of (ACB) African Caribbean in Barbados HapMap population
1000 Genomes Project (Owner)1000 Genomes Project (Owner)






Population Genome & Exome Sequencing: African
Whole genome sequencing of (GWD) Gambian in Western Division, The Gambia HapMap populationExome sequencing of (GWD) Gambian in Western Division, The Gambia HapMap population
1000 Genomes Project (Owner)1000 Genomes Project (Owner)
Whole genome sequencing of (MSL) Mende in Sierra Leone HapMap populationExome sequencing of (MSL) Mende in Sierra Leone HapMap population
1000 Genomes Project (Owner)1000 Genomes Project (Owner)






Population Genome & Exome Sequencing: African
Whole genome sequencing of (YRI) Yoruba HapMap populationExome sequencing of (YRI) Yoruba in Ibadan Nigeria HapMap population
1000 Genomes Project (Owner)1000 Genomes Project (Owner)
Whole genome sequencing of (ESN) Esan in Nigeria HapMap populationExome sequencing of (ESN) Esan in Nigeria HapMap population
1000 Genomes Project (Owner)1000 Genomes Project (Owner)







     
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