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Dataset Title Keywords Date Released Description
E. histolytica and E. invadens RNA-seq of non coding RNA 08-19-2015 This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
Tbx3 controls Dppa3 levels to regulate exit from pluripotency towards mesodermal lineage RNA-seq of coding RNA
ChIP-seq
08-19-2015 Tbx3, a member of the T-box family, plays important roles in development, stem cells, nuclear reprog...
Conversion of MyoD to a neurogenic factor: binding site specificity determines lineage [RNA-seq] RNA-seq of coding RNA 08-19-2015 MyoD and NeuroD2 are master regulators of myogenesis and neurogenesis and bind to a "shared&quo...
Small RNAs during E. histolytica stress response RNA-seq of non coding RNA 08-19-2015 We analyzed ~27nt small RNAs from Entamoeba histolytica trophozoites in basal conditions and after h...
Integrative ‘omic analysis of experimental bacteremia identifies a metabolic signature that distinguishes human sepsis from SIRS RNA-seq of coding RNA 08-19-2015 Rationale: Sepsis is a leading cause of morbidity and mortality; early diagnosis and prediction of p...
Lung adenocarcinoma metastasis is suppressed by the alveolar lineage transcription factors GATA6 and HOPX. RNA-seq of coding RNA 08-18-2015 Molecular programs that mediate normal cell differentiation are required for oncogenesis and tumor c...
Transcription profiling by 3'-end sequencing of whole blood from pancreatic ductal adenocarcinoma (PDAC) patients and healthy controls for PDAC diagnosis RNA-seq of coding RNA 08-14-2015 We sequenced the transcriptomes using massive analysis of cDNA ends (MACE) of whole blood samples fr...
LEF-1 and TCF-1 orchestrate T follicular helper (Tfh) cell differentiation by regulating Tfh differentiation circuits upstream of Bcl6 RNA-seq of coding RNA 08-19-2015 This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
Fgf and Esrrb integrate epigenetic and transcriptional networks that regulate self-renewal of Trophoblast Stem Cells RNA-seq of coding RNA
ChIP-seq
08-18-2015 Derivation and maintenance of TS cells depends on the presence of Fgf signalling. Numerous gene knoc...
High-throughput sequencing of mouse liver transcriptome in Clock mutant animals RNA-seq of coding RNA 08-19-2015 Circadian profile of polyA RNA by RNA-Seq, collected from ClockΔ19 mouse liver at CT22, CT28, CT34,...
RNA-Seq profiling of single bovine oocyte transcript abundance and its modulation by cytoplasmic polyadenylation RNA-seq of coding RNA 08-19-2015 Polyadenylated RNA from individual germinal vesicle and metaphase II ooyctes was amplified and proce...
Molecular anatomy of palate development RNA-seq of coding RNA 08-19-2015 Background: The FACEBASE consortium was established in part to create a central resource for craniof...
Transciptional response to acute thermal stress in Chinook salmon RNA-seq of coding RNA 08-19-2015 Thermal stress is a serious and growing challenge facing Chinook salmon (Oncorhynchus tshawytscha) l...
Interactions of melanoma cells with distal keratinocytes trigger metastasis via Notch signaling inhibition of MITF RNA-seq of non coding RNA 08-19-2015 The most critical stage in initiation of melanoma metastasis is the radial to vertical growth transi...
Innate lymphoid cell development requires TOX-dependent generation of a common ILC progenitor RNA-seq of coding RNA 08-05-2015 Subtypes of innate lymphoid cells (ILC), defined by effector function and transcription factor expr...
Varicella-Zoster Virus (VZV) quiescent and productive infection of neurons derived from human embryonic stem cells RNA-seq of coding RNA 06-22-2015 quiescent and productive infection of varicella zoster virus in human embryonic stem stem cell-deriv...
The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis (RNA-Seq) RNA-seq of coding RNA 06-27-2015 SOX9 is a transcriptional activator required for chondrogenesis, and SOX5 and SOX6 are closely relat...
Transcriptomic gene profiling of porcine muscle tissue depending on histological properties RNA-seq of coding RNA 12-12-2015 Purpose: Next-generation sequencing (NGS) was used to select genes potentially associated with fiber...
TET-catalyzed 5-hydroxymethylcytosine regulates gene expression in differentiating colonocytes and colon cancer RNA-seq of coding RNA
methylation profiling by high throughput sequencing
12-12-2015 5-hydroxymethylcytosine (5-mC) and gene expression profiling of T84 cell differentiation; 5-hmC prof...
Next generation sequencing identifies differentially localized transcripts in Xenopus laevis and Xenopus tropicalis oocytes RNA-seq of coding RNA 12-12-2015 RNA-seq technology was used to identify differentially localized transcripts from Xenopus laevis and...
Global transcript analysis of quantitative trait loci (QTL) associated with meat tenderness in pigs RNA-seq of coding RNA 12-12-2015 We sequenced mRNA from 32 muscles (n=16 semimembranosus,n=16 longisimus dorsi) of two pig breeds (Pu...
Differential RNA-seq of Plant Beneficial Rhizobacterium Bacillus amyloliquefaciens FZB42 Reveals sRNA Bas01 involved in Sporulation and Biofilm Formation RNA-seq of coding RNA 12-08-2015 Bacillus amyloliquefaciens FZB42 is a representative organism for Gram positive soil bacteria associ...
Identifying Glioblastoma Gene Networks Based on Hypergeometric Test Analysis RNA-seq of coding RNA 12-08-2015 Patient specific therapy is emerging as an important possibility for many cancer patients. However,...
RNA-seq analysis of Bacteroides xylanisolvens XB1AT grown on pectin or xylan RNA-seq of coding RNA 12-08-2015 Dietary fiber degradation is a key function of the human gut microbiota. The aim of this study was ...
Broiler responses to virulent and avirulent Clostridium perfringens RNA-seq of coding RNA 12-08-2015 Purpose: Analyze gene expression during C. perfringens colonization in the chicken Transcriptomic pr...
Next Generation Sequencing identifies Cdh11 and Mrc1 as novel translational biomarkers of kidney fibrosis RNA-seq of coding RNA 12-08-2015 Chronic kidney disease (CKD) is the gradual, asymptomatic loss of kidney function and current tests ...
Transcription factor trapping by RNA in gene regulatory elements other
RNA-seq of coding RNA
12-08-2015 This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
Drug-based modulation of endogenous stem cells promotes functional remyelination in vivo RNA-seq of coding RNA 08-19-2015 Multiple sclerosis involves an aberrant autoimmune response and progressive failure of remyelination...
Genome-wide mapping of promoter-enhancer interactions with HiCap other
RNA-seq of coding RNA
08-19-2015 This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
Transcript profiles of juvenile female brown trout exposed to glyphosate and Roundup herbicides. RNA-seq of coding RNA 08-19-2015 This study aimed to investigate the hepatic transcriptional response of brown trout to glyphosate, a...
Global identification of genes specific for rice meiosis RNA-seq of coding RNA 08-19-2015 The leptotene-zygotene transition is a major step in meiotic progression during which pairing betwee...
Genome-wide mapping of promoter-enhancer interactions with HiCap [RNA-seq] RNA-seq of coding RNA 08-19-2015 Although the locations of promoters and enhancers have been identified in several cell types, we hav...
EZH2 inhibitor efficacy in non-Hodgkin lymphoma does not require suppression of H3K27 mono-methylation [RNA-Seq] RNA-seq of coding RNA 08-19-2015 Here we report the discovery of highly potent and selective EZH2 small molecule inhibitors, their va...
Leucegene: AML sequencing (part 4) RNA-seq of coding RNA 08-19-2015 RNA sequencing of human leukemia The goals of this project are to obtain a comprehensive study of mu...
A novel analytical brain block tool to enable functional annotation of discriminatory transcript biomarkers among discrete regions of the fronto-limbic circuit in primate brain RNA-seq of coding RNA 08-19-2015 We describe a novel method for obtaining discrete regions from the fronto-limbic circuits of a 4 yea...
High-throughput sequencing of mouse liver transcriptome. RNA-seq of coding RNA 08-19-2015 Circadian profile of polyA RNA by RNA-Seq, collected from mouse liver at CT23, CT29, CT35, CT41, CT4...
The carbonic anhydrase inhibitor ethoxzolamide inhibits the Mycobacterium tuberculosis PhoPR regulon and Esx-1 secretion and attenuates virulence RNA-seq of coding RNA 08-19-2015 The purpose of this study was to examine how ethoxzolamide modulates gene M. tuberculosis gene expre...
Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development RNA-seq of coding RNA 08-19-2015 To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA s...
Small RNA mediated immune responses: insights from analyses of nine soybean R-gene near-isogenic lines and their susceptible parent RNA-seq of non coding RNA 08-19-2015 Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are negative regulators...
dsRNA-seq of Physcomitrella patens rdr mutants RNA-seq of coding RNA 08-19-2015 To investigate the effects of rdr2 and rdr6 mutations upon the strucutred component of the Physcomit...
IFN-g Regulates mTORC1, Cellular Metabolism and mRNA Translation to Potentiate Inflammatory Macrophage Activation [miRNA-Seq] RNA-seq of non coding RNA 08-19-2015 IFN-g primes macrophages for enhanced inflammatory activation by TLRs and microbial killing, but lit...
Identification of MEDIATOR16 as the Arabidopsis COBRA suppressor, MONGOOSE1   RNA-seq of coding RNA 01-03-2016 RNAseq data for Col-0. cob-6, sfr6-3 and cob-6sfr6-3 7 days old seedlings grown in 24h light with 0
Vascular niche induction of hematopoietic progenitors from pluripotent stem cells RNA-seq of coding RNA 01-01-2016 Pluripotent stem cells (PSC) represent an alternative source of hematopoietic stem cells (HSCs). Cli...
Global Analysis of the Transcriptional Response of Chinese cabbage (Brassica rapa ssp. pekinensis) to Methyl Jasmonate Reveals JA Signaling on Enhancement of Secondary Metabolism Pathways RNA-seq of coding RNA 01-03-2016 We conducted a RNA-Seq analysis of MeJA-treated Chinese cabbage leaf transcriptome. Total 14,619,469...
Genome-wide mapping of TEL-AML1 targets in acute leukemia RNA-seq of coding RNA 01-03-2016 Around 20-25% of childhood acute lymphoblastic leukemias carry the TEL-AML1 (TA) fusion gene. It is ...
Transcription profiling by high throughput sequencing of Arabidopsis estradiol-inducible tor-es mutant RNA-seq of coding RNA 01-04-2016 To validate that the transcriptional program rapidly activated by PP242, WYE354, KU63794 and Torin2 ...
Assessment of ability of hTSLP to maintain primary CRLF2 B-ALL cells in a xenograft model in a state more similar to the parent leukemia RNA-seq of coding RNA 01-02-2016 Xenograft models represent an excellent method for expanding primary leukemias, but their ability to...
Small RNAs in stress-related rice cultivars RNA-seq of non coding RNA 01-01-2016 In this study, we sequenced small RNA content from three different rice cultivars employing Illumina...
Next generation sequencing of miRNAs in folic acid-induced kidney damage RNA-seq of non coding RNA 12-26-2015 We have used small RNA sequencing to measure the expression of all miRNAs present in the kidneys dur...
Cryptochromes interact directly with PIFs to control plant growth in limiting blue light RNA-seq of coding RNA 01-02-2016 Sun-loving plants have the ability to detect and avoid shading through sensing of both blue and red ...
Transcription profiling by high throughput sequencing of maize seedlings segregating for gl3, a recessive mutant involved in the accumulation of epicuticular wax RNA-seq of coding RNA 01-11-2016 Bulked segregant analysis (BSA) is an efficient method to rapidly and efficiently map genes responsi...
A novel RAF kinase inhibitor with DFG-out binding mode: high efficacy in BRAF-mutant tumor xenograft models in the absence of normal tissue hyperproliferation RNA-seq of coding RNA 01-10-2016 Purpose: Seek for differential gene expression in vemurafenib-resistant A375 tumors vs. untreated co...
Transcription profiling by high throughput sequencing in protonemata of Physcomitrella patens after heat shock treatments RNA-seq of coding RNA 01-13-2016 We used heat shock (HS) treatments and high-throughput mRNA sequencing to obtain HS transcriptomes i...
Transcriptome profiling of zebrafish embryos from the SAT Sanger AB Tubingen strain 2 RNA-seq of coding RNA 01-12-2016 Total RNA was extracted from zebrafish embryos from the SAT (Sanger AB Tubingen) strain. The RNA was...
Transcription profiling by high throughput sequencing of Arabidopsis pollen and seedlings RNA-seq of coding RNA 01-12-2016 Pollen grains of Arabidopsis thaliana contain two haploid sperm cells enclosed in a haploid vegetati...
Circadian rhythm in NIH3T3 cells RNA-seq of coding RNA 01-11-2016 Identification of cyclical expressed coding and non-coding genes during the circadian rhythm in NIH3...
RNA-seq of N. gansuense-infected (E+) vs. non-infected (E-) A. inebrians RNA-seq of coding RNA 01-10-2016 The molecular regulation mechanisms involved in stress tolerance remain largely unknown. Drunken hor...
Cells with Surface Expression of CD133highCD71low are Enriched for Colony-Forming Progenitor Cells in the Adult Murine Pancreas RNA-seq of coding RNA 01-10-2016 Previously, we identified tripotent colony-forming progenitor cells in the adult murine pancreas tha...
Transcriptional responses of an indigenous and an invasive whitefly to different host plants reveal their different capacity of adaptation RNA-seq of coding RNA 01-10-2016 The whitefly Bemisa tabaci is a species complex with global distribution and extensive genetic diver...
Rapid conversion of fibroblasts into functional forebrain GABAergic interneurons by direct genetic reprogramming RNA-seq of coding RNA 12-19-2015 Transplantation of GABAergic interneurons (INs) can sustain long-standing benefits in animal models ...
HSB-2 cells stably expressing LDB1 or mutant LDB1 proteins RNA-seq of coding RNA 12-19-2015 LMO2 is a component of multisubunit DNA-binding transcription factor complexes that regulate gene ex...
Trophoblast stem cells (TSC) global transcriptome in stemness and differentiation conditions after treatment with PF1-3 RNA-seq of coding RNA 12-18-2015 Here we report a potent, acetyl-lysine competitive and cell active inhibitor, PFI-3, that tightly bi...
NSD3-short is an adaptor protein that couples BRD4 to the CHD8 chromatin remodeler RNA-seq of coding RNA
ChIP-seq
12-18-2015 This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
AKT Inhibition Promotes Non-autonomous Cancer Cell Survival [RNA-Seq] RNA-seq of coding RNA 12-12-2015 Small-molecule inhibitors of AKT signaling are being in evaluated in patients with various cancer ty...
Human Embryoid Body Transcriptomes Reveal Maturation Differences Influenced by Size and Formation in Custom Microarrays RNA-seq of coding RNA 12-12-2015 Stem cell differentiation strategies and optimization for generating lineage-specific cells and tiss...
RNA-sequencing analysis of 5' capped RNAs identifies novel differentially expressed genes in sessile serrated colon polyps (SSPs) RNA-seq of coding RNA 12-18-2015 RNA-sequencing of SSP RNA from patients with serrated polyposis syndrome identifies VSIG1 and MUC17 ...
Aedes aegypti Cry11Aa intoxication curve transcriptome RNA-seq of coding RNA 12-19-2015 Transcriptomic analysis of mosquito larvae exposed to LC50 of Cry11Aa toxin from Bti at different ti...
Gene expression analysis to identify Klf2 target genes in B-cell progenitors [Klf2_KO] RNA-seq of coding RNA 12-19-2015 The sequential activation of distinct developmental gene networks governs the ultimate identity of a...
Identification of MEF2B, EBF1, and IL6R as chromosome bound targets of EBNA1 essential for EBV infected B-lymphocyte survival RNA-seq of coding RNA
ChIP-seq
12-19-2015 EBNA1 is the EBV-encoded nuclear antigen required for viral episome maintenance during latency. EBN...
BMP signaling in mouse embryonic stem cells (ESCs) in the naïve and primed pluripotent states [RNA-Seq] RNA-seq of coding RNA 12-12-2015 Carrying out both RNA-seq and Smad1/5 genome-wide chromatin immunoprecipitation and sequencing (ChIP...
Limiting cholesterol biosynthetic flux engages type I IFN signaling in a STING-dependent manner RNA-seq of coding RNA 12-20-2015 Cellular lipid requirements are achieved through a combination of biosynthesis and import programs. ...
A XEN-like state bridges somatic cells to pluripotency during chemical reprogramming RNA-seq of coding RNA 12-20-2015 Pluripotent stem cells can be generated from somatic cells by using pure chemicals.However, the cell...
The life history of retrocopies illuminates the evolution of new mammalian genes RNA-seq of coding RNA 12-19-2015 New genes contribute substantially to adaptive evolutionary innovation, but the functional evolution...
Somatosensory Neuron Types Identified by High-Coverage Single-Cell RNA-Sequencing and Functional Heterogeneity RNA-seq of coding RNA 12-20-2015 Sensory neurons are distinguished by distinct signaling networks and receptive characteristics. Thus...
Parallel single-cell bisulfite- and RNA-sequencing link transcriptional and epigenetic heterogeneity RNA-seq of coding RNA
methylation profiling by high throughput sequencing
12-26-2015 This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
Identifying transcription start sites and active enhancer elements using BruUV-seq RNA-seq of coding RNA 12-26-2015 BruUV-seq utilizes UV light to introduce transcription-blocking DNA lesions randomly in the genome p...
Identification and characterization of MCF01A circular RNAs [RNA-seq] RNA-seq of coding RNA 12-27-2015 Circular RNAs (circRNAs) are widespread circular forms of non-coding RNAs with largely unknown funct...
Response to different types of stress converge in mitochondrial metabolism RNA-seq of coding RNA 12-27-2015 The budding yeast Saccharomyces cerevisiae was used to study 9 different stress conditions in chemos...
A serum microRNA panel as potential biomarkers for hepatocellular carcinoma related with hepatitis B virus RNA-seq of non coding RNA 12-27-2015 Background: The identification of new high sensitivity and specificity markers for HCC are essential...
Quantitative BrdU immunoprecipitation method demonstrates that Fkh1 and Fkh2 are rate-limiting activators of replication origins that reprogram replication timing in G1 phase (BrdU) other
RNA-seq of coding RNA
12-27-2015 The S. cerevisiae Forkhead Box (FOX) proteins, Fkh1 and Fkh2, regulate diverse cellular processes in...
RNA-seq for monitoring expression changes in absence of chromatin anchoring RNA-seq of coding RNA 12-20-2015 RNA-seq for monitoring expression levels in mutants that do not anchor chromatin at the nuclear peri...
RNA Seq in wild type and zfs1 deficient C. albicans RNA-seq of coding RNA 12-20-2015 Members of the tristetraprolin (TTP) family of CCCH tandem zinc finger proteins bind to AU-rich regi...
RNA Polymerase II-associated factor 1 regulates the release and phosphorylation of paused RNA Polymerase II RNA-seq of coding RNA
ChIP-seq
12-20-2015 Release of promoter-proximal paused RNA polymerase II (Pol II) during early elongation is a critical...
A microfluidic platform enabling single cell RNA-seq of multigenerational lineages RNA-seq of coding RNA 12-26-2015 We introduce a microfluidic platform that enables off-chip single-cell RNA-seq after multigeneration...
The role of antigen presenting cells in the induction of HIV-1 latency in resting CD4+ T-cells RNA-seq of coding RNA 12-26-2015 BACKGROUND: Combination antiretroviral therapy (cART) is able to control HIV-1 viral replication, ho...
Dual RNA-seq – sRNA profiling in various cell types RNA-seq of coding RNA 12-20-2015 Bacteria possess many small noncoding RNAs whose regulatory roles in pathogenesis are little underst...
Long non-coding RNAs display higher natural expression variability than protein-coding genes in healthy humans RNA-seq of coding RNA 01-09-2016 Background: Long non-coding RNAs (lncRNAs) are increasingly implicated as gene regulators and may ul...
Transcriptome-wide regulation of pre-mRNA splicing and expression by the RNA-binding protein Quaking during monocyte to macrophage differentiation [RNA-Seq] RNA-seq of coding RNA 01-09-2016 Expression levels of the RNA-binding protein Quaking (QKI) are low in monocytes of early, human athe...
Multiple waves of transcriptome changes during extended hypoxic induction in human pulmonary microvascular endothelial cells RNA-seq of coding RNA 01-02-2016 We profile the expression pattern of human pulmonary microvascular endothelial cells (HPMECs) at dif...
Transcription profiling by high throughput sequencing of somatic and reproductive tissues of Brassica rapa plants following heat shock stress exposure. RNA-seq of coding RNA 01-07-2016 In the current study we have profiled changes in the transcriptome of somatic and reproductive tissu...
Transcription profiling by high throughput sequencing of a maize IBM (Intermated B73×Mo17) RIL population derived from the cross of the inbred lines B73 and Mo17 RNA-seq of coding RNA 01-08-2016 Gene transcription is an essential step of gene function and transcriptome variation is of agronomic...
A conserved factor Dhp1/Rat1/Xrn2 triggers premature transcription termination and nucleates heterochromatin to promote gene silencing ChIP-chip by tiling array
RNA-seq of non coding RNA
01-09-2016 This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
The chicken erythrocyte epigenome other
RNA-seq of coding RNA
ChIP-seq
01-10-2016 This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
Transcription profiling by high throughput sequencing of Arabidospsis ref8-1, med5a/5b, and med5a/5b ref8-1 mutants RNA-seq of coding RNA 01-07-2016 Mutation of the lignin biosynthetic gene REF8, which encodes p-coumaroylshikimate 3'-hydroxylase, ca...
Transcription profiling by RNA-seq of fetal liver from poly(C) binding protein 2 (Pcbp2) knockout mice RNA-seq of coding RNA 01-08-2016 RNA-binding proteins participate in a complex array of post-transcriptional controls essential to ce...
Ubiquitin-dependent turnover of MYC promotes loading of the PAF complex on RNA Polymerase II to drive transcriptional elongation RNA-seq of coding RNA
ChIP-seq
01-09-2016 This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
Adult mouse cortical cell taxonomy by single cell transcriptomics RNA-seq of coding RNA 01-09-2016 Nervous systems are composed of numerous cell types, but the extent of cell type diversity is poorly...
MAGE-A1 Promotes Proliferation, Migration and Invasion of Human Melanoma Cells through RNA-SEQ Analysis via Affecting C-JUN-IL8-ARHGAP29 Network RNA-seq of coding RNA 01-09-2016 To define the role of MAGE-A1 in melanoma growth and metastasis, we performed RNA-seq analysis on MA...
Transcription profiling by high throughput sequencing of maize third node in la1-ref mutant plants RNA-seq of coding RNA 01-05-2016 The classical maize mutant lazy1 (la1), displayed prostrate growth with reduced shoot gravitropism. ...
SIRT6 regulates redox homeostasis in human mesenchymal stem cells by the transactivation of NRF2 RNA-seq of coding RNA
ChIP-seq
01-09-2016 We investigated the effect of SIRT6-knockout on gene expression and H3K4me3 modification profile in ...