Contributors : Emil H Pallesen ; Ieva Bagdonaite ; Hiren J JoshiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe used RNA_Seq to quantify cellular transcripts in human spontaneously immortalized HaCaT keratinocytes upon knock out of GALNT1, GALNT2, or GALNT3 - most abundantly expressed enzyme isoforms initiating mucin-type O-linked glycosylation.
1h
Contributors : M Chen ; M S SundrudSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusCD4+ T cells are tightly regulated by microbiota in the intestine, but whether intestinal T cells interface with host-derived metabolites is less clear. Here, we show that CD4+ T effector (Teff) cells upregulated the xenobiotic transporter, Mdr1, in the ileum to maintain homeostasis in the presence of bile acids. Whereas wild-type Teff cells upregulated Mdr1 in the ileum, those...
1h
Contributors : Shichao Xing ; Qiulan lvSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculuswe detected the gen expression of ileum,jejunum and colon in hyperuricemia and wildtype mice
1h
Contributors : M Chen ; M S SundrudSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusCD4+ T cells are tightly regulated by microbiota in the intestine, but whether intestinal T cells interface with host-derived metabolites is less clear. Here, we show that CD4+ T effector (Teff) cells upregulated the xenobiotic transporter, Mdr1, in the ileum to maintain homeostasis in the presence of bile acids. Whereas wild-type Teff cells upregulated Mdr1 in the ileum, those...
1h
Contributors : Christopher DeVera ; Gianluca TosiniSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose: The presence of a phagocytic peak of photoreceptor outer segments by the retinal pigment epithelium (RPE) one or two hours after the onset of light has been reported for several diurnal and nocturnal species. This peak in phagocytic activity also persists under constant lighting conditions (i.e., constant light or dark) thus demonstrating that the...
1h
Contributor : Yan YimingSeries Type : Methylation profiling by high throughput sequencingOrganism : Gallus gallusWe bed ALV-J-susceptible and ALV-J-resistant chickens. In this work, we find the difference DNA methylation states between ALV-J-susceptible and ALV-J-resistant chickens
1h
Contributors : Randee E Young ; Xin SunSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe goals of this study are to evalute the role of airway smooth muscle during mouse lung development. We have compared Tbx4rtTA;tetOcre;Mycocdf/f (MyocdCKO) mutants to control mice and generated next generation sequencing transcriptome profiling (RNA-seq) to compare the transcriptomes of each genotype.
1h
Contributors : Shannon M Murray ; Daniel C Douek ; Rafick P SekalySeries Type : Expression profiling by arrayOrganism : Homo sapiensMyeloid dendritic cells (mDC) were isolated from antiretroviral therapy (ARV)-treated and untreated people living with HIV (PLWH), and from HIV uninfected Individuals. The results indicate that mDC are altered in genes expression from PLWH. Some RNA transcriptional changes are not completely restored by ARV. This provides more data on myeloid cells, an understudied cell...
1h
Contributors : Misuzu Kurihara ; Kagayaki Kato ; Chiaki Sanbo ; Shuji Shigenobu ; Yasuyuki Ohkawa ; Takeshi Fuchigami ; Yusuke MiyanariSeries Type : OtherOrganism : Mus musculusTo address specificity of ALaP-seq for PMLwt, we performed genome-wide profiling of genomic regions associated with NLS-APEX or PMLca-APEX. Cells were treated with H2O2 to trigger labeling of chromatin with biotin (H2O2+). Experimental negative control for PMLca (H2O2-), where the H2O2 treatment was omitted, was also...
1h
Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.CD4+ T cells are tightly regulated by microbiota in the intestine, but whether intestinal T cells interface with host-derived metabolites is less clear. Here, we show that CD4+ T effector (Teff) cells upregulated the xenobiotic transporter, Mdr1, in the ileum to maintain homeostasis in the presence of bile acids. Whereas wild-type Teff cells upregulated...
1h
Contributors : Misuzu Kurihara ; Kagayaki Kato ; Chiaki Sanbo ; Shuji Shigenobu ; Yasuyuki Ohkawa ; Takeshi Fuchigami ; Yusuke MiyanariSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Mus musculusTo address the roles of PML bodies in transcription under stress condition, we performed ALaP-seq and RNA-seq with paraquat treated mESCs.
1h
Contributors : Francesco Aulicino ; Francesco Sottile ; Elisa Pedone ; Frederic Lluis ; Lucia Marucci ; Maria P CosmaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe Wnt/β-catenin signalling pathway is a key regulator of embryonic stem cell self-renewal and differentiation. Constitutive activation of this pathway has been shown to significantly increase mouse embryonic stem cell (mESC) self-renewal and pluripotency marker expression. In this study, we...
1h
Contributors : Randall J Smith Jr ; Julien V Kann ; Jonathan E Bard ; Donald Yergeau ; Stelios T AndreadisSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe examined the global transcriptome of individual cells in the three cell populations, starting MC from three donors after 1hr adherence to FN pooled, MC-derived EC subjected to shear stress, and HCAEC subjected to shear stress using single cell RNA-sequencing (scRNA-Seq). Analysis showed that the initial...
1h
Contributors : Akshayalakshmi Sridhar ; Akina Hoshino ; Connor Finkbeiner ; Thomas A RehSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo study the development of human retina, we used single cell RNAseq at key fetal stages and followed the development of the major cell types, as well as populations of transitional cells. We also analyzed stem cell (hPSC)-derived retinal organoids; although organoids have a very similar cellular composition at equivalent...
1h
Contributors : Z Zhang ; J W Leavenworth ; E S YangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe report the changes in the transcription profiles of the 4T1 breast cancer cells (control, RNF2 knockout (KO), and RSF1 KO), isolated and enriched from the tumor implanted in the 4th mammary pads by Fluorescence activated cell sorting, and the changes in the infiltrated NK cells. The transcription profiles were measured by RNA sequencing. We found that upon...
1h
Contributors : Thomas Wallach ; Vasudha Srivastava ; Zev GartnerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensbulk sequencing outputs of Caco2 cells after exposure to permeability modifying and permeability rescuing agents.To identify the molecular drivers for methotrexate-induced barrier dysfunction, we conducted RNA sequencing on Caco2 spheroids treated with methotrexate and lactoferrin. Given our observation that barrier function was compromised as early...
1h
Contributors : Binhua P Zhou ; Ren XuSeries Type : Expression profiling by arrayOrganism : Homo sapiensSnail and Twist are two EMT inducer, expression of Snail or Twist will induce EMT in HMLE and MCF10A cells. By introducing Snail or Twist in HMLE and MCF10A cells, which lack the expression of these two proteins, will identify the genes are induced during EMT.We used microarray analysis to compare the gene expression profiles between the mammamry epithleial cells and the cells undergone EMT.
1h
Contributors : Vikram Mathews ; Saravanan Ganesan ; Hamenth Kumar PalaniSeries Type : Expression profiling by arrayOrganism : Homo sapiensAbout 5-10% newly diagnosed and about 20-30% of relapsed acute promyelocytic leukemia (APL) patients will have disease recurrence after receiving currently accepted standards of care. While there are reports of micro-environment mediated drug resistance (EM-DR) in AML, there is no data on the effect of malignant promyelocyte and stromal interaction on Arsenic...
1h
Contributors : Yuan Yuan ; Yilu Zhou ; Yali Li ; Zhenglin Jiang ; Yihua WangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusHyperbaric oxygen (HBO) is widely applied to treat a number of hypoxia-related diseases. Previous studies focused on the immediate effect of HBO-exposure induced oxidative stress on lungs, but knowledge regarding the chronic effects from repetitive HBO exposure is limited, especially at the gene expression level. We found that repetitive...
1h
Contributors : Jung-Woo Eun ; Suk-Woo NamSeries Type : Expression profiling by arrayOrganism : Mus musculusTo better characterize the pathogenesis of hepatocarcinogenesis, we established mouse HCC model by diethylnitrosamine (DEN) exposures and performed whole genome expression profiling.
1h
Contributors : Rafal Donczew ; Linda Warfield ; Derek Pacheco ; Ariel Erijman ; Steven HahnSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeDeletions within genes coding for subunits of the transcription coactivator SAGA caused strong genome-wide defects in transcription and SAGA-mediated chromatin modifications. In contrast, rapid SAGA depletion produced only modest transcription defects at 13% of protein-coding genes – genes that...
5h
Contributors : Rafal Donczew ; Linda Warfield ; Derek Pacheco ; Ariel Erijman ; Steven HahnSeries Type : Expression profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeDeletions within genes coding for subunits of the transcription coactivator SAGA caused strong genome-wide defects in transcription and SAGA-mediated chromatin modifications. In contrast, rapid SAGA depletion produced only modest transcription defects at 13% of protein-coding genes – genes that are generally...
5h
Contributors : Rafal Donczew ; Linda Warfield ; Derek Pacheco ; Ariel Erijman ; Steven HahnSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeDeletions within genes coding for subunits of the transcription coactivator SAGA caused strong genome-wide defects in transcription and SAGA-mediated chromatin modifications. In contrast, rapid SAGA depletion produced only modest transcription defects at 13% of protein-coding genes – genes that...
5h
Contributors : Guanjue Xiang ; Cheryl A Keller ; Elisabeth Heuston ; Belinda M Giardine ; Lin An ; Alexander Q Wixom ; Amber Miller ; April Cockburn ; Michael E Sauria ; Kathryn Weaver ; Jens Lichtenberg ; Berthold Göttgens ; Qunhua Li ; David Bodine ; Shaun Mahony ; James Taylor ; Gerd A Blobel ; Mitchell J Weiss ; Yong Cheng ; Feng Yue ; Jim Hughes ; Douglas R Higgs ; Yu Zhang ; Ross C HardisonSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism...
5h
Contributors : Guanjue Xiang ; Cheryl A Keller ; Elisabeth Heuston ; Belinda M Giardine ; Lin An ; Alexander Q Wixom ; Amber Miller ; April Cockburn ; Michael E Sauria ; Kathryn Weaver ; Jens Lichtenberg ; Berthold Göttgens ; Qunhua Li ; David Bodine ; Shaun Mahony ; James Taylor ; Gerd A Blobel ; Mitchell J Weiss ; Yong Cheng ; Feng Yue ; Jim Hughes ; Douglas R Higgs ; Yu Zhang ; Ross C HardisonSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism...
5h
Contributors : Guanjue Xiang ; Cheryl A Keller ; Elisabeth Heuston ; Belinda M Giardine ; Lin An ; Alexander Q Wixom ; Amber Miller ; April Cockburn ; Michael E Sauria ; Kathryn Weaver ; Jens Lichtenberg ; Berthold Göttgens ; Qunhua Li ; David Bodine ; Shaun Mahony ; James Taylor ; Gerd A Blobel ; Mitchell J Weiss ; Yong Cheng ; Feng Yue ; Jim Hughes ; Douglas R Higgs ; Yu Zhang ; Ross C HardisonSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism...
5h
Contributors : Guanjue Xiang ; Cheryl A Keller ; Elisabeth Heuston ; Belinda M Giardine ; Lin An ; Alexander Q Wixom ; Amber Miller ; April Cockburn ; Michael E Sauria ; Kathryn Weaver ; Jens Lichtenberg ; Berthold Göttgens ; Qunhua Li ; David Bodine ; Shaun Mahony ; James Taylor ; Gerd A Blobel ; Mitchell J Weiss ; Yong Cheng ; Feng Yue ; Jim Hughes ; Douglas R Higgs ; Yu Zhang ; Ross C HardisonSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThousands...
5h
Contributors : Michael R Howitt ; Y G Cao ; Matthew Gologorsky ; Jessica Li ; Adam L Haber ; Moshe Biton ; Jessica Lang ; Monia Michaud ; Aviv Regev ; Wendy S GarrettSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTuft cells are an epithelial cell subset critical for initiating type 2 immune responses to parasites and protozoa in the small intestine. To respond to these stimuli, intestinal tuft cells use taste chemosensory signaling pathways, but the role...
7h
Contributors : Jie Su ; Joan MassagueSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusEpithelial-to-mesenchymal transitions (EMT) play prominent roles during development, regeneration and tumor progression. EMTs are triggered by TGF-β, RAS and other signals that cooperatively induce the expression of master EMT transcription factors such as SNAIL. Here, we elucidate how the TGF-β and RAS pathways jointly trigger EMTs and tie them to broader developmental programs....
10h
Contributors : Jie Su ; Joan MassagueSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusEpithelial-to-mesenchymal transitions (EMT) play prominent roles during development, regeneration and tumor progression. EMTs are triggered by TGF-β, RAS and other signals that cooperatively induce the expression of master EMT transcription factors such as SNAIL. Here, we elucidate how the TGF-β and RAS pathways...
10h
Contributors : Diego R Gelsinger ; Gherman Uritskiy ; Rahul Reddy ; Adam Munn ; Katie Farney ; Jocelyne DiRuggieroSeries Type : Expression profiling by high throughput sequencingOrganism : halite metagenomeRegulatory small RNAs (sRNAs) represent a major class of regulatory molecules that play large-scale and essential roles in many cellular processes across all domains of life. Microbial sRNAs have been primarily investigated in a few model organisms and little is known about the dynamics of...
11h
Contributors : C D Scharer ; J E KohlmeierSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo examine differences in the transcriptome of resident memory CD8 T cells in the lung, influenza nucleoprotein-specific CD8 T cells from the airways , lung parenchyma, and spleen were FACS sorted and RNA isolated for RNA-seq.
12h
Contributors : C D Scharer ; J E KohlmeierSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusTo examine differences in chromatin accessibility of resident memory CD8 T cells in the lung, influenza nucleoprotein-specific CD8 T cells from the airways , lung interstitium, and spleen were FACS sorted and ATAC-seq performed.
12h
Contributors : C D Scharer ; J E KohlmeierSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusTo examine differences in chromatin accessibility of resident memory CD8 T cells in the lung, influenza nucleoprotein-specific CD8 T cells from the airways , lung parenchyma, and spleen were FACS sorted and DNA isolated for ATAC-seq.
12h
Contributors : C D Scharer ; J E KohlmeierSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo examine differences in the transcriptome of resident memory CD8 T cells in the lung, influenza nucleoprotein-specific CD8 T cells from the airways , lung interstitium, and spleen were FACS sorted and RNA isolated for RNA-seq.
12h
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.
12h
Contributors : C D Scharer ; J E KohlmeierSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo examine how the transcriptome of circulating memory CD8 T cells isolated from the spleen are reprogrammed in the lung airways, influenza nucleoprotein-specific CD8 T cells from the spleen were FACS sorted and RNA isolated for RNA-seq or the cells were transferred to the lung airways and allowed to rest for 2 days. Following 2 days, donor influenza nucleoprotein-specific...
12h
Contributors : C D Scharer ; J E KohlmeierSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo examine differences in the transcriptome of resident memory CD8 T cells in the lung, influenza nucleoprotein-specific CD8 T cells from the airways , lung interstitium, lung vasculature, and spleen were FACS sorted and RNA isolated for RNA-seq. In some experiments, FACS sorted cells were transferred into the airways, peritoneum, or in vitro culture before subsequent isolation...
12h
Contributors : Vichaya Ruenjaiman ; Yu-Wei Leu ; Asada Leelahavanichkul ; Monnat Pongpanich ; Tanapat PalagaSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusIn this study, we compared active histone marks (trimethylation on lysine 4 on histone 3 (H3K4me3)) in LPS-stimulated macrophages and LPS/IC-stimulated macrophages using bone marrow derived murine macrophages using ChIP-seq approach.
13h
Contributors : Sandrine Le Guillou ; Antoine Leduc ; Johann Laubier ; Sarah Barbey ; Marie-Noëlle Rossignol ; Rachel Lefebvre ; Sylvain Marthey ; Denis Laloë ; Fabienne Le Provost ; Diane EsquerreSeries Type : Expression profiling by high throughput sequencingOrganism : Bos taurusThe concept of milk as a healthy food has opened the way for studies on milk components, from nutrients to microRNAs, molecules with broad regulatory properties present in large quantities in milk. Characterization...
15h
Contributors : Toomas Silla ; Manfred Schmid ; Yuhui Dou ; Miha Milek ; Koshi Imami ; Dennis Johnsen ; Patrik Polak ; Jens S Andersen ; Mathias Selbach ; Markus Landthaler ; Torben H JensenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRecruitment of the human ribonucleolytic RNA exosome to nuclear polyadenylated (pA+) RNA is facilitated by the Poly(A) Tail eXosome Targeting (PAXT) connection. Besides its core dimer, formed by the exosome co-factor...
16h
Contributors : Lucia Moreira-Teixeira ; Anne O'GarraSeries Type : Expression profiling by arrayOrganism : Mus musculusCharacterisation of blood and lung global transcriptional responses to Mycobacterium tuberculosis infection in distinct mouse models of Tuberculosis
17h
Contributors : Lucia Moreira-Teixeira ; Anne O'GarraSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusCharacterisation of blood and lung global transcriptional responses to Mycobacterium tuberculosis infection in distinct mouse models of Tuberculosis
17h
Series Type : Expression profiling by array ; Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.
17h
Contributors : Lucia Moreira-Teixeira ; Anne O'GarraSeries Type : Expression profiling by arrayOrganism : Mus musculusCharacterisation of blood and lung global transcriptional responses to Mycobacterium tuberculosis infection in distinct mouse models of Tuberculosis
17h
Contributors : Lucia Moreira-Teixeira ; Anne O'GarraSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusCharacterisation of blood and lung global transcriptional responses to Mycobacterium tuberculosis infection in distinct mouse models of Tuberculosis
17h
Contributor : Xuexia ZhouSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe generated the SRSF1 knockdown U87MG and U251 cells by infecting with shRNA virus. Then, we extracted RNAs and performed next generation sequencing. By comparing sequencing data from WT and KD samples in each cell type, we profiled the alternative splicing events and gene expression regulated by SRSF1 in GBM.
18h
Contributors : Natalie Wolf ; Michael Bussmann ; Abigail Koch-Koerfges ; Nino Katcharava ; Julia Schulte ; Tino Polen ; Johannes Hartl ; Julia A Vorholt ; Meike Baumgart ; Michael BottSeries Type : Expression profiling by arrayOrganism : Corynebacterium glutamicum ATCC 13032The cAMP-dependent transcriptional regulator GlxR serves as a central hub in the regulatory network of the actinobacterial model organism Corynebacterium glutamicum and controls expression of ~10% of all genes. The consequences...
19h
Contributors : Lan-Sun Chen ; Waldemar KanczkowskiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAltogether, this is the first study presenting the global changes of the transcriptome in the adrenal microvascular cells. The results of RNA sequencing and subsequent bioinformatics analysis revealed that adrenal vascular endothelial cells are active players not only involved in maintenance of the adrenal gland microenvironment, but also they play a key role...
20h
Contributors : Masood Abu-Halima ; Nicole LudwigSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiensBACKGROUND: Molecular signaling in in vitro fertilization procedures seems to play a crucial role for embryonic development. In a prospective blinded cohort study, we investigated the role of microRNAs (miRNA) and extracellular vesicles (EV) as potential carriers of miRNAs in embryonic culture media. METHODS: Embryonic culture media from 56 female partners undergoing infertility...
20h
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