Ki67 is a nuclear protein expressed during the active phases of the cell cycle, which makes it a biomarker of cell proliferation. In clinical pathology settings, immunohistochemical (IHC) detection of Ki67 is used to calculate Ki67 proliferation indices (PIs), which have prognostic information and are used to subdivide breast carcinomas and neuroendocrine neoplasias. Calculation of Ki67 PIs is notoriously hard and prone to intraobserver and interobserver variance. In addition, IHC protocol settings...
now
Contributors : Manonmani Soundararajan ; Tobias A OelschlaegerSeries Type : Expression profiling by high throughput sequencingOrganism : Escherichia coliRapidly growing antibiotic resistance among gastrointestinal pathogens, and the ability of antibiotics to induce the virulence of these pathogens makes it increasingly difficult to rely on antibiotics to treat gastrointestinal infections. The probiotic E. coli strain Nissle 1917 (EcN) is the active component of the pharmaceutical preparation Mutaflor®...
7h
Contributors : Alexia Martinez de Paz ; Leila Khajavi ; Helene Martin ; Rafael Claveria-Gimeno ; Susanne tom Dieck ; Manjinder Cheema ; Jose Sanchez-Mut ; Malgorzata Moksa ; Annaïck Carles ; Nick Brodie ; Taimoor Sheikh ; Melissa Freeman ; Evgeniy Petrotchenko ; Christoph Borchers ; Erin Schuman ; Matthias Zytnicki ; Adrian Velazquez-Campoy ; Olga Abian ; Martin Hirst ; Manel Esteller ; John Vincent ; Cecile Malnou ; Juan AusioSeries Type : Genome binding/occupancy profiling...
9h
Contributors : Alexander N Dabrowski ; Anshu Shrivastav ; Claudia Conrad ; Kassandra Komma ; Markus Weigel ; Kristina Dietert ; Achim D Gruber ; Wilhelm G Bertrams ; Bernd Schmeck ; Katrin Reppe ; Philippe D N'Guessan ; Sahar Aly ; Norbert Suttorp ; Torsten Hain ; Janine Zahlten ; Jochen WilhelmSeries Type : Expression profiling by arrayOrganism : Mus musculusStreptococcus pneumoniae is the most frequent cause of community-acquired pneumonia. Endogenous antimicrobial proteins such as...
10h
Contributors : Jochen Wilhelm ; Alexander N Dabrowski ; Anshu Shrivastav ; Claudia Conrad ; Kassandra Komma ; Markus Weigel ; Stephanie Plog ; Kristina Dietert ; Achim D Gruber ; Wilhelm G Bertrams ; Bernd Schmeck ; Katrin Reppe ; Philippe D N'Guessan ; Sahar Aly ; Norbert Suttorp ; Torsten Hain ; Janine ZahltenSeries Type : Expression profiling by arrayOrganism : Mus musculusStreptococcus pneumoniae is the most frequent cause of community-acquired pneumonia. Endogenous antimicrobial...
10h
Contributors : Razvan V Chereji ; Terri D Bryson ; Steven HenikoffSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Drosophila melanogasterChromatin mapping using micrococcal nuclease (MNase) has been the standard tool for mapping nucleosomes for >40 years. When coupled with DNA sequencing, MNase-seq can provide base-pair-resolution nucleosome maps. However, determining nucleosome occupancy using MNase-seq has been hampered by its aggressive endo-/exo-nuclease...
10h
Contributor : Yun ZhengSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Macaca mulattaMicroRNAs are small non-coding RNAs that are critical in post-transcriptional regulation. According to the latest miRBase (v22), there are 617 annotated pre-miRNAs in Macaca mulatta, which is much less than 1917 in human, although both of these two species are primates. To improve the annotation of miRNAs in Macaca mulatta, we generated 12 small RNA profiles from 8 tissues and perform...
12h
Contributors : Nicolás Martínez-Calle ; Marien Pascual ; Raquel Ordoñez ; Xabier Agirre ; Felipe ProsperSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensIn this study we have interrogated the DNA methylome of myelofibrosis (MF) patients using high-density DNA methylation arrays. Interestingly, primary and secondary MF showed no differences in DNA methylation profiles, whereas a total of 35,238 differentially methylated CpGs (DMC) corresponding to 10,904 genes...
12h
Contributors : Will Mair ; Anne LanjuinSeries Type : Expression profiling by high throughput sequencingOrganism : Caenorhabditis elegansEvaluating gene expression changes between wildtype worms, raga-1 mutants (loss of gene), and a neuronal rescue worm model
13h
Contributors : Cyril J Peter ; Atsushi Saito ; Schahram Akbarian ; Atsushi Kamiya ; Joan HanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMany neuropsychiatric risk genes contribute to epigenetic regulation of gene expression but very little is known about specific chromatin-associated mechanisms governing the formation and maintenance of neuronal connectivity. Here we show that transcallosal connectivity is critically dependent on C11orf46 (also known...
14h
Contributors : Muthiah Kumaraswami ; Hackwon Do ; Nishanth MakthalSeries Type : Expression profiling by high throughput sequencingOrganism : Streptococcus pyogenesThe goal was to perform global transcriptome analysis on MGAS10870 serotype to investigate and compare the gene expression alterations between ΔmtsR mutant to WT or WT grown in the presence or absence of 100 µM Manganese (MnCl2) to WT grown in the presence of 100µM Manganese (MnCl2)
15h
Contributors : Yong Dong ; Jinyong WangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusHematopoietic stem cell (HSC) gives rise to all the hematopoietic cells. The stemness of HSC is strictly controlled by some transcription factors. Here we show that both of Nras mutation (NrasG12D) and Nup98-Hoxa10HD (NA) improve the transplantation competition ability of HSC. Pathways and differential expression genes analysis show that NrasG12D and NA proteins enhance...
16h
Contributors : Tao Sun ; Jay Kolls ; Wei Chen ; Kong ChenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRationale: Ivacaftor is a recently FDA-approved drug for the treatment of cystic fibrosis (CF) patients with at least one copy of the G511D mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The transcriptomic effect of Ivacaftor in CF patients remains unclear.Objectives: We aim to examine if and how the transcriptome of...
16h
Contributors : Jifan Hu ; Jiuwei Cui ; Yijing ZhaoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMitochondria, the powerhouse of the cell, has been recognized as the key players in cancer cell biology, including cancer metabolism, metastasis, and drug resistance. Recent studies have demonstrated a functional interplay between mitochondria and epithelial-mesenchymal transition (EMT) in cancer. To delineate the role of mitochondrial components in this interplay,...
16h
Contributors : Antonin Papin ; Benoit Tessoulin ; Céline Bellanger ; Anne Moreau ; Yannick Le Bris ; Hervé Maisonneuve ; Philippe Moreau ; Cyrille Touzeau ; Martine Amiot ; Catherine Pellat-Deceunynck ; Steven Le Gouill ; David ChironSeries Type : Expression profiling by arrayOrganism : Homo sapiensThe microenvironment strongly influences mantle cell lymphoma (MCL) survival, proliferation and chemoresistance. However, little is known regarding the molecular characterization of lymphoma...
16h
Contributors : Steven Poser ; Mathias Lesche ; Andreas Dahl ; Yan Ge ; Carlo CannistraciSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCancer stem cells are responsible for the regenerative properties of tumors, manifested as recurrence and metastasis. They can adopt different states, some of which may not be sensitive to current therapies. Modeling distinct states in culture will contribute towards efficient drug discovery. We previously demonstrated...
16h
Contributors : Cyril Carvalho ; Regis Courbeyrette ; Celine Derbois ; Robert Olaso ; Jean-François Deleuze ; Carl Mann ; Jean-Yves ThuretSeries Type : Expression profiling by arrayOrganism : Homo sapiensAnalysis of the transcriptional response to treatment with glucocorticoids in human fibroblasts entering oncogene-induced senescence.
21h
Contributors : Cyril Carvalho ; Regis Courbeyrette ; Cyril Denby-Wilkes ; Carl Mann ; Jean-Yves ThuretSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensAnalysis of the differential binding of EGR1 to chromatin in human fibroblasts entering oncogene-induced senescence, with and without clobetasol.
21h
Contributors : Ya Gao ; Yifang Zhang ; Qingfeng LiSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensHDFs were cultured for 24 hrs for adhesion and to reach 50-70% confluence before mechanical tension was applied. Cyclic mechanical stretch (CMS) with a 0.5-Hz sinusoidal curve at 10-20% elongation was applied using a Flexcell○RFX-5000TM Tension System during the stretching. Cells were harvested immediately after the application of CMS stimulation...
22h
Contributors : Sarah K Sasse ; Margaret Gruca ; Mary A Allen ; Vineela Kadiyala ; Tengyao Song ; Fabienne Gally ; Arnav Gupta ; Miles A Pufall ; Robin D Dowell ; Anthony N GerberSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThis study combined ChIP-seq using two different GR antibodies and stable GR knockdown in Beas-2B airway epithelial cells to determine whether glucocorticoid-mediated repression of inflammatory enhancers requires local...
23h
Contributors : Hui Chen ; Weiwei Feng ; Kun Chen ; Xuchun Qiu ; Hai Xu ; Guanghua Mao ; Ting Zhao ; Yangyang Ding ; Xiangyang WuSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioPhthalate esters (PAEs), a notable plasticizer, could be prolific contaminants in the aquatic environment, and have been shown to induce reproductive toxicity. However, studies concerning the toxicity towards aquatic species are based upon individual chemicals and the combined...
23h
Contributors : Sarah K Sasse ; Margaret Gruca ; Mary A Allen ; Vineela Kadiyala ; Tengyao Song ; Fabienne Gally ; Arnav Gupta ; Miles A Pufall ; Robin D Dowell ; Anthony N GerberSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThis study combined ChIP-seq using two different GR antibodies and stable GR knockdown in Beas-2B airway epithelial cells to determine whether glucocorticoid-mediated repression of inflammatory enhancers requires local...
23h
Contributors : Sarah K Sasse ; Margaret Gruca ; Mary A Allen ; Vineela Kadiyala ; Tengyao Song ; Fabienne Gally ; Arnav Gupta ; Miles A Pufall ; Robin D Dowell ; Anthony N GerberSeries Type : OtherOrganism : Homo sapiensThis study addressed mechanisms through which glucocorticoids exert repressive effects on pro-inflammatory TNF signaling using Global Run-on Sequencing (GRO-seq) in Beas-2B airway epithelial cells treated with dexamethasone and/or TNF for 10 or 30 minutes.
23h
Series Type : Expression profiling by arrayOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.
23h
Contributors : Antwi-Boasiako Oteng ; Anke Loregger ; Michel van Weeghel ; Noam Zelcer ; Sander KerstenSeries Type : Expression profiling by arrayOrganism : Mus musculusScope: Consumption of industrial trans fatty acids unfavourably alters plasma cholesterol and has been linked to NAFLD. However, the mechanisms underlying these deleterious effects of trans fatty acids are unclear. Here, we aim to investigate the molecular mechanisms of action of industrial trans fatty acids. Methods & Results:...
23h
Contributors : Antwi-Boasiako Oteng ; Anke Loregger ; Michel van Weeghel ; Noam Zelcer ; Sander KerstenSeries Type : Expression profiling by arrayOrganism : Mus musculusScope: Consumption of industrial trans fatty acids unfavourably alters plasma cholesterol and has been linked to NAFLD. However, the mechanisms underlying these deleterious effects of trans fatty acids are unclear. Here, we aim to investigate the molecular mechanisms of action of industrial trans fatty acids. Methods & Results:...
23h
Contributors : Antwi-Boasiako Oteng ; Anke Loregger ; Michel van Weeghel ; Noam Zelcer ; Sander KerstenSeries Type : Expression profiling by arrayOrganism : Mus musculusScope: Consumption of industrial trans fatty acids unfavourably alters plasma cholesterol and has been linked to NAFLD. However, the mechanisms underlying these deleterious effects of trans fatty acids are unclear. Here, we aim to investigate the molecular mechanisms of action of industrial trans fatty acids. Methods & Results:...
23h
Contributors : Razvan V Chereji ; Peter R Eriksson ; Josefina Ocampo ; David J ClarkSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusDNA accessibility is thought to be of major importance in regulating gene expression. We test this hypothesis using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors. We measured the digestion rate and the fraction of accessible DNA at all genomic AluI sites in budding...
1d
Contributors : Razvan V Chereji ; Peter R Eriksson ; Josefina Ocampo ; David J ClarkSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeDNA accessibility is thought to be of major importance in regulating gene expression. We test this hypothesis using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors. We measured the digestion rate and the fraction of accessible DNA at all genomic AluI sites...
1d
Series Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculus ; Saccharomyces cerevisiaeThis SuperSeries is composed of the SubSeries listed below.
1d
Contributors : Razvan V Chereji ; Peter R Eriksson ; Josefina Ocampo ; David J ClarkSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeDNA accessibility is thought to be of major importance in regulating gene expression. We test this hypothesis using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors. We measured the digestion rate and the fraction of accessible DNA at all genomic AluI sites...
1d
Contributors : Razvan V Chereji ; Peter R Eriksson ; Josefina Ocampo ; David J ClarkSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeDNA accessibility is thought to be of major importance in regulating gene expression. Here we test this hypothesis, using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors. We measured the digestion rate and the fraction of accessible DNA at all genomic AluI...
1d
Surgical Infections, Ahead of Print.
2h
Abstract Background The immune reconstitution after initiation of highly active antiretroviral therapy (HAART) among HIV-infected individuals substantially affects patients’ prognosis. However, the dynamic characteristics and predictors of reconstitution outcome remain unclear. Methods In this study, the HIV/AIDS patients with sustained virological...
2h
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.
2h
Contributors : Luigi Ombrato ; Ilaria Malanchi ; Probir Chakravarty ; Miriam Llorian-SopenaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe analysed the signature of the non-immune cells from the metastatic niche and the distal lung using the breast tumour 4T1 cell line as a model of lung metastasis from breast cancer
2h
Series Type : Expression profiling by arrayOrganism : Homo sapiensTo comprehensively screen for the changed genes in the MSCs that make up the microenvironment of cancer cells, the characteristics of the risk genes considered in this analysis were compared using microarray analysis.
2h
Contributors : Aurélie Bousard ; Ana Raposo ; Jan J Zylicz ; Christel Picard ; Vanessa Borges Pires ; Yanyan Qi ; Laurène Syx ; Howard Chang ; Edith Heard ; Simão Teixeira da RochaSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusXist RNA has been established as the master regulator of X-chromosome inactivation in female eutherian mammals but its mechanism of action remain unclear. By creating novel Xist mutants at the endogenous locus in...
2h
Contributor : Matthew J LozaSeries Type : Expression profiling by arrayOrganism : Homo sapiensCSF-1 is a key regulator of the macrophage lineage. Macrophages are key mediators of inflammation, cancer, and homeostasis and in some cases differentiate from infiltrating blood monocytes. To better understand the the impact of CSF-1 on blood monocytes, transcriptomic changes in ex vivo cultured human whole blood were measured 4 and 24 hrs after addition of CSF-1 and compared to blood cultured without...
2h
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