title: Acetate Fermentation facilitates survival of Mtb when respiration is inhibited

status: Public on Dec 31 2012

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: Respiratory ATP-synthesis is at present the only known mechanism for ATP synthesis in Mtb. This makes Mtb particularly vulnerable to inhibition of respiratory ATP synthase inhibitors such as TMC207, a novel compound for treatment of tuberculosis. We now provide first evidence that Mtb possesses a pathway that is fermentative in nature that could compensate lack of respiratory ATP synthesis. We identified acetate as a fermentation product in Mtb. Production of acetate was mediated by phosphotransacetylase (Pta) and acetate kinase (AckA). In acetate fermenting Mtb cultures, ATP levels remained stable despite inhibition of respiratory ATP synthase. Deletion of the PtaAckA pathway in Mtb decreased ATP content and impaired survival. This study provides evidence that in Mtb substrate level phosphorylation can compensate lack of oxidative phosphorylation, and thus facilitates survival of Mtb in the absence of respiration. Acetate fermentation contributes to adaptation to respiration-limiting conditions, and plays an important role in the emerging field of fermentative metabolism of Mtb.

overall_design: We performed DNA microarray analysis to validate the reduction of oxygen concentration  by comparing aerobic and hypoxic cultures. RNA was prepared from Mtb after two days of cultivation in aerobic and in hypoxic cultures. At each condition, Mtb were cultured in medium supplemented with glycerol and glucose. Labelled cDNA from three independent experiments was subjected to array analysis.

first: R

first: N

last: Ruecker

first: F

last: Bange


title: Expression data from wild type Sinorhizobium meliloti and mutants in the NSR grown under conditions of high and low nitrogen availability

status: Public on Jan 18 2013

city: Pullman

first: Jennifer

last: Rice

state: WA

address: 100 Dairy Road

country: USA

institute: WSU

summary: Acquisition and utilization of nitrogen is governed by the Nitrogen Stress Response regulatory cascade.  GlnD is the primary nitrogen sensor in this system, and modifies the PII proteins to effect changes in the expression of target genes. We used microarrays to evaluate changes in gene expression due to nitrogen availability, mutation of the glnD gene, and deletion of both PII proteins.

platform_organism:
Sinorhizobium meliloti
Medicago truncatula

overall_design: Sinorhizobium meliloti cultures were grown at 30C to mid-log phase (0.5–0.6 OD600) for RNA extraction and hybridization on Affymetrix microarrays.  Wild-type 1021, a strain containing a mutation in glnD, and a strain with both PII proteins deleted were grown in media containing either 0.05% ammonium chloride or 0.02% sodium glutamate as the nitrogen source.

first: Svetlana

middle: N

last: Yurgel

first: Michael

middle: L

last: Kahn


title: Thrombocythemic Platelets microRNA Profiling

status: Public on Nov 06 2012

city: Stony Brook

first: Xiao

last: Xu

state: NY

address: Stony Brook University

institute: Stony Brook University BME

summary: Post-transcriptional and translational controls mediated by microRNAs (miRNA) regulate diverse biological processes and disease.  We systematically dissected regulatory effects of miRNAs relevant to megakaryocytopoiesis and platelet biology by analyzing expression patterns in 79 subjects with thrombocytosis and healthy controls, and integrated these data with transcriptomic and proteomic platforms.  We identified and validated a unique 21-miRNA genetic fingerprint associated with thrombocytosis, and demonstrated that a discrete 3-member subset effectively defines ET phenotypes.  The genetic signature includes functional guide and passenger strands of the previously-uncharacterized miR 490 (5p and 3p), both of which displayed restricted, low-level expression in megakaryocytes/platelets (compared to leukocytes), and aberrant expression during thrombocytosis, most profound in essential thrombocythemia (ET).  Overexpression of miR 490 in a bilineage differentiation model of megakaryocyte/erythroid progenitor formation was insufficient for hematopoietic stem cell colony differentiation and/or lineage specification.  Systematic integration of transcriptomic and mass spectrometric datasets with functional reporter assays identified dishevelled associated activator of morphogenesis 1 (DAAM1) as a unique miR 490 5p protein target demonstrating decreased expression in ET platelets, putatively modulated by translational control (and not by mRNA target degradation).  Our data define a dysregulated miRNA fingerprint in thrombocytosis, and collectively support a developmentally-restricted function of miR 490 (and its putative DAAM1 target) to conditions associated with exaggerated megakaryocytopoiesis and/or proplatelet formation.

overall_design: Human platelets from a total of 79 samples in 3 phenotypic groups: essential thrombocythemia (ET, N =27), reactive thrombocytosis (RT, N=22) and healthy controls (NO, N=30) were measured on array platform

first: Ian

middle: S

last: Hitchcock

first: Jean

last: Wainer

first: Dmitri

middle: V

last: Gnatenko

first: Wadie

middle: F

last: Bahou


title: Dual RpoH sigma factors in Sinorhizobium meliloti

status: Public on Oct 02 2012

city: Stanford

first: Melanie

middle: J

last: Barnett

state: CA

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

summary: Sinorhizobium meliloti can live as a soil saprophyte, and can engage in a nitrogen fixing symbiosis with plant roots.  To succeed in such diverse environments, the bacteria must continually adjust gene expression.  Transcriptional plasticity in eubacteria is often mediated by alternative sigma factors interacting with core RNA polymerase.  The S. meliloti genome encodes 14 of these alternative sigmas, including two putative RpoH (heat shock) sigmas.  We used custom Affymetrix Symbiosis Chips to characterize the global transcriptional response of S. meliloti rpoH1, rpoH2 and rpoH1 rpoH2 mutants during heat shock and stationary phase growth.  Under these conditions, expression of over 300 genes is dependent on rpoH1 and rpoH2.

overall_design: Gene expression profiling of Sinorhizobium meliloti Rm1021 and its isogenic rpoH1, rpoH2, and rpoH1rpoH2 mutants, subjected to heat shock or stationary phase growth, was performed using custom Affymetrix GeneChips

first: Alycia

last: Bittner

first: Carol

last: Toman

first: Valerie

last: Oke

first: Sharon

middle: R

last: Long


title: Prospective isolation and characterization of renal cancer stem cells from human Wilms' tumor xenografts leads to tumor eradication

status: Public on Dec 01 2012

city: Pittburgh

first: Marcus

middle: James

last: Magister

state: PA

address: 3500 Terrace St.

department: Medicine - PACCM

institute: University of Pittsburgh Medical Center - UPMC

summary:
Downregulation of specific microRNAs contribute to epithelial-mesenchymal transition of Wilms' tumor cancer initiating cells.
In order to gain insight into the biology of initiating cells/cancer stem cells (CIC/CSCs) in Wilms' tumor, we compared the microRNA expression profile of un-sorted propagatable WT xenografts (p-WT Xn), p-WT NCAM+ALDH1+-derived Xn and human fetal kidneys (hFKs). Global microRNA expression analysis showed specific microRNAs to differentially express identifying a strong miRNA signature for the NCAM+ALDH1+ WT CICs.

overall_design: 3 different tissue types (described in 'summary') each with n=4 were homoginized and analyzed for their global miRNA expression profiles. Human Fetal Kidney tissues were used as a control.

first: Naftali

last: Kaminski

first: Naomi

last: Pode-Shakked

first: Benjamin

last: Dekel


title: Microarray Analysis of MicroRNA Expression in Peripheral Blood Mononuclear Cells of critically ill Patients with Influenza A (H1N1)

status: Public on Dec 28 2012

city: Xi’an

first: Hao

last: Song

state: Shaanxi Province

address: NO.3 Xinong Road，Yangling

department: College of Veterinary Medicine

country: China

institute: Northwest A & F University

summary: To determine whether differential expression of cellular microRNAs plays a role in the host response to Influenza A (H1N1) infection, we have employed the Agilent miRNA microarray (V3) as a discovery platform to identify microRNAs between the critically ill Patients with Influenza A (H1N1) and the healthy controls.

overall_design: Five critically ill patients with a diagnosis of 2009 Inflluenza A (H1N1) and three healthy controls were included in the study. The Peripheral Blood Mononuclear Cells (PBMCs) were isolated and total RNA was extracted respectively.

first: Qi

last: Wang

first: Yang

last: Guo

first: Li

middle: D

last: Zhang

first: Jun

last: Cheng


title: The Conserved Polarity Factor PodJ1 Impacts Multiple Cell Envelope-Associated Functions in Sinorhizobium meliloti

status: Public on Aug 10 2012

summary: Although diminutive in size, bacteria possess highly diverse and spatially confined cellular structures.  Two related alpha-proteobacteria, Sinorhizobium meliloti and Caulobacter crescentus, serve as models for investigating the genetic basis of morphologic variations.  S. meliloti, a symbiont of leguminous plants, synthesizes multiple flagella and no prosthecae, whereas C. crescentus, a freshwater bacterium, has a single polar flagellum and stalk.  The podJ gene, originally identified in C. crescentus for its role in polar organelle development, is split into two juxtaposed open reading frames, podJ1 and podJ2, in S. meliloti.  Deletion of podJ1 interferes with flagellar motility, exopolysaccharide production, cell envelope integrity, cell division, and normal morphology, but not symbiosis.  As in C. crescentus, the S. meliloti PodJ1 protein appears to act as a polarity beacon and localizes to the newer cell pole.  Microarray analysis indicates that podJ1 affects the expression of at least 129 genes, the majority of which correspond to observed mutant phenotypes.  The combination of phenotypic characterization, microarray analysis, and suppressor identification suggests that PodJ1 controls a core set of conserved elements, including flagellar and pili genes, the signaling proteins PleC and DivK, and the TacA transcriptional activator, while alternate downstream targets have evolved to suit the distinct lifestyles of individual species.

overall_design: Gene expression profiling of Sinorhizobium meliloti Rm1021 or its isogenic podJ1 deletion mutant, grown to mid exponential phase in rich medium, was performed using custom Affymetrix GeneChips.

first: Alexander

middle: T

last: Fields

first: Joseph

middle: C

last: Chen


title: Whole Transcriptome Analysis of the Silicon Response of the Diatom Thalassiosira pseudonana

status: Public on Oct 01 2012

city: Rockville

first: Ravi

last: Sanka

state: Maryland

address: 9704 Medical Center Drive

institute: JCVI

summary: Diatom cell walls, made of nanostructured silica, are of interest in diverse areas ranging from cellular structure, to hierarchical organization in biomineralization, to nanotechnology. Thus far, only cell surface proteins and proteins tightly associated with silica matrix have been characterized, and essential components of the silica deposition vesicle (SDV) are unknown, including components of the SDV membrane, cytoskeletal-interacting proteins, and proteins involved in trafficking associated with the SDV.  Thus, an understanding of most of the molecular components and the dynamics of cellular processes involved in cell wall synthesis is lacking.  In this work we report the first whole-cell response analysis using whole genome microarrays to identify genes potentially involved in diverse aspects of diatom cell division or cell wall synthesis.  Thalassiosira pseudonana transcript profiles from precise time points, known to be associated with specific cell wall formation processes in cell-cycle synchronized cultures, suggests that this gene set includes extracellular proteins, silica matrix proteins, and proteins involved in signal transduction, vesicle trafficking, and transport. Protein localization experiments further confirm the first discovery of proteins associated with the SDV membrane. We propose that these proteins provide the interface between extra-SDV organization by the cytoskeleton and intra-SDV organization of silica polymerization determinants, which lead to the higher order organization of diatom silica structure.

overall_design: Analyzed mRNA from 0, 2, 4, 7, 8 and 9 hr of synchronized cell cycle  using the Affymetrix GeneChip whole genome tiling array. Initial analysis of gene level expression was performed using Affymetrix Expression Console Software, version 1.1. No biological replicates were performed. 0 hr is used as reference point.

first: Roshan

middle: P

last: Shrestha

first: Benoit

last: Tesson

first: Trina

last: Norden-Krichmar

first: Stephen

last: Federowicz

first: Mark

last: Hildebrand

first: Andrew

middle: E

last: Allen


title: Gene expression and epigenetic profiling of CD34+ hematopoietic progenitor cells in multiple sclerosis patients (miRNA)

status: Public on Sep 05 2012

city: Hamburg

first: Christian

last: Schulze

address: Falkenried 94

country: Germany

institute: ZMNH

summary: Intense immunosuppression followed by autologous hematopoietic stem cell transplantation (aHSCT) is a potential treatment for patients suffering from aggressive multiple sclerosis (MS). However it remains unresolved whether autologous CD34+ hematopoietic progenitor cells of MS patients show gene expression differences prior to aHSCT that indicate a preset proinflammatory state, which would then also predispose to or predetermine recurrence of the autoimmune disease. To approach this key point we compared the micro RNA gene expression signature of CD34+ cells collected from MS patients and healthy donors (HD). Gene expression of CD34+ cells was analysed with the Human miRNA Microarray (Agilent-Technologies) chip. No substantial alterations in the gene expression profile of CD34+ HPCs in MS were observed.

overall_design: Samples of CD34+ cells were obtained from 4 female MS patients and 4 age matched  healthy donors (3 female) mobilized by G-CSF (2x5μg/kg/day). White blood cells, containing the CD34+ cell fraction, were collected by leucocytapheresis from peripheral blood, frozen and stored in liquid nitrogen. All samples were thawed and processed at one center and CD34+ HPCs purified by magnetic bead separation using the autoMACS system (Miltenyi). Purity and viability of CD34+ cells was analyzed by Fluorescence Activated Cell Sorter (FACS). Total cellular RNA were extracted with TRIzol reagent and analyzed with the Human miRNA Microarray (Agilent-Technologies).

first: Andreas

last: Lutterotti

first: Ilijas

last: Jelcic

first: Sven

last: Schippling

first: Petra

last: Breiden

first: Benedetta

last: Mazzanti

first: Stefanie

last: Reinhard

first: Massimo

last: DiGioia

first: Annamaria

last: Repice

first: Luca

last: Massacesi

last: Sputtek

first: Gabriela

last: Salinas-Riester

first: Nicolaus

last: Kroeger

first: Mireia

last: Sospedra

first: Riccardo

last: Saccardi

first: Axel

last: Zander

first: Roland

last: Martin


title: Differential expression of microRNAs between oral squamous cell carcinoma and healthy control tongues

city: Bethesda

first: Hyun Min

last: Jung

state: MD

address: 6 Center Drive

department: Division of Developmental Biology

institute: National Institutes of Health

summary: In order to identify aberrantly expressed microRNAs in oral squamous cell carcinomas (OSCCs), we have employed microRNA microarray profile using healthy tongue samples as control. All seventeen human OSCCs and three normal tongue tissues were collected from the Tissue Bank at the Moffitt Cancer Center and approved by the University of Florida institutional review board. Majority (15 out of 17) of the OSCCs were derived from tongue cancers. The tumor samples contained greater than 80% of cancerous cells, confirmed by microscopic examination by a head and neck pathologist. The normal tongues were taken from a non-cancerous region. Tissues were snap-frozen and stored at -80°C until further use. Total RNAs were isolated from human tissues using mirVana miRNA Isolation kit (Ambion/Applied Biosystems, Austin, TX) according to the manufacturer’s instruction. NanoDrop® ND-100 spectrophotometer (Thermo Scientific, Wilmington, DE) was used to quantify the isolated RNA. The Agilent 2100 Bioanalyzer from the Interdisciplinary Center for Biotechnology Research at the University of Florida was used to detect the size distribution of total RNA and to determine the quality as well. Expression of microRNAs from this signature was quantified in the same RNA samples by real-time PCR, confirming the expression pattern.

overall_design: Human tissues of oral squamous cell carcinoma and healthy normal tongues were used for microRNA microarray profile to identify aberrantly expressed microRNAs in oral squamous cell carcinomas.

first: Hyun

middle: M

first: Rushi

last: Patel

first: Jin

middle: Q

last: Cheng

first: Edward

middle: K

last: Chan


title: Inducible Astrocytomas in Genetically Engineered Mice: Agilent

status: Public on Sep 13 2012

city: Seattle

first: Burak

last: Kutlu

address: 1441 North 34th Street

institute: Institute for Systems Biology

summary:
To determine the regulatory pathways necessary for astrocytoma formation within complex adult brain microenvironments, we engineered mice for adult astrocyte-specific disruption of key regulators (pRb, Kras and Pten). Drivers of all astrocytoma grades were identified using CreERTM-inducible alleles. Inactivation of pRb was necessary to initiate grade II disease, and was the only lesion to do so.  Additional activation of Kras progressed disease to grade III, while further Pten inactivation facilitated grade IV (glioblastoma) progression. These outcomes were elicited whether somatic events were induced broadly or focally. In vivo inactivation of pRb, which induced astrocyte proliferation and apoptosis, activated the MAPK pathway, while Kras activation and Pten loss triggered PI3K pathways.
TRPhet denotes mice with Inhibition of Rb, Over-expression of Kras and Deletion of one Copy of PTEN.

overall_design: high grade astrocytoma tumors were obtained from tamoxifen induced mice

first: Yurong

last: Song


title: Contribution of microRNA-1275 to Claudin11 protein suppression via a polycomb-mediated silencing mechanism in human glioma stem-like cells.

status: Public on Jul 31 2012

city: Nagoya

first: Keisuke

last: Katsushima

address: 1-1 Kanokoden

country: Japan

institute: Aichi Cancer Center Research Institute

summary: Glioblastomas show heterogeneous histological features, in which tumor cells show distinct phenotypic states that confer different functional attributes. This functional and morphological heterogeneity characterizes aggressive glioblastoma; however, molecular mechanisms underlying the heterogeneity are poorly understood. Glioma stem-like cells (GSCs) are considered able to aberrantly differentiate into diverse cell types and may contribute the establishment of tumor heterogeneity. Using the GSC model, we investigated the differentially expressed microRNAs(miRNAs) and associated epigenetic mechanism that regulate the differentiation of GSCs. MiRNA-microarray showed that 13 and 34 miRNAs were commonly upregulated and downregulated in two independent GSC lines during differentiation, respectively. Among those miRNAs, quantitative-PCR analysis showed that miR-1275 was consistently downregulated during the GSC differentiation along with the upregulation of its target, CLDN11, a marker of oligodendroglial-lineage differentiation. Compellingly, inhibition of miR-1275 with specific antisense oligonucleotide (anti-miR-1275) in GSC increased the expression of CLDN11, together with significant growth suppression. Epigenetic analysis revealed that gain of histone H3 lysine 27 trimethylation (H3K27me3) and loss of H3K9Ac in the pri-miR-1275 promoter were closely associated with the miR-1275 expression. Treatment of 3-Dezaneplanocin-A, an inhibitor of H3K27 methyltransferase, impaired the GSC differentiation in parallel with sustained miR-1275 expression. Our results illuminated the epigenetic regulatory pathways of miR-1275 closely associated with oligodendroglial differentiation, which may contribute to the tissue heterogeneity formation of glioblastomas. Inhibition of miR-1275 induces the GSC differentiation and suppresses tumor cell proliferation, miR-1275 may be a potential therapeutic target for glioblastomas.

overall_design: Human miRNA Microarray V3 kits (G4470C; Agilent Technologies, Santa Clara, California) were used according to the manufacturer’s protocols.  This microarray system contains probes for all 866 human and 89 human viral miRNAs reported from the Sanger database v12.0 (http://microrna.sanger.ac.uk/sequences/).  Each miRNA species is printed 20 times with replicate probes on the array.  Total RNA was isolated with TRIzol reagent (Invitrogen).　One hundred ng of total RNA was labeled with pCp-Cy3 (Agilent Technologies) and 15 units of T4 RNA ligase (GE Healthcare, Little Chalfont, Buckinghamshire, UK) at 16°C for 2 hours.  Labeled samples were purified with MicroBio-Spin 6 columns (Bio-Rad, Richmond, CA) and hybridized to microarray at 55 °C with rotation at 20 rpm for 20 hours.  Microarrays were scanned by an Agilent Scanner (Agilent Scan Control 7.0 software) and analyzed using Agilent Feature Extraction 10.7 software for miRNA microarray.

first: Keiko

last: Shinjo

first: Atsushi

last: Natsume

first: Fumiharu

last: Ohka

first: Makiko

last: Fujii

first: Hirotaka

last: Osada

first: Yoshitaka

last: Sekido

first: Yutaka

last: Kondo


title: Fat body

status: Public on Jun 04 2012

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

type: Genome variation profiling by genome tiling array

summary:
modENCODE_submission_5522
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Most terminally differentiated Drosophila tissues are either polyploid or polytene.  Unlike  normal chromosomes, where the entire chromosome must be replicated exactly once, polytene chromosomes are often differentially replicated with many regions underreplicated and some overreplicated. We will characterize five different polytene tissues using comparative genomic hybridization (CGH) to identify differentially replicated regions of each chromosome. These studies will also identify tissue specific amplicons, where the replication mediated amplification of specific loci is essential for up-regulation of mRNA levels encoding proteins critical for development. The differential replication of polytene chromosomes in Drosophila will provide a unique opportunity to understand how developmental cues and chromosomal domains influence replication initiation.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CGH. BIOLOGICAL SOURCE 1: Strain: Oregon-R Orr-Weaver(genotype : TBA outcross : TBA description : Wild-type Oregon-R population maintained by Terry Orr-Weaver. made_by : wt population ); Tissue: Fatbody; Developmental Stage: cleavage stage; Genotype: TBA; Sex: Unknown; BIOLOGICAL SOURCE 2: Strain: Oregon-R Orr-Weaver(genotype : TBA outcross : TBA description : Wild-type Oregon-R population maintained by Terry Orr-Weaver. made_by : wt population ); Tissue: Fatbody; Developmental Stage: cleavage stage; Genotype: TBA; Sex: Unknown;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Tissue Fatbody

first: David

last: MacAlpine

first: Terry

last: Orr-Weaver

first: Helena

last: Kashevsky


title: miR-34a is downregulated in cis-diamminedichloroplatinum treated sinonasal squamous cell carcinoma patients with poor prognosis.

status: Public on Jun 14 2012

city: Sendai

first: yuriko

last: saiki

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

department: Molecular Pathology

institute: Tohoku University School of Medicine

summary: For the purpose of analyzing mechanisms related to the cis-diamminedichloroplatinum (CDDP) resistance in head and neck squamous cell carcinoma (head and neck SCC), we employed a nasal squamous cell carcinoma (nasal SCC) cell line RPMI2650 and its CDDP resistant substrain RPMI2650CR previously described. The identification of the resistance-related microRNA (miR) clusters was conducted between RPMI2650CR and RPMI2650 using microRNA microarray.

overall_design: microRNA expression of parental and CDDP resistant was measured with or without CDDP treatment in duplicate.

first: Yuriko

last: Saiki

first: Takenori

last: Ogawa

first: Akira

last: Horii


title: Evaluation of microRNA expression in vehicle and metformin-treated breast cancer cells and evaluation of the dicer relevance

status: Public on Jun 05 2012

city: rome

first: andrea

last: sacconi

address: via elio chianesi

country: Italy

institute: regina elena cancer institute

summary: We have evaluated the microRNA expression profile of SUM159 cells stably infected with a control shRNA or a dicer-targeting shRNA treated with vehicle or metformin for 24 hrs at non cytotoxic doses.

overall_design: microRNA expression was evaluated from total RNA extracted from logaritmically growing SUM159 cells stably expressing a control shRNA or a dicer-targeting shRNA and  treated with vehicle (PBS) or metformin (0.5mM) for 24 hrs.

first: Andrea

last: Sacconi

first: Giovanni

last: Blandino


title: Malpigian tubules

summary:
modENCODE_submission_5521
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Most terminally differentiated Drosophila tissues are either polyploid or polytene.  Unlike  normal chromosomes, where the entire chromosome must be replicated exactly once, polytene chromosomes are often differentially replicated with many regions underreplicated and some overreplicated. We will characterize five different polytene tissues using comparative genomic hybridization (CGH) to identify differentially replicated regions of each chromosome. These studies will also identify tissue specific amplicons, where the replication mediated amplification of specific loci is essential for up-regulation of mRNA levels encoding proteins critical for development. The differential replication of polytene chromosomes in Drosophila will provide a unique opportunity to understand how developmental cues and chromosomal domains influence replication initiation.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CGH. BIOLOGICAL SOURCE 1: Strain: Oregon-R Orr-Weaver(genotype : TBA outcross : TBA description : Wild-type Oregon-R population maintained by Terry Orr-Weaver. made_by : wt population ); Tissue: Malpighian tubules; Developmental Stage: cleavage stage; Genotype: TBA; Sex: Female; BIOLOGICAL SOURCE 2: Strain: Oregon-R Orr-Weaver(genotype : TBA outcross : TBA description : Wild-type Oregon-R population maintained by Terry Orr-Weaver. made_by : wt population ); Tissue: Malpighian tubules; Developmental Stage: cleavage stage; Genotype: TBA; Sex: Unknown;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Tissue Malpighian tubules


title: Adult Midgut

summary:
modENCODE_submission_5520
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Most terminally differentiated Drosophila tissues are either polyploid or polytene.  Unlike  normal chromosomes, where the entire chromosome must be replicated exactly once, polytene chromosomes are often differentially replicated with many regions underreplicated and some overreplicated. We will characterize five different polytene tissues using comparative genomic hybridization (CGH) to identify differentially replicated regions of each chromosome. These studies will also identify tissue specific amplicons, where the replication mediated amplification of specific loci is essential for up-regulation of mRNA levels encoding proteins critical for development. The differential replication of polytene chromosomes in Drosophila will provide a unique opportunity to understand how developmental cues and chromosomal domains influence replication initiation.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CGH. BIOLOGICAL SOURCE 1: Strain: Oregon-R Orr-Weaver(genotype : TBA outcross : TBA description : Wild-type Oregon-R population maintained by Terry Orr-Weaver. made_by : wt population ); Tissue: Midgut; Developmental Stage: cleavage stage; Genotype: TBA; Sex: Female; BIOLOGICAL SOURCE 2: Strain: Oregon-R Orr-Weaver(genotype : TBA outcross : TBA description : Wild-type Oregon-R population maintained by Terry Orr-Weaver. made_by : wt population ); Tissue: Midgut; Developmental Stage: cleavage stage; Genotype: TBA; Sex: Unknown;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Tissue Midgut


title: microRNA expression profile in endometrioid endometrial carcinoma (EEC)

status: Public on Jun 01 2012

city: Lublin

first: Anna

last: Torres

address: Jaczewskiego 4

department: Human Anatomy Department

country: Poland

institute: Medical University of Lublin

summary:
The aim of the presented study was to define tissue and plasma miRNA signatures, which could potentially serve as diagnostic and prognostic markers in endometrioid endometrial cancer (EEC), and to investigate miRNA profiles in regard to clinicopathological characteristics of the tumors.

Results: qPCR validation revealed regulation of 14 miRNAs in EEC tissues (miR-9, miR-141,miR-205,miR-203,miR-183,miR-200a*,miR-200b*,miR-200a,miR-200c,miR-429,miR-200b,miR-410,miR-92a,miR-1305) and 9 in plasma samples (miR-449a,miR-1290,miR-1228,miR-203,miR-200a,miR-141,miR-92a, miR-9, miR-301b). Expression of certain miRNAs showed association with FIGO stage, grade and relapse. Two miRNA signatures, miR-205/miR-410 and miR-410/miR-429/miR-92a, classified tumor tissues with higher accuracy in comparison to single miRNAs (AUC 0.972, 95% CI 0.919-0.995 and 0.991, 95% CI 0.948-1.000, resepctively). miRNA signature composed of miR-205 and miR-200a predicted relapse with AUC of 0.854 (95% CI 0.691-0.951). Tissue miRNA signatures were independent prognostic markers of overall (miR-1228/miR-200c/miR-429, HR 2.98) and progression-free survival (miR-1228/miR-429, HR 4.149). Plasma miRNA signatures classified EEC plasma samples with high accuracy.

Conclusions: We conclude that miRNA signatures hold great promise for becoming non-invasive biomarkers for early EEC detection and prognosis.

overall_design: Tissue samples were collected from 122 women (77 EEC and 45 controls). Expression profiling of 866 human miRNAs and 89 human viral miRNAs was performed in 24 samples and was followed by qPCR validation in 104 patients. Of 24 samples analyzed by microarrays, 22 (18 EEC, 4 normal controls) were available for final analysis. Expression of 14 miRNAs was analysed in 48 plasma samples by qPCR.

first: Kamil


title: MeHg exposure zebrafish embryos vs control

status: Public on May 15 2012

city: Eggenstein-Leopoldshafen

first: Jessica

last: Legradi

state: Baden-Wuerttemberg

address: Hermann-von-Helmholtz-Platz 1

department: Institute of Toxicology and Genomics ITG

institute: Karlsruhe Institute of Technology

summary: Gene respons in the central nervous system of zebrafish embryos exposed to the neurotoxicant methyl mercury

overall_design: Two-condition experiment, control vs MeHg exposure embryos (60 µg/l), Biological replicates: 4, dye swaps

first: J

first: N

middle: Y

last: Ho

first: L

last: Yang


title: Longitudinal Genome Wide Analysis of Chronic Lymphocytic Leukemia Reveals Complex Evolution of Clonal Architecture at Disease Progression and at the Time of Relapse

status: Public on Jun 30 2012

city: Scottsdale

first: Esteban

last: Braggio

state: AZ

address: 13208 East Shea Boulevard, MCRB 3-024

department: Biochemistry

institute: Mayo Clinic

summary: Little is known about the extent of intraclonal heterogeneity of CLL tumor cells.  We performed longitudinal whole genome analysis in 22 CLL cases with evidence of clinical progression and/or clinical relapse post therapy.  We demonstrate the striking and unanticipated presence of genetic clonal heterogeneity, with at least 27% of patients exhibiting clonal evolution and 18% showing evidence of multiple subclones.  We show that CLL progression can occur with multiple genetic subclones evolving either in a linear or branching manner.  The analysis reveals a shift in the relative dominance of subclones with the emergence of initially minor clones after therapy all of which were very resistant to secondary therapies.  This study uncovers the clinical importance of tracking subclone diversity in CLL.

overall_design:
All patients had genome wide genetic analysis performed by aCGH on at least two sequential tumor samples >6 months apart.  For the purposes of this study, we classified samples as; time point 1 (TP1) collected >6 months before starting first-line treatment for disease progression; time point 2 (TP2) consisting of tumor samples at the time of progression requiring treatment; and time point 3 (TP3) consisting of tumor samples collected >6 months after initial treatment but prior to subsequent treatments.  Overall, aCGH assay was performed in 54 samples from 22 patients (2 to 4 time points analyzed per patient).  Thus, 6 patients were analyzed at TP1 and TP2, 8 patients at TP2 and TP3, 2 patients at TP1 and TP3, and the remaining 6 patients were analyzed at TP1, TP2 and TP3.
Keyword : array comparative genomic hybridization

first: Rafael

last: Fonseca

first: Neil

last: Kay


title: Lieb SDQ3517_ZFP1_N2_MXEMB

status: Public on Apr 23 2012

first: DCC

last: modENCODE

type: Genome binding/occupancy profiling by genome tiling array

summary:
modENCODE_submission_3561
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Mixed Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Mixed Embryo; temp (temperature) 20 degree celsius; Antibody SDQ3517 ZFP1 (target is ZFP-1); Strain N2

first: Morten

last: Jensen

first: Jason

last: Lieb


title: Strome HK00001_H3K36ME3_13C9_N2_L3_s5

summary:
modENCODE_submission_3557
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temp (temperature) 20 degree celsius; Antibody HK00001 H3K36me3:13C9 (target is H3K36me3); Strain N2

first: Thea

last: Egelhofer

first: Susan

last: Strome


title: Strome HK00001_H3K36ME3_13C9_N2_L4_s6

summary:
modENCODE_submission_3558
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L4 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage L4 Larva; temp (temperature) 20 degree celsius; Antibody HK00001 H3K36me3:13C9 (target is H3K36me3); Strain N2


title: Strome HK00001_H3K36ME3_13C9_N2_YA_s7

summary:
modENCODE_submission_3559
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Germline containing young adult; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage Germline containing young adult; temp (temperature) 20 degree celsius; Antibody HK00001 H3K36me3:13C9 (target is H3K36me3); Strain N2


title: Identification of a Transcription Factor That Is Critical for Malaria Liver Stage Development

status: Public on May 01 2012

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

institute: mie university

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

overall_design: Refer to individual Series


title: Strome HK00001_H3K36ME3_13C9_N2_L2_s4

summary:
modENCODE_submission_3556
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L2 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage L2 Larva; temp (temperature) 20 degree celsius; Antibody HK00001 H3K36me3:13C9 (target is H3K36me3); Strain N2


title: Comparison of gene expression between wild type and AP2-L KO parasites

summary: In the rodent malaria parasite Plasmodium berghei, we found that an AP2 family transcription factor designated AP2-L plays a critical role in the development of the liver stage. Using DNA microarray analysis we showed that the expression of several genes, including those of parasitophorous vacuole membrane proteins, was significantly decreased in the early liver stage of AP2-L-depleted parasites.

overall_design: Gene expression of P. berghei  liver stages was compared between wild type and AP2-L KO parasites. Liver stage parasites were cultured for 24h using HepG2 cells. Ten and seven biologically independent experiments were performed for wild type and AP2-L KO parasites, respectively.

first: Masao

last: Yuda

first: Izumi

last: Kaneko


title: Strome HK00001_H3K36ME3_13C9_N2_L1_s3

summary:
modENCODE_submission_3555
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L1 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage L1 Larva; temp (temperature) 20 degree celsius; Antibody HK00001 H3K36me3:13C9 (target is H3K36me3); Strain N2


title: Strome HK00001_H3K36ME3_13C9_N2_LTEMB_s2

summary:
modENCODE_submission_3554
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Late Embryos; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage Late Embryos; temp (temperature) 20 degree celsius; Antibody HK00001 H3K36me3:13C9 (target is H3K36me3); Strain N2


title: Strome HK00001_H3K36ME3_13C9_N2_EEMB_s1

summary:
modENCODE_submission_3553
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Antibody HK00001 H3K36me3:13C9 (target is H3K36me3); Strain N2


title: Strome WA30534819_H3K4ME3_N2_YA_s7

summary:
modENCODE_submission_3552
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Germline containing young adult; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage Germline containing young adult; temp (temperature) 20 degree celsius; Antibody WA305-34819 H3K4me3 (target is H3K4me3); Strain N2


title: Strome WA30534819_H3K4ME3_N2_L4_s6

summary:
modENCODE_submission_3551
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L4 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage L4 Larva; temp (temperature) 20 degree celsius; Antibody WA305-34819 H3K4me3 (target is H3K4me3); Strain N2


title: Strome WA30534819_H3K4ME3_N2_L2_s4

summary:
modENCODE_submission_3549
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L2 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage L2 Larva; temp (temperature) 20 degree celsius; Antibody WA305-34819 H3K4me3 (target is H3K4me3); Strain N2


title: Strome WA30534819_H3K4ME3_N2_L1_s3

summary:
modENCODE_submission_3548
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L1 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage L1 Larva; temp (temperature) 20 degree celsius; Antibody WA305-34819 H3K4me3 (target is H3K4me3); Strain N2


title: Strome WA30534819_H3K4ME3_N2_LTEMB_s2

summary:
modENCODE_submission_3547
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Late Embryos; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage Late Embryos; temp (temperature) 20 degree celsius; Antibody WA305-34819 H3K4me3 (target is H3K4me3); Strain N2


title: Desai ABAB817_8WG16_N2_LTEMB

summary:
modENCODE_submission_3545
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Late Embryos; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Developmental Stage Late Embryos; temp (temperature) 20 degree celsius; Antibody ABAB817 8WG16:346588 (target is RNA polII CTD domain unphosophorylated); Strain N2

first: Reto

last: Gassmann

first: Arshad

last: Desai


title: Strome WA30534819_H3K4ME3_N2_EEMB_s1

summary:
modENCODE_submission_3546
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Antibody WA305-34819 H3K4me3 (target is H3K4me3); Strain N2


title: Desai ABAB817_8WG16_N2_EEMB

summary:
modENCODE_submission_3544
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Antibody ABAB817 8WG16:346588 (target is RNA polII CTD domain unphosophorylated); Strain N2


title: Ahringer DISN147_H4K20ME1_001_N2_L3

summary:
modENCODE_submission_3538
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temp (temperature) 20 degree celsius; Antibody DISN147 H4K20me1:001 (target is H4K20me1); Strain N2

first: Anne

last: Canonge

first: Julie

last: Ahringer


title: MiRNA profiling in lung epithelial cells during infection with influenza A virus

status: Public on Mar 01 2013

city: Shatin, New Territories

first: Wai Yip

last: Lam

address: Area 39, Lo Kwee-Seong Integrated Biomedical Sciences Building

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong


title: Strome SDQ2324_HPL2_N2_LTEMB

summary:
modENCODE_submission_3438
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Late Embryos; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Late Embryos; temp (temperature) 20 degree celsius; Antibody SDQ2324-HPL2 (target is HPL-2); Strain N2

first: Jacob

last: Garrigues


title: Strome JL00001_DPY27_N2_EEMB

summary:
modENCODE_submission_3435
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Antibody JL00001 DPY27 (target is DPY-27); Strain N2


title: Lieb SDQ2357_AMA1_N2_MXEMB_1

summary:
modENCODE_submission_3432
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Mixed Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Developmental Stage Mixed Embryo; temp (temperature) 20 degree celsius; Antibody SDQ2357-AMA1 (target is AMA-1); Strain N2

first: Christine

last: Whittle


title: Strome DISN147_H4K20ME1_001_N2_EEMB

summary:
modENCODE_submission_3434
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Antibody DISN147 H4K20me1:001 (target is H4K20me1); Strain N2


title: Strome MP07030_H3K4ME2_DAM1570816_N2_EEMB

summary:
modENCODE_submission_3199
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Antibody MP07030 H3K4me2:DAM157816 (target is H3K4me2); Strain N2


title: Strome TJ00001_H3K27ME18835_N2_EEMB

summary:
modENCODE_submission_3180
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Antibody TJ00001 H3K27me1:8835 (target is H3K27me1); Strain N2


title: StromeWA30834809_H3K4ME2_N2_EEMB

summary:
modENCODE_submission_3198
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Antibody WA308-34809 H3K4me2 (target is H3K4me2); Strain N2


title: Lieb SDQ4129_Y39G10AR18_N2_MXEMB

summary:
modENCODE_submission_2970
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Mixed Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Mixed Embryo; temp (temperature) 20 degree celsius; Antibody SDQ4129 Y39G10AR18 (target is Y39G10AR.18); Strain N2


title: Valvular heart disease and atrial fibrillation regulate microRNA expression profiles in left and right atria differently

status: Public on Dec 21 2011

city: Darlinghurst

first: Mark

last: Cowley

state: NSW

address: 384 Victoria St.

department: Genome Informatics & Clinical Genomics

country: Australia

institute: Garvan Institute of Medical Research

summary:
Background: Chronic atrial fibrillation (AF) is a complication associated with the dilated atria of patients with valvular heart disease and contributes to worsened pathology.
Methods and Results: Using microarray technology, we examined microRNA (miR) expression profiles in right and left atrial appendage tissue from valvular heart disease (VHD) patients. Right atrial appendage from patients undergoing coronary artery bypass grafting (CABG) and left atrial (LA) appendage from healthy hearts not used for transplant were used as controls. VHD induced different changes in miR expression in LA compared with right atria (RA). Fifty-two (52) miRs were altered by VHD in LA, compared with 5 in RA tissue. There was no detectable effect of chronic AF on miR expression in LA tissue, but miR expression in RA was strongly influenced by AF, with 47 miRs showing differential expression. LA volume correlated with miR expression changes in both LA and RA, but the affected miRs were different for the two atrial groups.
Conclusions: VHD and AF influence miR expression patterns in LA and RA, but these are affected differently by disease progression and by the development of AF. These findings provide new insights into the progression of VHD. RA tissue is not a useful surrogate for LA in studies of mitral valve disease.

overall_design: 34 arrays from either the left or right atrium from patients with Valvular Heart Disease (VHD), patients undergoing coronary artery bypass grafting (CABG), or healthy controls. Arrays in this series were generated on V2 and V3 Agilent microRNA arrays and analysed in combination.

first: Nicola

last: Cooley

first: Ruby

last: Lin

first: Silvana

last: Marasco

first: Chiew

last: Wong

first: David

last: Kaye

first: Anthony

last: Dart

first: Elizabeth

middle: A

last: Woodcock


title: Identification of a biomarker panel for the intake of the common dietary trans fat elaidic acid (trans∆9-C18:1)

status: Public on Nov 30 2011

city: Aarhus

first: Toke

middle: Krogager

last: Hansen

address: gustav wieds vej 10c

department: Molecular Biology

country: Denmark

institute: Aarhus University

summary: Elaidic acid is an abundant industrial produced trans fatty acid in foodstuffs. Trans fatty acid intake has been correlated to an unfavorable plasma lipoprotein profile and an increased cardiovascular disease risk. The present study aimed to identify a plasma protein biomarker panel related to human intake of elaidic acid. The human liver cell line HepG2-SF was used as a model system, and the cells were maintained for seven days in serum-free medium containing 100 µM elaidic acid (trans∆9-C18:1), oleic acid (cis∆9-C18:1) or stearic acid (C18:0). The secretomes were analyzed by stable isotope labeling of amino acids in cell culture (SILAC), difference in gel electrophoresis (DIGE) and gene expression microarray analysis. Twelve proteins were found to be differentially regulated based on SILAC data (>1.3 fold change, P-value < 0.05), 13 proteins were found to be differentially regulated based on DIGE analysis (>1.3 fold change, P-value < 0.05), and 17 mRNA transcripts encoding extracellular proteins were determined to be affected (>1.3 fold change, P-value < 0.01) following the addition of elaidic acid compared to oleic acid or stearic acid.   The results revealed that 37 proteins were regulated specifically in response to elaidic acid exposure, and nine of these proteins were confirmed to be regulated in this manner by using selected reaction monitoring mass spectrometry.

overall_design: HepG2 cells kept used in serum free conditions. The cells were incubated for seven days in either 100 µM oleic, elaidic or stearic acid, before total RNA was extracted. For each group four biological replicates were made and from the each RNA extraction two technical replicates were made. There is a control group without fatty acid incubation.

last: Krogager

first: Lone

last: Nielsen

first: Jan

last: Enghild


title: The Rpd3 Core Complex is a Chromatin Stabilization Module

status: Public on Jan 01 2012

city: Los Angeles

first: Xiao-Fen

last: Chen

state: California

address: 615 Charles E. Young Dr

department: Biological Chemistry

institute: University of California Los Angeles

summary: The S. cerevisiae Rpd3 large (Rpd3L) and small (Rpd3S) histone deacetylase (HDAC) complexes are prototypes for understanding transcriptional repression in eukaryotes [1]. The current view is that they function by deacetylating chromatin, thereby limiting accessibility of transcriptional factors to the underlying DNA. However, an Rpd3 catalytic mutant retains substantial repression capability when targeted to a promoter as a LexA fusion protein [2]. We investigated the HDAC-independent properties of the Rpd3 complexes biochemically and discovered a chaperone function, which promotes histone deposition onto DNA, and a novel activity, which prevents nucleosome eviction but not remodeling mediated by the ATP-dependent RSC complex. These HDAC-independent activities inhibit Pol II transcription on a nucleosomal template. The functions of the endogenous Rpd3 complexes can be recapitulated with recombinant Rpd3 core complex comprising Sin3, Rpd3, and Ume1. To test the hypothesis that Rpd3 contributes to chromatin stabilization in vivo, we measured histone H3 density genomewide and found that it was reduced at promoters in an Rpd3 deletion mutant but partially restored in a catalytic mutant. Importantly, the effects on H3 density are most apparent on RSC-enriched genes [3]. Our data suggest that the Rpd3 core complex could contribute to repression via a novel nucleosome stabilization function.

overall_design: H3 were ChIP'd from yeast strains and normalized to input.

first: Benjamin

last: Kuryan

first: Tasuku

last: Kitada

first: Nancy

last: Tran

first: Jing-Yu

last: Li

first: Siavash

last: Kurdistani

first: Michael

last: Grunstein

first: Bing

last: Carey


title: Microarray expression analysis of Drosophila DrosDel deficiency lines

status: Public on Apr 03 2012

first: Brian

last: Oliver

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary: Microarray data of DrosDel deficiency (Df/+) and parental strain diploid flies along with spike-in controls was performed on the Nimblegen 12-plex array platform. Samples are named in this dataset according to the following sample naming scheme: tissue_genotype shorthand_sex_biological replicate #.

overall_design: PolyA+ mRNA was isolated in triplicate to quadruplicate from 5 day old adult female or male whole flies.  Female and male mRNA were labeled with Cy3 or Cy5 dyes separately and hybridized to Drosophila 12-plex Nimblegen arrays.

first: John

middle: H

last: Malone

first: Dong-Yeon

last: Cho

first: Nicolas

last: Mattiuzzo

first: Carlo

middle: G

last: Artieri

first: Lichun

last: Jiang

first: Ryan

last: Dale

first: Harold

last: Smith

first: Jennifer

last: McDaniel

first: Sarah

last: Munro

first: Marc

last: Salit

first: Justen

last: Andrews

first: Teresa

last: Przytycka


title: Differential Expressions of miRNAs in resting and activated human in vitro-differentiated NK cells

status: Public on Nov 21 2011

city: Daejeon

first: Tae-Don

last: Kim

address: 125 Gwahak-ro, Yuseong

department: Cell Therapy Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: To investigate miRNA expressions of miRNA upon activation.

overall_design: In vitro-differentiated human NK cells were freshly incubated in the presence of IL15 after 24h deprivation of IL-15. The cells were harvested at the times (0h, resting-Sample 1 and 2; 6h, activated-Sample 3 and 4) and analyzed by microarray.

first: Inpyo

last: Choi


title: MicroRNA expression in primate postnatal brain through lifespan

status: Public on Dec 09 2011

city: Leipzig

first: Mehmet

last: Somel

address: Deutscher Platz 6

department: Evolutionary Genetics

institute: Max Planck Institute for Evolutionary Anthropology

summary: While multiple studies have reported the accelerated evolution of brain gene expression in the human lineage, the mechanisms underlying such change remain poorly understood. Here we address this issue from a developmental perspective, by analyzing mRNA and microRNA (miRNA) expression in two brain regions within macaques, chimpanzees and humans throughout their lifespan. We find that developmental profiles of trans-regulators, such as miRNA, as well as their target genes, show the fastest rates of human-specific evolutionary change. Changes in expression of a few key regulators may be a major driving force behind human brain evolution.

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens

overall_design: Human, chimpanzee and rhesus macaque post-mortem brain samples from the prefrontal cortex and cerebellar cortex were collected. The age ranges of the individuals in all three species covered the respective species' postnatal maturation period from infancy to old adulthood. RNA extracted from the dissected tissue was hybridized to B72.

first: Xiling

last: Liu

first: Hu

last: Haiyang

first: Zheng

last: Yan

first: Philipp

last: Khaitovich


title: Strome WA30534819_H3K4ME3_N2_L3_s5

status: Public on Jul 19 2011

first: DCC

last: modENCODE

summary:
modENCODE_submission_3550
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temp (temperature) 20 degree celsius; Antibody WA305-34819 H3K4me3 (target is H3K4me3); Strain N2

first: Thea

last: Egelhofer

first: Susan

last: Strome


title: A conserved transcriptional regulator governs fungal morphology in widely diverged species [ChIP-chip, Transcriptional regulation by Mit1 and orthologs]

status: Public on Oct 04 2011

city: san francisco

first: Chris

last: Cain

address: 600 16th street

institute: UC San Francisco

summary: In this paper, we examine orthologs of a transcriptional regulator in three fungal species, Saccharomyces cerevisiae, Candida albicans, and Histoplasma capsulatum. We show that, despite an estimated 600 million years since those species diverged from a common ancestor, Wor1 in C. albicans, Ryp1 in H. capsulatum, and Mit1 in S. cerevisiae recognize the same DNA motif. Previous work established that Wor1 regulates white-opaque switching in C. albicans and that its ortholog Ryp1 regulates the yeast to mycelial transition in H. capsulatum. Here we show that the ortholog Mit1 in S. cerevisiae also regulates a morphological transition, in this case pseudohyphal growth. Full genome chromatin immunoprecipitation experiments show that Mit1 binds to the control regions of approximately 94 genes including the previously known regulators of pseudohyphal growth. Through a comparison of full genome chromatin immunoprecipitation experiments for Mit1 in S. cerevisiae, Wor1 in C. albicans, and Wor1 ectopically expressed in S. cerevisiae, we conclude that genes controlled by the orthologous regulators overlap only slightly between these two species. We suggest that the ancestral Wor1/Mit1/Ryp1 protein controlled aspects of cell morphology and that evolutionary movement of genes in and out of the Wor1/Mit1/Ryp1 regulon is responsible, in part, for the differences of morphological forms among these species. Consistent with this idea, ectopic expression of C. albicans Wor1 or H. capsulatum Ryp1 can drive the pseudohyphal growth program in S. cerevisiae.

overall_design: IP strains were compared to untagged or deletion control strains

first: C

middle: W


title: Distinctive microRNA expression profile and potential funtional role in K562 cells

status: Public on Oct 21 2011

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

summary:
Our objective is to decipher a miRNA expression signature associated with Chronic myeloid leukemia (CML), with or without Imatinib or Dasatinib and compared to normal blood leukocytes, and to determine potential target genes and signaling pathways affected by these signature miRNAs.
Background/Aims: MicroRNAs (miRNAs) are short non-coding regulatory RNAs that control gene expression and play an important role in cancer development and progression. However, little is known about the role of miRNAs in chronic myeloid leukemia (CML). Our objective is to decipher a miRNA expression signature associated with CML and to determine potential target genes and signaling pathways affected by these signature miRNAs.  Results: Using miRNA microarrays we characterized the miRNAs expression profile of K562 cells in reference to healthy blood. We also looked into the expression profile of K562 cells treated with imatinib or dasatinib. We identified a miRNA signature that distinguishes K562 cells from healthy blood that included downregulation of miRNAs such as miR-31, miR-34a, miR-143, miR-145, miR-155, miR-196b and miR-564 and upregulation of miR-128. We also identified a miRNA signature that distinguishes untreated K562 cells from the treated ones that included downregulation of miRNAs such as miR-128 and upregulation of miR-564.
Results: Using miRNA microarrays we characterized the miRNAs expression profile of K562 cells in reference to healthy blood. We also looked into the expression profile of K562 cells treated with imatinib or dasatinib. We identified a miRNA signature that distinguishes K562 cells from healthy blood that included downregulation of miRNAs such as miR-31, miR-34a, miR-143, miR-145, miR-155, miR-196b and miR-564 and upregulation of miR-128. We also identified a miRNA signature that distinguishes untreated K562 cells from the treated ones that included downregulation of miRNAs such as miR-128 and upregulation of miR-564.
We next analyzed predicted targets and affected pathways of the deregulated miRNAs. Reassuringly, the analysis identified CML as the main disease associated with these miRNAs. MAPK, TGF-beta and Wnt were the main molecular pathways related with these expression patterns. Utilizing Venn diagrams we found appreciable overlap between the CML-related miRNAs and the MAPK and TGF-beta signaling pathways and focal adhesion-related miRNAs.
Conclusions: The miRNAs identified in this study might offer a pivotal role in CML. Nevertheless, while these data point to a central disease, the precise molecular pathway/s targeted by these miRNAs is variable implying a high level of complexity of miRNA target selection and regulation. These deregulated miRNAs highlight new candidate gene targets allowing for a better understanding of the molecular mechanism underlying the development of CML, and propose possible new avenues for therapeutic treatment.

overall_design: MiRNA profiling of CML: With the objective of deciphering a potential miRNA expression signature associated with CML, we analyzed the miRNAs expression profile of K562 in reference to a pool of 3 healthy blood samples using an miRNA-based microarray chip assay. In addition, to search for Bcr-Abl-dependent or Src-dependant miRNA expression patterns, K562 cells were treated or not with imatinib or with dasatinib to inhibit Bcr-Abl tyrosine kinase activity or Bcr-Abl and Src tyrosine kinase activity, respectively. In order to validate the microarray data and to ensure that the variability observed among samples was not technical, we carried out Taqman miRNA quantitative real-time PCR analysis (Applied Biosystems, USA) on miRNAs that we find to be most relevant, according to bioinformatics analysis (see below) and published data.

first: Rokah

middle: O

last: Hershkovitz

first: G

last: Granot

first: A

last: Ovcharenko

first: S

last: Modai

first: M

last: Toren

first: N

last: Shomron

first: O

last: Shpilberg