title: Transcriptional trajectories of human kidney injury progression

status: Public on Feb 21 2019

city: Lugano

first: Pietro

middle: Ernesto

last: Cippa

address: Via Tesserete 46

department: Nephrology

institute: Ente Ospedaliero Cantonale

summary: RNAseq analysis on protocol biopsies obtained from 42 kidney transplant recipients at 4 time points after kidney transplantation.

overall_design: Protocol biopsies obtained before reperfusion, after reperfusion, 3 months and 12 months after kidney transplantation.

middle: E

last: Cippà

first: Andrew

last: McMahon


title: Fatty acid biosynthesis is insufficient in HSCs cultured in serum-free culture conditions

status: Public on Jul 24 2018

city: Tokyo

first: Keiyo

last: Takubo

address: 1-21-1 Toyama Shinjuku-ku

department: Department of Stem Cell Biology

country: Japan

institute: National Center for Global Health and Medicine

summary: Hematopoietic stem cells (HSCs) maintain lifelong hematopoiesis by remaining quiescent in the bone marrow niche. Recapitulation of a quiescent state in culture has not been achieved, as cells rapidly proliferate and differentiate in vitro. By modulating environmental factors mimicking physiological conditions, we were able to maintain engraftable quiescent HSCs for 1 month in culture under low cytokine concentrations, hypoxia, and high fatty acid concentration, the latter required due to suppression of intrinsic fatty acid synthesis. By contrast, high cytokine concentrations or normoxia induced HSC proliferation and differentiation. Our novel culture system provides a means to evaluate properties of steady state HSCs and test effects of defined factors in vitro under near-physiological conditions.

overall_design: CD150+CD41-CD48-CD34-Flt3-LSK cells of pooled bone marrow from 20 mice were sorted into SF-O3 medium and then and either lysed for the fresh sample or cultured for 16 hours either in the serum-free or 10% serum conditions. Cultured cells were centrifuged at 340 x g for 5 min at 4°C and lysed with 75µL RLT buffer + 0.75µL 2-ME. RNA extraction, cDNA synthesis, microarray analysis, and data normalization were outsourced to DNA Chip Research Inc.

first: Hiroshi

last: Kobayashi

first: Ayumi

last: Okinaga


title: Gene expression profiling of tamoxifen-resistant breast cancer MCF7L cells

status: Public on Nov 01 2016

city: Houston

first: Xiaoyong

last: Fu

state: Tx

address: 1 Baylor Plaza

department: Breast Center

country: USA

institute: Baylor College of Medicine

type: Expression profiling by high throughput sequencing

summary: Endocrine resistance is a major obstacle in treating estrogen receptor α (ER)-positive (+) breast cancer.  In order to better understand the mechanism of endocrine resistance, we established a stable tamoxifen-resistant (TamR) MCF7L cell model by culturing the parental (P) MCF7L cells in the presence of 100 nM of 4-hydroxytamoxifen (4HT) for over 6 months.  To characterize the transcriptomic profiles in these cells, we performed an RNA-seq analysis.

overall_design: Gene expression profiles (by RNA-seq) were taken of a TamR cell model.  The tamoxifen-sensitive P cells and TamR cells were compared to each other.

first: Obi

middle: L

last: Griffith

first: Rachel

last: Schiff


title: scMNase-seq measures chromatin accessibility and nucleosome positioning in single cells

status: Public on Jul 23 2018

city: Bethesda

first: Keji

last: Zhao

state: MD

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Nucleosome positioning is critical to chromatin accessibility, and is associated with gene expression programs in cells. Previous nucleosome mapping methods assemble profiles from cell populations and reveal a cell-averaged pattern: nucleosomes are positioned and form a phased array surrounding the transcription start sites (TSSs ) of active genes and DNase I hypersensitive sites (DHSs). However, cells exhibit remarkable expression heterogeneity in response to active signaling even in a homogenous population of cells, which may be related to the heterogeneity in chromatin accessibility. Here, we report a technique, termed single-cell MNase-seq (scMNase-seq), to measure genome-wide nucleosome positioning and chromatin accessibility simultaneously in single cells. Application of scMNase-seq to NIH3T3, mouse primary naïve CD4 T and embryonic stem cells (mESC) reveals two novel principles of nucleosome organization: (1) nucleosomes surrounding TSSs of silent genes or in heterochromatin regions show large positioning variation across different cells but are highly uniformly spaced along the nucleosome array and, (2) In contrast, nucleosomes surrounding TSSs of active genes and DHSs show small positioning variation across different cells but show relatively low spacing uniformness along the nucleosome array. We found a bimodal distribution of nucleosome spacing at DHSs, which corresponds to inaccessible and accessible states and is associated with nucleosome variation and accessibility variation across cells. Nucleosome variation within single cells is smaller than that across cells and variation within the same cell type is smaller than that across cell types. A large fraction of naïve CD4 T cells and mESCs show depleted nucleosome occupancy at the de novo enhancers detected in their respectively differentiated lineages, revealing the existence of cells primed for differentiation to specific lineages in undifferentiated cell populations.

overall_design: Measuring chromatin accessibility and nucleosome positioning in single-cells by applying single-cell MNase-seq to 48 NIH3T3 cells, 198 mouse embryonic stem cells (mESCs), and 278 mouse naïve CD4 T cells.

first: Binbin

last: Lai

first: Weiwu

last: Gao

first: Kairong

last: Cui

first: Wanli

last: Xie

first: Qingsong

last: Tang

first: Wenfei

last: Jin

first: Gangqing

last: Hu

first: Bing

last: Ni


title: A systematically-revised ribosome profiling protocol for bacteria reveals translational pauses at single-codon resolution

status: Public on Feb 08 2019

city: Baltimore

first: Allen

middle: R

last: Buskirk

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: In eukaryotes, ribosome profiling provides insight into the mechanism of protein synthesis at the codon level. In bacteria, however, the method has been more problematic and no consensus has emerged for how to best prepare profiling samples. Here, we identify the sources of these problems and describe new solutions for arresting translation and harvesting cells in order to overcome them. These improvements remove confounding artifacts and improve the resolution to allow analyses of ribosome behavior at the codon level. With a clearer view of the translational landscape in vivo, we observe that filtering cultures leads to translational pauses at serine and glycine codons through the reduction of tRNA aminoacylation levels. This observation illustrates how bacterial ribosome profiling studies can yield insight into the mechanism of protein synthesis at the codon level and how these mechanisms are regulated in response to changes in the physiology of the cell.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Ribosome profiling of E. coli MG1655 using a variety of lysis buffers and cell harvesting conditions


title: Environmental Optimization Enables Maintenance of Quiescent Hematopoietic Stem Cell Ex Vivo

overall_design: CD150+CD41-CD48-CD34-Flt3-LSK cells of pooled bone marrow from 10 mice were sorted into SF-O3 medium and then and either lysed for the fresh sample or cultured for 7 days either in the 4% nBSA or 4% reconstituted BSA conditions. Cultured cells were centrifuged at 340 x g for 5 min at 4°C and lysed with 75µL RLT buffer + 0.75µL 2-ME. RNA extraction, cDNA synthesis, microarray analysis, and data normalization were outsourced to DNA Chip Research Inc.


title: Influence on PPFIA1 knock-down and overexpression to gene expression in primary and metastatic head and neck squamous cell carcinoma cell lines by exon and gene Affymetrix microarrays.

status: Public on Dec 01 2016

city: Helsinki

first: Outi

last: Monni

address: Haartmaninkatu 8

department: Department of Biomedicine

country: Finland

institute: University of Helsinki

summary: 11q13 amplification is one of the most common amplifications in several epithelial cancers and is often related to poor prognosis. The role of several genes mapping to this region, such as PPFIA1, is not well-known. The purpose of our study was to identify genes whose expression is altered due to PPFIA1 knock-down or overexpression. The overall goal was to gain insight into the mechanism by which PPFIA1 affects on progression of head and neck cancers.

overall_design: Three replicates of UT-SCC-24B cell lines were infected with shScramble control and shPPFIA1 shRNA construct. UT-SCC-95 cell line was infected with one control (emptry vector) and two different overexpression constructs targeting PPFIA1. We compared the effect of knockdown and overexpression of PPFIA1 to gene expression profiles of the control samples.

first: Henna

last: Pehkonen

first: Maria

last: Lehtivaara

first: Riku

last: Louhimo


title: Abnormal neutrophil signature in the blood and pancreas of pre-symptomatic and symptomatic type 1 diabetes

status: Public on Nov 30 2018

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Analysis of neutrophils purified from peripheral blood of patients with symptomatic and pre-symptomatic type 1 diabetes (T1D), at risk of T1D, and healthy controls.

overall_design: Subjects were classified into four groups based on type 1 diabetes (T1D) risk or diagnosis. Healthy control subjects with no family history of T1D (N=16) were donors undergoing surgery. Patients with family history of T1D were enrolled in the Type 1 Diabetes TrialNet Pathway to Prevention Trial; these subjects were divided into pre-symptomatic T1D (N=8) or at risk of T1D (N=13) based on the presence/absence (respectively) of 2 or more T1D-related autoantibodies. Symptomatic T1D subjects had clinical diagnosis of T1D, with first insulin injection no more than 10 days prior to the blood draw.

first: Federica

last: Vecchio

first: Nicola

last: Lo Buono

first: Angela

last: Stabilini

first: Laura

last: Nigi

first: Matthew

middle: J

last: Dufort

first: Susan

last: Geyer

first: Paola

middle: M

last: Rancoita

last: Cugnata

first: Andrea

last: Valle

first: Alessandra

last: Mandell

first: Pia

last: Leete

first: Lars

last: Krogvold

first: Francesca

last: Mancarella

first: Norma

last: Maugeri

first: Kevan

last: Herold

first: Helena

last: Larsson

first: Sarah

last: Richardson

first: Noel

last: Morgan

first: Knut

last: Dahl-Jørgensen

first: Peter

middle: S

last: Linsley

first: Jochen

last: Hecht

first: Guido

last: Sebastiani

first: Francesco

last: Dotta

first: Emanuele

last: Bosi

first: Manuela

last: Battaglia


title: PhyloChip-based characterization of stool samples from Familial Mediterranean Fever patients and the effects of probiotic Lactobacillus acidophilus INMIA 9602 Er 317/402

status: Public on Mar 16 2018

city: Berkeley

first: Yvette

last: Piceno

state: CA

address: 1 Cyclotron Rd., MS 70A-3317

department: Ecology

institute: LBNL

summary: Familial Mediterranean fever (FMF) is an inflammatory genetic disease characterized by elevated systemic reactivity against commensal gut microbiota and high levels of gut Candida albicans.  The current study investigated the effects of Lactobacillus acidophillus INMIA 9602 Er 317/402 strain (probiotic “Narine”) on the relative abundance of gut enteric bacteria, lactobacilli, Staphylococcus aureus, and Enteroccocus faecalis in Candida albicans-carrier and non-carrier FMF patients in remission with the main MEFV mutation patterns M694V/V726A- the prevalent MEFV gene mutation within FMF patients in the Armenian cohort.   Our data revealed that M694V/V726A mutations in PURIN inflammasome leading to FMF disease brought to gender specific differences in microbial community structure in FMF patients. Possibly, long-term colchicine use suppresses the PURIN inflammasome/inhibits NLRP3 inflammasome-dependent IL-1β release influencing on overgrowth of C. albicans in gut microbiota of FMF patients.  The comparison of Operational Taxonomic Units (OTUs) of enteric bacteria in C. albicans-carrier and non-carrier female patients revealed the statistically significant increase in OTUs of enterobacteria in C. albicans-carriers. In contrast to this, there were no differences in abundance of Enteroccocus faecalis between female FMF C. albicans-carriers compared with non-carriers, while male FMF C. albicans-carriers have increased abundance of  E. faecalis  in their gut microbiota compared with that of male patients with none carriers. The gut microbiota of FMF patients (both male and female) with C. albicans below baseline level contains high abundance of lactobacilli compared with C. albicans-carriers.  The adoption of Lactobacillus acidophilus INMIA 9602 Er 317/402 leads to changes in gut microbiota composition of FMF patients. It reduces, in particularly, the abundance of enterobacteria in females, and Enteroccocus faecalis in men parallel with reducing the numbers of yeast in gut microbiota of FMF patients.  We hypothesize that colchicine treatment changes the already-altered gut microbiota of FMF patients, thereby affecting the regulation of immune system by inhibition of NLRP3 inflammasome. Colchicine could lead to overgrowth of C. albicans in gut microbiota of FMF patients, whereas the Lactobacillus acidophilus INMIA 9602 Er 317/402 works on activation of inflammasome by new changes in gut microbiota of patients.

platform_organism: Bacteria Archaea

overall_design:
166 samples, patients diagnosed with Familial Mediterranean Fever were given either placebo or treated with Narine or Colibacteron. The human fecal metagenome was analyzed pre- and post-treatment.

Please note that the array probe sequences are under patent therefore no CDF or probe mapping file is available.

first: Astghik

last: Pepoyan

first: Marine

last: Balayan

first: Shigeru

last: Kamiya

first: Tamas

last: Torok

first: Michael

last: Chikindas


title: Gene expression profiling and TF occupancy upon treatment with the FXR agonist obeticholic acid

status: Public on Jan 27 2016

city: Innsbruck

first: Jose Miguel

last: Ramos Pittol

address: Innrain 80-82

department: Institute of Biochemistry

country: Austria

institute: University of Innsbruck

summary: The farnesoid X receptor (FXR) is a nuclear receptor activated by bile acids and regulates bile acid metabolism, glucose and cholesterol homeostasis. From mouse studies we know that the novel FXR agonist obeticholic acid (OCA) regulates expression of many genes in the liver, but there is currently no data on the effects of OCA on human liver gene expression. This is especially relevant since the novel FXR agonist OCA is currently tested in clinical trials for the treatment of several diseases, such as nonalcoholic steatohepatitis (NASH), nonalcoholic fatty liver disease (NAFLD) and Type 2 Diabetes. In this study we investigate the effect of OCA treatment on gene expression profiles and localization of FXR to the genome in relevant liver samples.

overall_design: ChIP-Seq for FXR in Liver tissue from 2 male mice treated with OCA/INT-747 (10mg/kg/day) and 2 male mice treated with vehicle (1% methyl cellulose).

first: Jose

first: Alexandra

last: Milona

first: Michal

last: Mokry

first: Danielle

last: Hollman


title: Single-cell chromatin accessibility data using scATAC-seq

status: Public on Jun 01 2016

city: Cambridge

first: Jason

middle: Daniel

last: Buenrostro

state: MA

address: 415 Main Street

institute: Broad Institute

summary: A single hematopoietic stem cell can give rise to all blood cells with remarkable fidelity. Here, we define the chromatin accessibility and transcriptional landscape controlling this process in thirteen primary cell types that traverse the hematopoietic hierarchy. Exploiting the finding that enhancer landscapes better reflect cell identity than mRNA levels, we enable "enhancer cytometry" for accurate enumeration of pure cell types from complex populations. We further reveal the lineage ontogeny of genetic elements linked to diverse human diseases. In acute myeloid leukemia, chromatin accessibility reveals distinctive regulatory evolution in pre-leukemic HSCs (pHSCs), leukemia stem cells, and leukemic blasts. These leukemic cells demonstrate unique lineage infidelity, confirmed by single cell regulomes. We further show that pHSCs have a competitive advantage that is conferred by reduced chromatin accessibility at HOXA9 targets and is associated with adverse patient outcomes. Thus, regulome dynamics can provide diverse insights into human hematopoietic development and disease.

overall_design: Single-cell ATAC-seq of LMPPs, Monocytes, LSCs and Luekemic blast cells.


title: Nuclear actin is required for transcription during Drosophila oogenesis [ChIP-seq]

status: Public on Aug 01 2018

first: Maria

last: Sokolova

address: Viikinkaari 5

department: Institute of Biotechnology

summary: We demonstrate that actin interacts with essentially all transcribed genes and co-occupies most gene promoters together with RNA polymerase II (Pol II). On highly expressed genes, actin and Pol II can be found also on the gene bodies.

overall_design: chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) of Mrtf-GFP, actin (AC-74 and AC-15) and Pol II phosphorylated at serine 5 (Pol II S5P) in ovaries of wild type (w1118) and Mrtf mutant (mal-dΔ7) flies, where Mrtf expression is abolished in ovaries,  as well as in flies ubiquitously expressing GFP-tagged version of Mrtf (tub mal-d3xGFP)


title: Gene expression profiling in a rat model of monocrotaline-induced heart failure

status: Public on Dec 01 2015

city: Brasília

first: Rolando

middle: Andre Rios

last: Villacis

state: DF

address: Asa Norte

department: Genetics and Morphology

country: Brazil

institute: University of Brasília - UnB

summary: Cardiac cachexia is a common complication of heart failure in severe cases and is associated with a poor prognosis. Several skeletal muscle abnormalities have been described in patients and animals with cardiac cachexia; these include atrophy, fibrosis, altered myosin heavy chain composition, and decreased oxidative capacity. It is also well established that gene expression patterns are substantially altered in cardiac cachexia, but the reasons for such differences are not clear.

overall_design: Total RNA was extracted from skeletal muscle (soleus) samples of three animals with cardiac cachexia (CC) and three control animals (CT). The Affymetrix RaGene 1.0 ST Array platform was used to compare CC and CT samples and identify genes potentially associated with the cardiac cachexia process.

first: Leonardo

middle: N

last: Moraes

middle: A


title: Age and Fasting in C. elegans

status: Public on Dec 08 2017

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

institute: Graduate School of Biostudies, Kyoto University

type: Expression profiling by genome tiling array

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Comparison of miRNA profile of uninfected and Leishmania donovani infected THP1 diffentiated macrophages.

status: Public on Jun 19 2017

city: NEW DELHI

first: Amitabha

last: Mukhopadhyay

state: Delhi

address: Aruna Asaf Ali Marg

department: Cell biology

country: India

institute: National Institute of Immunology

summary: Several intracellular pathogens target the host miRNA to modulate the expression of host proteins for their successful infection and survival. For example, S. typhimurium (Schulte et al., 2011) and Mycobacterium tuberculosis (Kumar et al., 2015) downregulate miRNAs of let-7 family to modulate immune response in host; H. pylori infection induces the expression of miR-155 to inhibit the release of IL-8 (Xiao et al., 2009); L. monocytogens triggers the expression of anti- inflammatory cytokine IFN-β by downregulation of miR-145 (Izar et al., 2012). Similarly, Leishmania infection also modulates the expression of various miRNA in macrophages (Lemaire et al., 2013). Consequently, it has been shown that L. donovani infection downregulates miR-122 expression which lowers serum cholesterol to facilitate infection (Ghosh et al., 2013). Whereas, Leishmania significantly enhances the miR30A- 3p expression and modulates autophagic pathway in macrophages (Singh et al., 2016). To understand how Leishmania modulate the expression of various genes in infected macrophages, we have compared the miRNA profile of uninfected and infected macrophages.

overall_design: miRNA profiling of uninfected and Leishmania donovani infected THP1  differentiated macrophages after 15 h of infection was done to understand the mechanism of regulation of various genes.

first: Jitender

middle: K

last: Verma

first: Ruchir

last: Rastogi


title: Genome wide transcript and miRNAanalysis of invitro and in-vivo  generated human cardiac samples

status: Public on May 12 2015

city: Seattle

first: Hannele

last: Ruohola-Baker

address: UW Medicine at South Lake Union, S580, 850 Republican Street

department: Department of Biochemistry

institute: University of Washington

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the identification of miRNAs and transcripts that are regulated during human cardiac maturation.

overall_design: Examination of  hESC-derived cardiomyocytes , human fetal  tissue and human adult heart tissue for cardiomyocyte maturation.

first: Kavitha

last: Kuppusamy

last: Baker


title: Enhanced T cell responses to IL-6 in type 1 diabetes are associated with early clinical disease and increased IL-6 receptor expression

status: Public on Sep 19 2016

first: Stephanie

last: Osmond

summary: IL-6 is a proinflammatory cytokine implicated in multiple autoimmune diseases. Here we show that IL-6 induced STAT3 and STAT1 phosphorylation is enhanced in CD4 and CD8 T cells from patients with T1D compared to healthy controls. Enhanced IL-6/pSTAT3 is associated with increased surface IL-6R and early clinical disease. The transcriptome of IL-6 treated CD4 T cells from T1D patients reveals upregulation of genes involved in T cell migration. The data suggest that individuals with type 1 diabetes may benefit from therapeutic targeting of the IL-6 pathway.

overall_design: CD4+CD25- T cells were purified from thawed PBMC of seven subjects with type 1 diabetes. Cells were left unstimulated or were treated with 10ng/ml IL-6 for 24 hours. RNA was extracted and RNA sequencing was performed.

first: Christian

last: Hundhausen

first: Elizabeth

last: Whalen

first: Vivian

last: Gersuk

first: Kimberly

last: O'Brian

first: Quynh-Anh

last: Nguyen

first: Dimitry

last: Popov

first: Alice

last: Long

first: Carla

last: Greenbaum

first: Karen

last: Cerosaletti

first: Jane

middle: H

last: Buckner


title: The antineoplastic drug, trastuzumab, dysregulates metabolism in iPSC derived cardiomyocytes.

status: Public on Mar 08 2017

city: Rochester

first: Xuewei

last: Wang

address: 200 1st street

institute: Mayo Clinic

summary:
Background: The targeted ERBB2 therapy, trastuzumab, has had a tremendous impact on management of patients with HER2+ breast cancer, leading to development and increased use of further HER2 targeted therapies. The major clinical side effect is cardiotoxicity but the mechanism is largely unknown. On the basis that gene expression is known to be altered in multiple models of heart failure, we examined differential gene expression of iPSC derived cardiomyocytes treated at day 11 with the ERBB2 targeted monoclonal antibody, trastuzumab for 48 hours and the small molecule tyrosine kinase inhibitor of EGFR and ERBB2.
Methods: Transcriptome sequencing was performed on four replicates from each group (48 hours untreated, 48 hours trastuzumab and 48 hours lapatinib) and differential gene expression analyses were performed on each treatment group relative to untreated cardiomyocytes.
Results: 517 and 1,358 genes were differentially expressed, p<0.05, respectively in cardiomyocytes treated with trastuzumab and lapatinib. Gene ontology analyses revealed in cardiomyocytes treated with trastuzumab, significant down-regulation of genes involved in small molecule metabolism (p=3.22x10-9) and cholesterol (p=0.01) and sterol (p=0.03) processing.
Conclusions: Our study suggests dysregulation of cardiac gene expression and metabolism as key elements of ERBB2 signaling that could potentially be early biomarkers of cardiotoxicity.

overall_design: Differential expression of iPSC-dervied cardiomyocytes treated with trastuzumab or lapatinib

first: Nadine

last: Norton

first: Daniel

last: Serie


title: Nucleosome maps in skeletal muscle in response to diet in vivo

status: Public on May 11 2012

city: Shreveport

first: Tara

last: Henagan

state: LA

address: 1501 Kings Hwy

department: Medical School

institute: Louisiana State University Health Sciences Center - Shreveport

summary: The nucleosome signature reflects the cellular epigenetic memory and contributes to the cellular phenotype and function. Obesity and type 2 diabetes pathogenesis is largely dependent on environmentally-induced epigenetic modifications and is marked by skeletal muscle insulin resistance; however, no in vivo skeletal muscle nucleosome maps exist to date. Herein, whole genome nucleosome maps via MNase-seq in skeletal muscle of mice on a low fat, high fat or high fat diet with the chromatin modifier sodium butyrate show that complex interactions among mitochondrial function, the tissue microenvironment, cellular phenotype and nucleosome landscape determine whole body phenotype and insulin resistance.

overall_design: Skeletal muscle samples (n=5 per group) were pooled after homogenization under liquid nitrogen with a motar and pestle to give one sample per group for MNase-seq


title: Topoisomerase II is required for proper dosage compensation in Drosophila

status: Public on Mar 30 2012

city: Atlanta

first: Edward

last: Ramos

state: GA

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

type: Genome binding/occupancy profiling by genome tiling array

summary:
Investigate Topo II levels in dosage compensated and non-dosage compensated genes
Dosage compensation refers to the equalization of most X-linked gene products between males and females. In Drosophila, it is mediated by the MSL complex that preferentially associates with numerous sites on the X chromosome in somatic cells of males, and is responsible for an enhancement of the transcriptional rate of a substantial number of X-linked genes. Here we show that topoisomerase II (Topo II) is an integral part of the mechanistic basis of dosage compensation and we highlight a novel function for this enzyme. A widely accepted model of transcription postulates that the moving bubble generated by an RNA polymerase elongating complex induces positive DNA supercoiling in the region ahead of the complex and negative supercoiling in its wake. These transitory changes in supercoiling are resolved by the action of topoisomerases. We have investigated the role of Topo II in dosage compensation by RNAi-mediated depletion, and we have used chromatin immunoprecipitation to determine its genomic distribution and relative abundance on X-linked genes. Topo II is enriched on dosage compensated genes and this enrichment is independent from the approximate two-fold enhancement in transcription of these genes. We have demonstrated an RNA-dependent association of Topo II with MLE, the ATPase-helicase subunit of the MSL complex. Our results indicate a role for Topo II that is additional to and different from its function in restoring normal DNA superhelicity during the transcription process.  We suggest that the enhanced level of Topo II alters the DNA supercoiling of compensated gene units to facilitate transcription and could provide a basis for the recent report that the MSL complex enhances transcription by increasing the rate of elongation of RNA polymerase II.

overall_design:
Investigation of dosage compensated gene expression levels in S2 and S2 Topo II RNAi knockdown cells. mRNA was isolated from S2 cells and S2 cells with RNAi knockdown of Topo II.  The mRNA was then converted to cDNA and hybridized to a NimbleGen D. melanogaster gene expression array. 2 replicates each.
S2 cells were ChIP with anti-Topo II antibody

first: John

last: Lucchesi

first: Simona

last: Cugusi


title: Gene expression profiling of parental and TAMR MCF7 cells after knock-down of ER or FOXA1 or overexpresion of FOXA1

status: Public on Nov 01 2016

first: Xiaoyong

last: Fu

summary: Gene expression profiles (RNA seq of parental MCF7 cells and tamoxifen resistant cells after ER or FOXA1 knock down and after overexpression of FOXA1 in parenatl cells).

overall_design: RNA-Seq data of MCF cells and tamoxifen resistant cell lines after ER knock-down/FOXA1 knock down or FOXA1 overexpression.

first: Jeselsohn

last: Rinath

first: Fu

last: Xiaoyong

first: Schiff

last: Rachel


title: The histone demethylase KDM1A sustains the oncogenic potential of MLL-AF9 leukemia stem cells

status: Public on Mar 29 2012

city: Manchester

first: Tim

middle: C

last: Somervaille

state: Lancashire

address: Wilmslow Road

country: United Kingdom

institute: Cancer Research UK Manchester Institute


title: Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling [MethylationEPIC]

status: Public on Sep 12 2016

city: Darlinghurst

first: Ruth

last: Pidsley

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

type: Methylation profiling by genome tiling array

summary: We performed a critical evaluation of the new Infinium MethylationEPIC BeadChip microarray. EPIC covers over 850,000 CpG sites, including >90% of the CpGs from the HumanMethylation450 (HM450) BeadChip and an additional 413,743 CpGs. Even though the additional probes improve the coverage of regulatory elements, including 58% of FANTOM5 enhancers, only 7% distal and 27% proximal ENCODE regulatory elements are represented.  Detailed comparisons of regulatory elements from EPIC and whole-genome bisulphite sequencing data (WGBS) show that a single EPIC probe is not always informative for those distal regulatory elements showing variable methylation across the region.  However, overall data from the EPIC array at single loci are highly reproducible across technical and biological replicates and demonstrate high correlation with HM450 and WGBS data. We show that the HM450 and EPIC arrays distinguish differentially methylated probes, but the absolute agreement depends on the threshold set for each platform.

overall_design: To assess the performance of the EPIC array we ran a series of technical analyses using DNA from different samples types (cell lines, clinical samples and blood) commonly profiled in array-based methylation studies: a transformed prostate cancer cell line (LNCaP); primary cell cultures of prostate epithelial cells (PrEC); patient-matched cancer associated fibroblasts (CAF) and non-malignant tissue associated fibroblasts (NAF); and infant blood from archival Guthrie cards. We first profiled the DNA on both the HM450 and EPIC arrays. LNCaP and PrEC samples were also profiled with WGBS.

first: Elena

last: Zotenko

first: Timothy

last: Peters

first: Susan

last: Clark


title: Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling [WGBS]

type: Methylation profiling by high throughput sequencing


title: Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling


title: Densely interconnected transcriptional circuits control cell states in human hematopoiesis

status: Public on Jan 21 2011

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: Tremendous progress has been made in identifying individual transcription factors that regulate hematopoietic differentiation, but many aspects of the global architecture of hematopoiesis remain unknown. Here, we profiled gene expression in 38 distinct purified populations of human hematopoietic cells and used probabilistic models of gene expression patterns and sequence-based analysis of motifs in gene promoters to decipher the general organization of their regulatory circuitry. We identified modules of highly co-expressed genes, some of which are restricted to a single lineage, but most are expressed at variable levels across multiple lineages. We found densely interconnected cis-regulatory circuits and a large number of transcription factors that are differentially expressed across hematopoietic states, suggesting a more complex regulatory system than previously assumed. We functionally validated a subset of candidate factors using RNA interference and ChIP-Seq. Our dataset, analytic tools, and findings, available on a web-based portal, provide a unique resource to study the regulatory architecture of hematopoiesis.

overall_design: We defined 38 distinct hematopoietic cell states based on cell surface marker expression, representing hematopoietic stem and progenitor cells, terminally differentiated cells, and intermediate states.  For each state, we purified samples separately from 4 to 7 independent donors by multiparameter flow cytometry, yielding 211 profiled samples.  Cells from all stem and progenitor populations were purified from umbilical cord blood. Terminally differentiated lymphocyte populations were purified from peripheral blood.


title: Integrative genomic analyses of neurofibromatosis tumors identify SOX9 as biomarker and survival gene

status: Public on Jul 15 2009

city: Cincinnati

first: Nancy

last: Ratner

state: OH

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital Medical Center

summary:
Understanding biological pathways critical for common neurofibromatosis type 1 (NF1) peripheral nerve tumors is essential, as tumor biomarkers, prognostic factors and therapeutics are all lacking.  We used gene expression profiling to define transcriptional changes between primary normal Schwann cells (n = 10), NF1-derived primary benign neurofibroma Schwann cells (n = 22), malignant peripheral nerve sheath tumor (MPNST) cell lines (n = 13), benign neurofibromas (n = 26) and MPNST (n = 6).  Dermal and plexiform neurofibromas were indistinguishable.  A prominent theme in the analysis was aberrant differentiation. Neurofibromas repressed gene programs normally active in Schwann cell precursors and immature Schwann cells.  MPNST signatures strongly differed; genes upregulated in the sarcomas were significantly enriched for genes activated in neural crest cells.  We validated differential expression of 82 genes including the neural crest transcription factor SOX9 and SOX9 predicted targets.  SOX9 immunoreactivity was robust in neurofibroma and MPSNT tissue sections and targeting SOX9 - strongly expressed in NF1-related tumors - caused MPNST cell death. SOX9 is a biomarker of neurofibroma and MPNST, and possibly a therapeutic target in NF1.

Keywords: tumor stage

overall_design: 86 microarrays, consisting of 77 samples and 9 batch reference samples: NHSC (10), dNFSC (11), pNFSC (11), MPNST cell lines (13), dNF (13), pNF (13), MPNST (6)

first: Walter

last: Jessen


title: The histone demethylase KDM1A sustains the oncogenic potential of MLL-AF9 leukemia stem cells (ChIP-Seq data)

summary: Using a mouse model of human MLL-AF9 leukemia, we identified the lysine-specific demethylase KDM1A (LSD1 or AOF2) as an essential regulator of leukemia stem cell (LSC) potential. KDM1A acts at genomic loci bound by MLL-AF9 to sustain expression of the associated oncogenic program, thus preventing differentiation and apoptosis. In vitro and in vivo pharmacologic targeting of KDM1A using tranylcypromine analogues active in the nanomolar range phenocopied Kdm1a knockdown in both murine and primary human AML cells exhibiting MLL translocations. By contrast, the clonogenic and repopulating potential of normal hematopoietic stem and progenitor cells was spared. Our data establish KDM1A as a key effector of the differentiation block in MLL leukemia which may be selectively targeted to therapeutic effect.

overall_design: To investigate the effects of Kdm1a KD on histone modifications, we performed chromatin immunoprecipitation followed by next-generation sequencing (ChIP-Seq) in control and Kdm1a KD MLL-AF9 AML cells for dimethyl-H3K4 and dimethyl-H3K9, as well as for trimethyl-H3K4 and trimethyl-H3K9. Dimethyl-H3K4 and dimethyl-H3K9 are targeted for demethylation by KDM1A. For each of these histone modifications, we compared the mean ChIP-Seq signal across and around protein coding genes bound by the MLL-AF9 oncoprotein (Bernt et al., 2011) with the mean signal from genes not bound by MLL-AF9 expressed at high, middle or low levels.


title: PTC versus paired normal thyroid tissue

status: Public on Jun 30 2006

city: Valhalla

first: Ismael

last: Reyes

state: NY

address: Microbiology department BSB room 311

institute: New York Medical College

summary:
we analyzed the gene expression profiles of 7 PTC samples compared to 7 paired normal samples using Affymetrix tools and dChip software. The objective was to find potential molecular markers for this disease
Keywords: gene expression analysis

overall_design: we used 7 PTC samples(tumor group) and 7 paired normal thyroid tissue samples (normal group)


title: Gene expression at E9.5 after deletion of type I BMP receptors in the mouse lens placode

status: Public on Mar 09 2015

city: Saint Louis

first: David

middle: Cy

last: Beebe

state: MO

address: 660 S. Euclid Ave.

department: Ophthalmology and Visual Science

institute: Washington University School of Medicine

summary: The type I BMP receptors, Bmpr1a and Acvr1 were conditionally deleted from the mouse lens placode with Le-Cre. The heads of wild type and knockout E9.5 mouse embryos were laser micodissected to isolate the lens ectoderm from three embryos of each genotype. Total RNA was purified and reverse transcribed and amplified using a NuGEN Ovation Pico WTA system kit. cDNA was biotinylated and hybridized to Illumina Mouse6 V1.1 bead arrays.

overall_design: Three wild type and three knockout embryos were used. RNA obtained from the lens ectoderm was pooled, amplified and used for microarray analysis. Statistical analysis was performed using the values from the 25-50 beads on each array.

first: Jie

last: Huang

first: Ying

last: Liu