Abstract Objectives Decompressive craniectomy is occasionally performed for patients with impending brain death, which is intended to relieve critically elevated intracranial pressure to keep effective intracranial perfusion. It has been in debate if this surgery later affects the result of brain perfusion scintigraphy performed as an ancillary test in the course of brain death diagnosis because rigid closed skull is deemed essential to...
19m
Contributors : Lina Zhang ; Wang Ying ; Mingxi Deng ; Yan YanSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterInvestigation of intratumor heterogeneity in the scrib¹ mutant wing imaginal discs.Method: Staged scrib¹ wing imaginal discs were dissected and transferred to DPBS. The wing imaginal discs were dissociated in 0.25% Trypsin-EDTA solution at 37 ℃ for 10 min. Cells were then washed in DPBS and passed through 35μm filter before library preparation....
27m
Contributors : Xiaowei Zhang ; Hanzhong WangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThis study finds that EV71 has oncolytic activity against experimental human malignant gliomas. RNA-seq analysis of infected glioma cells reveals transcriptional up-regulation, notably genes in apoptosis pathways. Application of virus targeting based on brain-specific microRNA-124 enhances the safety profile. Oncolysis with EV71 may be a potentially novel treatment...
27m
Contributors : Josyf C Mychaleckyj ; Alessandro DoriaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe performed RNA-Seq whole transcriptome analysis of H716 cells grown in two glucose concentrations.
27m
Contributors : Berkley E Gryder ; Xinyu Wen ; Javed KhanSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusWith emerging methods recently developed to capture protein-anchored 3D epigenome folding we herein report an experimental advance yielding a fundamental and systematic improvement in understanding the 3D genome: integrated normalization of orthologous chromatin for measurement of absolute changes in the landscape. With Absolute...
27m
Contributors : Idit Hazan ; Rami AqeilanSeries Type : OtherOrganism : Homo sapiensMapping physiological double strand breaks (DSBs) in cancer cells uncovers transcription-coupled repair mechanism at oncogenic super-enhancers in which RAD51 of the homologous recombination pathway plays a key role supporting the hyper-transcription of related oncogenes.
27m
Contributors : Yuanjun Guo ; Jennifer Y Sui ; Kyungsoo Kim ; Zhentao Zhang ; Xiaoyan A Qu ; Young-Jae Nam ; Robert N Willette ; Joey V Barnett ; Bjorn C Knollmann ; Thomas Force ; Hind LalSeries Type : Expression profiling by arrayOrganism : Mus musculusBackground: Cardiac kinases play a critical role in the development of heart failure, and represent potential tractable therapeutic targets. However, only a very small fraction of the cardiac kinome has been investigated. To identify novel cardiac...
27m
Contributors : Xiaohui Liu ; Donge TangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensOne of the most common congenital disorders of male infertility is Klinefelter syndrome. Because of its extreme heterogeneity in clinical and genetic presentation, the relationship between transcriptome and the clinical phenotype and the associated co-morbidities seen in KS has not been fully clarified yet. We reported here a 47 XXY karyotype Chinese male (KS) with infertility...
27m
Contributor : Li-Fang ChuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensLittle is known about human segmentation clock during somitogenesis. Human embryonic stem (ES) cell differentiation towards PSM and somite cells provide a window of opportunity to probe for the dynamics of oscillatory gene expression. Using high temporal RNA-seq, we captured a transcriptional signature highly reminiscent of segmentation clock during somite differentiation. Our study provides...
27m
Contributors : Laith Al-Eitan ; Amneh H Tarkhan ; Mansour A Alghamdi ; Firas A Al-Qarqaz ; Hadeel S Al-KofahiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe main purpose of this study is to investigate the differences between the gene expression profiles of common warts and healthy skin in HPV-positive individuals by RNA sequencing on the Illumina HiSeq 2500. After obtaining shave biopsies of common warts and healthy skin from twelve Arab males, we were...
27m
Contributor : Daniele M GilkesSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe designed a novel approach to fate-map hypoxic cells in order to determine their cellular response to physiological O2 gradients. Our system causes a change in the expressing fluorescent protein upon hypoxic exposure (DsRed -> GFP). We generated hypoxia fate-mapping tumors using MDA-MB-231 cells expressing our system. Metastatic lungs were resected 2 weeks after primary tumor...
27m
Contributors : Xin-Yu Shi ; Kan Zhai ; Huan-Zhong ShiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe interactions between tumor cells and the host vasculature and immune cells results in increased net fluid production via enhanced plasma extravasation into the pleural space.Understanding the regulatory mechanism of IL-10 in MPE formation is essential both for deciphering how IL-10 acts in regulating tumor immunity and for discovering key molecular targets...
27m
Contributors : Hanns L Ksstsch ; Reinhard UllmannSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIn this study, we describe a potential novel gene expression biomarker for early post-irradiation biodosimetry purposes in BARD1 and we portray the practicability of the established gene expression biomarkers AEN, FDXR and DDB2 after exposure to low dose radiation. Future in-vivo experiments and the inclusion of novel examination procedures present promising approaches...
27m
Contributors : Wenbiao Chen ; Hongyan DiaoSeries Type : Expression profiling by arrayOrganism : Homo sapiensTo explore the lncRNAs and mRNA expression profiles in CHB and asymptomatic HBsAg carriers (ASC) and construct mRNA-lncRNA co-expression profile and ceRNA networks to identify the potential targets of diagnosis and treatment in CHB.
27m
Contributors : Cuidong Wang ; Nathaniel HeintzSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain. Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the cortex-amygdala transition zone (CxA) of adult Lypd1-EGFP/Rpl10a (OI82) mice. This work was supported...
27m
Contributors : Luyi Tian ; Daniela Amann-Zalcenstein ; Jaring Schreuder ; Shalin H NaikSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusA classical view of blood cell development is that multipotent haematopoietic stem and progenitor cells (HSPCs) become lineage-restricted at defined stages. The Lin–c-kit+Sca1+Flt3+ stage, termed lymphoid-primed multipotent progenitors (LMPPs), have lost megakaryocyte and erythroid potential but are heterogeneous in their...
27m
Contributors : Marine Adlanmerini ; Bryce J Carpenter ; Jarrett R Remsberg ; Yann Aubert ; Lindey C Peed ; Hannah J Richter ; Mitchell A LazarSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusIdentification of temperature-selective RevErba binding sites in mice brown adipose tissue.
27m
Contributors : Peiwei Chai ; Xianqun FanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe identified aberrant CTCF binding lead to a 3D chromosomal interactional driver in NTS locus that accelerates tumorigenesis of uveal melanoma. Both enhancer deletion and abolishing CTCF binding lead to the loss of chromosomal looping and triggered therapeutic efficacy in inhibiting tumorigenesis. Our study shed light on a functional chromosomal architecture induced enhancer...
27m
Contributors : Walton Ashley ; Gryder Berkley ; Xinyu Wen ; Javed KhanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensActivation of identity determining transcription factors (TFs), or core regulatory TFs, is governed by cell-type specific enhancers, an important subset of these being super enhancers (SEs). This mechanism is distinct from constitutive expression of housekeeping genes. The characterization of drug-like small molecules to selectively inhibit...
27m
Contributors : Peiwei Chai ; Xianqun FanSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensWe identified aberrant CTCF binding lead to a 3D chromosomal interactional driver in NTS locus that accelerates tumorigenesis of uveal melanoma. Both enhancer deletion and abolishing CTCF binding lead to the loss of chromosomal looping and triggered therapeutic efficacy in inhibiting tumorigenesis. Our study shed light on a functional chromosomal architecture...
27m
Contributors : Bo Lv ; Chaojie LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe adopt mouse pre-implantation embryos to evaluate the effects of different exposure time and illumination intensity. The damage-causing time and intensity is chosen to treat embryos at 2-cell stage. Single-cell transcriptomes from 2-cell to blastocyst stage are analyzed under both control and high-intensity light conditions. These data show that embryo cells at each embryonic...
57m
Contributor : Debasish SinhaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe study was aimed at understanding the expression of known neutrophil regulating factors in the retinal pigment epithelium (RPE) cells with increasing age in a mouse model (Cryba1 cKO, mice lacking gene which codes for beta A3/A1-crystallin protein only in the RPE cells) of age-related macular degeneration
3h
Contributors : Paul Yan ; Athma A Pai ; Julia F Alterman ; Anastasia KhvorovaSeries Type : Expression profiling by high throughput sequencingOrganism : Macaca fascicularisExamine potential off-target effects of HTT targeting siRNA in cynomologus macaque brains.
8h
Contributors : Jeffrey Robinson ; Simon Turkington ; Sarah Abey ; Wendy HendersonSeries Type : OtherOrganism : Homo sapiensAdherent cell layers were grown on permeable membrane inserts culture system using multiple GI cell lines.
9h
Contributor : Marc-André SirardSeries Type : Methylation profiling by high throughput sequencingOrganism : Bos taurusComparison of mitochondrial DNA (mtDNA) methylation patterns in oocytes, blastocysts and ovarian granulosa cells indicates hitherto unsuspected dynamics. Oocytes and blastocysts recovered from animals subjected to ovarian stimulation and from abattoir ovaries were analyzed using bisulphite transformation of DNA followed by whole genome sequencing. The number of mtDNA copies is quite...
10h
Contributors : Clifton L Dalgard ; Harvey B PollardSeries Type : Expression profiling by high throughput sequencingOrganism : Rattus norvegicusWe have previously reported that the cardenolide drug digitoxin blocks TNFα/NFκB-driven proinflammatory signaling. We therefore hypothesized that digitoxin might break the collaborative process between NFκB and TGFβ by also inhibiting expression of TGFBR2. We therefore tested whether TGFβ-driven EMT and resulting metastases would be suppressed.
10h
Contributors : J E Fish ; N KhyzhaSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiensThe purpose of this study was to identify long noncoding RNAs (lncRNAs) that are dysregulated during vascular inflammation and contribute to mRNA regulation. Previous studies have suggested that many lncRNAs interact with protein complexes to regulate their neighboring mRNAs. Therefore, we performed the Human LncRNA Expression Microarray V3.0 (Arraystar) to simultaneously profile the expression...
10h
Contributors : Marcus W Butler ; Neil R Hackett ; Jacqueline Salit ; Yael Strulovici-Barel ; Ronald G CrystalSeries Type : Expression profiling by array ; Genome variation profiling by SNP arrayOrganism : Homo sapiensThe glutathione S-transferase (GST) gene family codes for enzymes that detoxify xenobiotics by catalyzing the conjugation of xenobiotics to glutathione. Based on reports that inherited copy number variations (CNV) in the genome modulate some GST expression levels and with the knowledge...
10h
Contributors : Natasha L Pacheco ; Michelle OlsenSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAstrocytic morphogenesis and maturation are critical steps in CNS development. The time window of astrocyte morphological development is well defined, but the molecular underpinnings are still unclear. BDNF is a critical growth factor involved in the development of the CNS, including synapse refinement. Here we demonstrate the BDNF receptor at Ntrk2 is enriched...
11h
Contributors : Tyler A Allen ; Jeffrey AYoder ; Xinxia PengSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMetastasis accounts for the majority of all cancer deaths, yet the process remains poorly understood. A pivotal step in the metastasis process is the exiting of tumor cells from the circulation, a process known as extravasation. However, it is unclear how tumor cells extravasate, and if multicellular clusters of tumor cells posses the ability to exit...
11h
Contributors : Adeline Berger ; Nicholas J Brady ; David S RickmanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusDespite recent advances in highly effective androgen receptor (AR)-directed therapies for the treatment of prostate cancer, a significant subset of patients with resistant disease develop AR-null, androgen signaling-indifferent neuroendocrine prostate cancer (NEPC). A majority of these NEPC cases that arise following anti-androgen...
12h
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusThis SuperSeries is composed of the SubSeries listed below.
12h
Contributors : Adeline Berger ; Nicholas J Brady ; David S RickmanSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensDespite recent advances in highly effective androgen receptor (AR)-directed therapies for the treatment of prostate cancer, a significant subset of patients with resistant disease develop AR-null, androgen signaling-indifferent neuroendocrine prostate cancer (NEPC). A majority of these NEPC cases that arise following anti-androgen...
12h
Contributors : Sander Lambo ; Marcel KoolSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensETMRs are aggressive pediatric embryonal brain tumors with universally dismal outcome. We collected 193 ETMR samples and an additional 23 matched relapses to investigate the genomic landscape of this distinct entity. We found that patients having tumors without C19MC amplification, the proposed driver, frequently harbor DICER1 germline mutations or other miRNA-related aberrations...
14h
Contributors : Sander Lambo ; Marcel KoolSeries Type : Expression profiling by arrayOrganism : Homo sapiensETMRs are aggressive pediatric embryonal brain tumors with universally dismal outcome. We collected 193 ETMR samples and an additional 23 matched relapses to investigate the genomic landscape of this distinct entity. We found that patients having tumors without C19MC amplification, the proposed driver, frequently harbor DICER1 germline mutations or other miRNA-related aberrations such as somatic...
14h
Contributors : Fei Li ; Jihye Paik ; Hongwu ZhengSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThe goal of this experiment is to determine the effect of ATRX depletion on telomeric chromatin compaction. We adapted the ATAC-seq to quantify telomere chromatin accessibility. By scoring the ratio of sequence reads that contained 3 - 12 tandem telomeric repeats over the total number of reads in wild-type and ATRX deplted cells, our analysis revealed...
15h
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