title: Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions

city: Freising

first: Richard

middle: B.

last: Landstorfer

address: Weihenstephaner Berg 3

department: Chair for Microbial Ecology

institute: Technische Universität München

summary: Multiple infection sources for enterohemorrhagic Escherichia coli O157:H7 are known, including food of animal origin and produce. The ecology of this pathogen outside its human host is largely unknown. One third of its annotated genes still are hypothetical. To identify genetic determinants expressed under environmental factors, we applied strand-specific RNA-sequencing of strain E. coli EDL933 under 11 different biotic and abiotic conditions: LB medium at pH4, pH7, pH9, or at 15°C; LB with nitrite or trimethoprim-sulfamethoxazole; LB-agar surface, M9 minimal medium, spinach leaf juice, surface of living radish sprouts, and cattle feces. Of 5379 annotated genes, only 144 are transcriptionally completely inactive under all conditions. Of 1,771 hypothetical genes, 1,672 exhibit significant transcriptional signals under at least one condition. The pathogenicity island LEE showed highest transcriptional activity in LB medium, minimal medium, and after treatment with antibiotics. Unique sets of genes, including many hypothetical genes, are highly up regulated on radish sprouts, cattle feces, or in the presence of antibiotics. For instance, azoR is biotechnologically important, but its environmental function has been elusive. This gene is highly active on radish sprouts. Further, we observed induction of the shiga-toxin carrying phages by antibiotics and confirmed active biofilm related genes on radish sprouts, in cattle feces, and on agar plates. Thus, environmental transcriptomics uncovers hitherto unknown gene functions and regulatory patterns of Escherichia coli O157:H7.

overall_design: Eleven different conditions were sequenced on the SOLiD system. Of two of the condtions, spinach medium and LB-nitrite, technical replicates were sequenced. Of LB medium and radish sprouts, biological replicates were sequenced on an Illumina MiSeq.

first: Svenja

last: Simon

first: Steffen

last: Schober

last: Keim

first: Siegfried

last: Scherer

first: Klaus

last: Neuhaus


title: Optimization of transcription factor binding map accuracy by utilizing their knockout-mouse models

status: Public on Jul 17 2014

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genome-wide assessment of protein-DNA interactions binding by ChIP-seq is a key technology to study transcription factor (TF) localization and regulation of gene-expression. In ChIP-seq, signal-to-noise-ratio as well as signal specificity depend on many variables including antibody quality, and efforts to improve ChIP-seq data thus far focused mostly on generating better reagents. Here we introduce KOIN (KO implemented normalization) as a novel strategy to increase signal specificity and reduce noise by using TF knockout-mice as a critical control for ChIP-seq.

overall_design: We tested our new peak calling strategy (KO implemented normalization = KOIN) on different ChIP-seq datasets to increase signal specificity and reduce noise.

first: W

last: Krebs

first: S

middle: V

last: Schmidt

first: A

last: Goren

first: D

last: De Nardo

first: L

last: Labzin

first: T

last: Ulas

first: H

last: Theis

first: M

last: Kraut

first: E

last: Latz

last: Beyer

first: J

middle: L


title: Diet-induced chromatin remodeling in mice livers

city: Duarte

first: Amy

last: Leung

address: 1500 E. Duarte Rd

department: Diabetes/Cancer

country: USA

institute: Beckman Research Institute, City of Hope

type: Expression profiling by high throughput sequencing

summary: The tissue-specific packaging of the genome into the nucleus through chromatin is fundamentally involved in gene regulation, and aberrant modifications to chromatin are a hallmark of many diseases. We show here that a high fat (HF) diet leads to substantial chromatin remodeling in the livers of C57BL/6J mice, as compared to mice fed a control diet. Regions of the genome that display the greatest variation in chromatin accessibility between HF and control regions are targeted by transcription factors with known roles in the liver including HNF4α, CEBP/α, and FOXA1. Whereas livers of DBA/2J mice fed a HF or control diet also demonstrate diet-induced chromatin remodeling, the regions displaying the greatest variation are largely distinct from those observed in B6 livers, indicating a crosstalk between genetic and epigenetic components in determining how diet-induced chromatin remodeling is associated with metabolic disease progression.

overall_design: Examination of chromatin remodeling with FAIRE-seq in livers of mice (C57BL/6J and DBA/2J) fed a high fat or control diet. Complemented with gene expression and H3K4me1 analyses

first: Brian

last: Parks

first: Juan

last: Du

first: Candi

last: Trac

first: Ryan

last: Setten

first: Kevin

last: Brown

first: Aldons

middle: J

last: Lusis

first: Rama

last: Natarajan

first: Dustin

middle: E

last: Schones


title: Integrative analysis of differentially expressed microRNAs in pulmonary alveolar macrophages from pigs infected with H1N1 swine influenza A virus at different time points

city: Yangling

first: Zhao

last: Xing

state: (Click to Select US State)

address: No.3 Taicheng Road, Yangling, Shaanxi, China

department: College of Veterinary Medicine

country: China

institute: NORTHWEST A&F UNIVERSITY

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: The goals of this study is to analyze differentially expressed microRNAs in pulmonary alveolar macrophages  from pigs infected with H1N1 swine influenza A virus at different time points.
Methods: miRNA profiles in PAMs from pigs infected with H1N1 SwIV at three time points were generated by deep sequencing. Differentially expressed miRNAs were then identified and their targets were predicted. For these targets, GO and KEGG analyses were performed and protein-protein interaction networks regulated by DE miRNAs were constructed.
Results: Comparing to control group, 70 and 16 DE miRNAs were respectively identified on post-infection day (PID) 4 and PID 7. 56 DE miRNAs were identified between PID4 and PID7. GO and KEGG analyses indicated that most of targets for these DE miRNAs were related to immune and inflammatory  responses.
Conclusions: Our study represents the first integrative analysis of DE miRNAs in PAMs infected with H1N1 SwIV at different time points. The results in this study would enable us to better understand the underlying pathogenesis of H1N1 SwIV infection in pigs. Furthermore, these data would be very useful for investigating the functions and regulatory mechanisms of miRNAs in human inﬂuenza because pig serves as an excellent animal model to study human diseases.

first: Pengfei

last: Jiang

last: Zhou

first: Xinyu

last: Chen

first: Xing

last: Zhao

first: Deli

last: Zhang


title: Regulation of DNA methylation by CK2-mediated phosphorylation of DNMT3A (Methyl-Seq)

city: Bruxelles

first: Matthieu

last: Defrance

address: CP614 route de Lennik 808

country: Belgium

institute: Université Libre de Bruxelles

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is a central epigenetic modification that has essential roles in cellular processes including chromatin structure, gene regulation, development and disease. The de novo DNA methyltransferases are responsible for the generation of genomic methylation patterns, but the underlying mechanisms are still poorly understood. Here, we show that phosphorylation of DNMT3A by the CK2 protein kinase regulates the establishment of DNA methylation patterns. We find that DNMT3A is phosphorylated by CK2 at two key residues located near its PWWP domain. We observed that, through phosphorylation of these residues, CK2 negatively regulates DNMT3A’s ability to methylate DNA and consistent with this, CK2 was found to decrease overall genomic level of 5-methylcytosine. Further, genome-wide DNA methylation analysis in CK2-depleted cells revealed that CK2 affects primarily CpG methylation of several heterochromatin repeats as well as Alu elements. Along these lines, we found that CK2-mediated phosphorylation of DNMT3A was required for its proper heterochromatin localization. Our results define phosphorylation as a new mode of regulation of de novo DNA methyltransferase function. These findings further uncover a previously unrecognized mechanism for the regulation of methylation at repetitive elements. They shed new light into the origin of DNA methylation patterns.

overall_design: MethylCap-seq experiment. DNA preparation, automated MethylCap, and Illumina sequencing and sequence read processing were done exactly as described previously (Bock et al., 2010; Martens et al., 2010). In this study, only the 600 mM NaCl MethylCap fraction was used.

first: Rachel

last: Deplus

first: Loïc

last: Blanchon

first: Arumugam

last: Rajavelu

first: Halim

last: Boukaba

first: Judith

last: Luciani

first: Sarah

last: Dedeurwaerder

first: Arie

middle: B

last: Brinkman

first: Femke

last: Simmer

first: Fabian

last: Müller

first: Maria

last: Berdasco

first: Pascale

last: Putmans

first: Emilie

last: Calonne

first: David

middle: W

last: Litchfield

first: Yvan

last: de Launoit

first: Tomasz

middle: P

last: Jurkowski

first: Hendrik

middle: G

last: Stunnenberg

first: Christoph

last: Bock

first: Mario

middle: F

last: Fraga

first: Manel

last: Esteller

first: Albert

last: Jeltsch

first: François

last: Fuks


title: Pharmacologic inhibition of histone demethylation as a therapy for pediatric brainstem glioma

status: Public on Jul 16 2014

city: San Francisco

first: Rintaro

last: Hashizume

address: 1450 3rd street

department: Neurosurgery

institute: UCSF

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

overall_design: Refer to individual Series


title: High-resolution mapping reveals a conserved, widespread, dynamic meiotically regulated mRNA methylation program [Mm]

status: Public on Jul 18 2014

city: Rehovot

first: Schraga

last: Schwartz

state: Choose a State or Province

address: Herzl 234, Department of Molecular Genetics

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

summary: N6-methyladenosine (m6A) is a common modification of mRNA, with potential roles in fine-tuning the RNA life cycle, but little is known about the pathways regulating this process and its physiological role. Here, we used mass-spectrometry to identify a dense network of proteins physically interacting with METTL3, a core component of the methyltransferase complex, and show that two of them, WTAP and KIAA1429, are required for methylation.  Combining high resolution m6A-Seq with knockdown of WTAP allowed us to define accurate maps, at near single-nucleotide resolution, of sites of mRNA methylation across four dynamic programs in human and mouse, including development, differentiation, reprogramming and immune response. Internal WTAP-dependent methylation sites were largely static across the different surveyed conditions and present in the majority of mRNAs. However, methylations were found at much lower levels within highly expressed mRNAs, and methylation is inversely correlated with mRNA stability, consistent with a role in establishing an overall basal, cell-type invariant, distribution of degradation rates. In addition, we identify thousands of WTAP-independent methylation sites at transcription initiation sites, forming part of the mRNA cap structure. We show that the methylations occur at the first transcribed nucleotide, and find that thousands of transcripts are present in different isoforms differing in the methylation state of the first transcribed nucleotide, a previously unappreciated complexity of the transcriptome. Together, our data sheds new light on the proteomic and transcriptional underpinnings of this epitranscriptomic modification in mammals.

overall_design: Examination of m6A methylation across different knockdowns using shRNAs in mouse embryonic fibroblasts, in embyronic and adult brains, and in dendritic cell stimulated with LPS.

first: Mumbach

last: Maxwell

first: Eric

middle: S

last: Lander

first: Aviv

last: Regev


title: Characterization of distinct classes of differential gene expression in osteoblast cultures from non-syndromic craniosynostosis bone

city: Atlanta

first: Monica

middle: L.

last: Rojas-Peña

state: GA

address: 310 Ferst Dr.

department: School of Biology

institute: Georgia Institute of Technology

summary: We report on explant osteoblast cultures from human patients, demonstrating that there are at least three sub-types of non-syndromic craniosynostosis defined by similarity of gene expression profiles.

overall_design: Osteoblast growth in culture, 23 craniosynostosis skull samples (7 metopic; 8 coronal; 3 lambdoid; 5 sagittal) and 8 normal (4 cranial bones and 4 long bones)

first: Rene

last: Olivares-Navarrete

first: Sharon

last: Hyzy

first: Dalia

last: Arafat

first: Zvi

first: Barbara

last: Boyan

first: Joseph

last: Williams

first: Greg

last: Gibson


title: Epigenetic regulation by chromatin activation mark H3K4me3 in primate progenitor cells within adult neurogenic niche

city: San Antonio

first: Chin-Hsing Annie

last: Lin

state: TX

address: One UTSA Circle

department: Biology

institute: University of Texas at San Antonio


title: RNA-seq of adult baboon subventricular zone primary cells

summary:
Histone 3 lysine 4 trimethylation (H3K4me3) is known to be associated with transcriptionally active or poised genes and required for postnatal neurogenesis within the subventricular zone (SVZ) in the rodent model. Previous comparisons have shown significant correlation between baboon (Papio anubis) and human brain. In this study, we demonstrate that chromatin activation mark H3K4me3 is present in undifferentiated progenitor cells within the SVZ of adult baboon brain. To identify the targets and regulatory role of H3K4me3 within the baboon SVZ, we developed a technique to purify undifferentiated SVZ cells while preserving the endogenous nature without introducing culture artifact to maintain the in vivo chromatin state for genome-wide studies (ChIP-Seq and RNA-Seq). We identified that H3K4me3 is significantly enriched for genes involved in cell cycle, cell signaling, nervous system development, metabolism, and ribosomal biogenesis. Among these genes, RNA-Seq identified that genes associated with cellular signaling/maintenance, DNA replication, metabolism, and protein synthesis are expressed.
We found that 72% of H3K4me3-enriched genes in undifferentiated SVZ cells are expressed (1913 genes are detectable by RNA-Seq; 2663 genes enriched with H3K4me3 by ChIP-Seq). On the other hand, 750 out of total 2663 H3K4me3-enriched genes are not detectable by RNA-Seq, suggesting 28% of genes in SVZ are poised for activation.

overall_design:
RNA-seq profiles were generated from adult baboon subventricular zone primary cells by paired-end deep sequencing with an Illumina HiSeq 2000.
RNA-Seq Analysis: Total RNA was extracted from purified baboon SVZ cells using TRIzol reagent, and sequencing libraries were generated with the Illumina RNA-Seq library kit. Paired-end RNA-deepSeq (76 base pair; >300 million tag reads; 269,081,636 mapped reads) were aligned to hg19. DESeq was used to normalize raw read counts, and Cufflink reports read counts and estimated FPKM (fragments per kilobase of exon per million fragments mapped; http://cufflinks.cbcb.umd.edu/faq.html#fpkm). Genes with expression values >1 FPKM were considered for subsequent analyses.

first: Richard

last: Sandstrom

first: Christopher

middle: T

last: Rhodes

first: Chin-Hsing

middle: A


title: Epigenetic regulation by chromatin activation mark H3K4me3 in primate progenitor cells within adult neurogenic niche [ChIP-seq]

summary: Histone 3 lysine 4 trimethylation (H3K4me3) is known to be associated with transcriptionally active or poised genes and required for postnatal neurogenesis within the subventricular zone (SVZ) in the rodent model. Previous comparisons have shown significant correlation between baboon (Papio anubis) and human brain. In this study, we demonstrate that chromatin activation mark H3K4me3 is present in undifferentiated progenitor cells within the SVZ of adult baboon brain. To identify the targets and regulatory role of H3K4me3 within the baboon SVZ, we developed a technique to purify undifferentiated SVZ cells while preserving the endogenous nature without introducing culture artifact to maintain the in vivo chromatin state for genome-wide studies (ChIP-Seq and RNA-Seq). Overall, H3K4me3 is significantly enriched for genes involved in cell cycle, metabolism, protein synthesis, signaling pathways, and cancer mechanisms. Additionally, we found elevated levels of H3K4me3 in the MRI-classified SVZ-associated Glioblastoma Multiforme (GBM), which has a transcriptional profile that reflects the H3K4me3 modifications in the undifferentiated progenitor cells of the baboon SVZ. Our findings highlight the importance of H3K4me3 in coordinating distinct networks and pathways for life-long neurogenesis, and suggest that subtypes of GBM could occur, at least in part, due to aberrant H3K4me3 epigenetic regulation.

overall_design: SVZ H3K4me3 ChIP-seq profile of an adult baboon brain was generated by deep sequencing with Illumina HiSeq 2000.

first: Chin


title: Perturbed adult sperm methylome after in utero undernutrition is associated with transmission of metabolic disease

city: Cambridge

first: Hui

last: Shi

address: Downing Street

department: Department of Physiology, Development and Neuroscience

country: United Kingdom

institute: University of Cambridge

summary: The pre and postnatal environment can affect both an individual’s risk of adult onset metabolic disease and that of subsequent generations.  Although animal models and epidemiological data implicate epigenetic inheritance, little is known of the mechanisms involved.  In a robust intergenerational model of developmental programming we demonstrate that the nutritional environment experienced in utero by F1 generation embryos alters the DNA methylome of the F1 adult male germ line in a locus-specific manner, without affecting overall methylation levels.  Differentially methylated regions are mostly hypomethylated and are enriched in nucleosome retaining regions in adult sperm.  A substantial fraction is resistant to early embryo methylation reprogramming, and thus have the potential to alter F2 generation development. Altered expression of transcripts neighbouring differentially methylated regions are evident in tissues of F2 offspring despite lack of persistence of differential methylation. Transmitted methylation variation in the germline at key regulatory loci may therefore contribute to the development of metabolic disease in the subsequent generation.

overall_design: 2 biological replicates of pooled sperm samples for each control (C) or undernutrition (UN) model

first: Elizabeth

last: Radford

first: Mitsiteru

last: Ito

first: Jennifer

last: Corish

first: Kazuki

last: Yamazawa

first: Elvira

last: Isganaitis

first: Stefanie

last: Seisenberger

first: Timothy

last: Hore

first: Wolf

last: Reik

first: Serap

last: Erkek

first: Antoine

last: Peters

first: Mary-Elizabeth

last: Patti

first: Anne

middle: C

last: Ferguson-Smith


title: An alternative, arginase-independent pathway for arginine metabolism in Kluyveromyces lactis involves guanidinobutyrase as a key enzyme

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

summary: Most available knowledge on fungal arginine metabolism is derived from studies on Saccharomyces cerevisiae, in which arginine catabolism is initiated by releasing urea via the arginase reaction. Orthologs of the S. cerevisiae genes encoding the first three enzymes in the arginase pathway were cloned from Kluyveromyces lactis and shown to functionally complement the corresponding deletion in S. cerevisiae. Surprisingly, deletion of the single K. lactis arginase gene KlCAR1 did not completely abolish growth on arginine as nitrogen source. Growth rate of mutant strongly increased during serial transfer in shake-flask cultures. A combination of RNAseq-based transcriptome analysis and 13C-15N-based flux analysis was used to elucidate the arginase-independent pathway. Isotopic 13C15N-enrichment in γ-aminobutyrate revealed succinate as the entry point in the TCA cycle of the alternative pathway. Transcript analysis combined with enzyme activity measurements indicated increased expression in the Klcar1Δ mutant of a guanidinobutyrase (EC.3.5.3.7), an enzyme not previously demonstrated in fungi. Expression of the K. lactis KLLA0F27995g (renamed KlGBU1) encoding guanidinobutyrase enabled S. cerevisiae to use guanidinobutyrate as sole nitrogen source and its deletion in K. lactis almost completely abolish growth on this nitrogen source. Phylogenetic analysis suggests that this enzyme activity is widespread in fungi.

overall_design: The goal of the present study was to characterize arginine catabolism in K. lactis. To this end, CAR1, CAR2 and PRO3 orthologs in K. lactis were identified and functionally analysed by deletion, expression in S. cerevisiae and enzyme activity assays. Since deletion of the arginase gene in K. lactis was found not to completely abolish growth on arginine as a sole nitrogen source, the alternative pathway for arginine catabolism operating in this yeast was studied by a combination of transcriptome analysis, 13C and 15N isotope-based flux analysis and enzyme activity assays in cell extracts. To investigate arginine metabolism in the arginase-negative K. lactis strain, strains GG1632 (Klku80Δ KlCAR1 reference strain) and IMS0367 (Klcar1Δ Arg+) were grown in aerobic bioreactor batch cultures on glucose chemically defined medium with arginine as sole nitrogen source. RNA sequencing of samples taken during the exponential phase of growth on glucose-arginine media of the reference strain  G1631 and the arginase less strain IMS0367 were compared resulting in the characterization of a new function.

first: Gabriele

last: Romagnoli

first: Marteen

last: Verhoeven

first: Marcel

last: van den Broek


title: Kat2a regulates hippocampal memory formation [small RNA-seq]

city: Cork

first: Roman

middle: M

last: Stilling

address: Western Road

department: Anatomy and Neuroscience

country: Ireland

institute: University College Cork

summary: We sequenced small RNAs from 12 samples extracted from mouse CA1 tissue to generate the first CA1-specific murine miRNome under normal and Kat2a-loss-of-function conditions.

overall_design: Samples were divded in 4 groups: A: Control (n=6), C: Kat2a cKO naïve (n=6)

first: Vincenzo

last: Capece

first: Stefan

last: Bonn

first: Andre

last: Fischer


title: Profiling of miRNA expression of HeLa cells infected with Salmonella Typhimurium

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: We identified miRNAs differentially regulated upon Salmonella infection by comparative deep-sequencing analysis of cDNA libraries prepared from the small RNA population (10–29 nt) of HeLa cells infected with Salmonella (20 hpi) and mock-treated cells. Considering that at a MOI of 25 Salmonella is internalized in only 10-15% of the HeLa cells, we separated the fraction of cells which had internalized Salmonella (Salmonella+) from the bystander fraction (Salmonella-) by fluorescence-activated cell sorting (FACS), and extended the analysis of miRNA changes to these samples. Interestingly, we observed that Salmonella infection induces a significant decrease in the expression of all the detected members of the miR-15 family

overall_design: miRNA profiles of HeLa cells infected with Salmonella Typhimurium were generated by deep sequencing, using Illumina HiSeq2000.

first: Claire

last: Maudet

first: Miguel

last: Mano

first: Ushasree

last: Sunkavalli

first: Malvika

last: Sharan

first: Mauro

last: Giacca

middle: U

first: Ana

last: Eulalio


title: Human intestinal DC and MNP

status: Public on Jul 15 2014

city: New York

first: Randy

last: Longman

state: NY

address: 1315 York Avenue

department: Medicine

institute: Weill Cornell Medical College

summary: Parallel subpopulations of CD11c+ MNPs present in the mouse intestine similarly exist in the human intestine (Fig. 6A and Ref. (Merad et al., 2013)). To evaluate whether these distinct subpopulations of MNPs from human intestinal tissue functioned similarly, we examined the phenotypic properties of CD103+ DCs and CD14+ MNPs (which express CX3CR1 (Kamada et al., 2008)) within the CD11c+ MHCII+ fraction of LPMCs (Fig. 6B).  In contrast to CD103+ DCs, CD14+ MNPs expressed CD64 as well as higher levels of CD86.  Consistent with the phenotypic characterization of these subsets, transcriptional analysis of these populations by RNA-seq revealed higher levels of CLEC9A, XCR1, and CD207 expression in the CD103+ cells, while MERTK, STAB1, and CX3CR1 were higher in the CD14+ cells (Fig. 6C).  We tested the potential of these subsets to induce IL-22 production by co-culturing TLR-stimulated CD14+ MNPs and CD103+ DCs from human intestinal resections with intestinal ILCs.  Intracellular cytokine staining at 18 hours revealed that the CD14+ MNP were more effective than the CD103+ DCs at stimulating IL-22 production by ILCs (Fig. 6D).  Neither cell population induced significant IL-17 or IFNg production by ILCs (Fig. 6D, 6E).

overall_design: RNA seq of sorted cell population.  2 biologic replicates for each sample.

first: Dan

middle: R

last: Littman


title: Kat2a regulates hippocampal memory formation


title: Kat2a regulates hippocampal memory formation [RNA-seq]

summary: We sequenced mRNA from 24 samples extracted from mouse CA1 tissue to generate the first CA1-specific murine transcriptome and the first CA1-transcriptome in response to environmental novelty under normal and Kat2a-loss-of-function conditions.

overall_design: Samples were divded in 4 groups: A: Control naïve (n=6), B: control novelty-exposed (n=5), C: Kat2a cKO naïve (n=6), D: Kat2a cKO novelty-exposed (n=7). Pairwise comparisons for AvsB, AvsC, BvsD and CvsD were performed using DESeq2.


title: The CNS-Heart Axis is a Source of Cardiac Dysfunction in Mouse Models   of Huntington’s Disease

city: London

first: Michal

last: Mielcarek

state: London

address: Great Maze Pond

department: Molecular and Medical Genetics

institute: King's College London

summary:
Purpose: Transcriptome profiling (RNA-seq) to microarray to evaluate transcriptional changes in the heart of HD mouse models
Methods: Heart mRNA profiles of 4-weeks-old wild-type (WT) and R6/2 transgenic; 15-weeks-old WT and R6/2 transgenic mice; 8-month-old WT and HdhQ150 knock-in mice; 22-month-old WT and HdhQ150 knock-in mice were generated by deep sequencing, in triplicate, using Illumina Hi-seq 2000.
Conclusions: Our study showed that there is no major transcriptional deregulation in the heart of mouse models of HD.

first: Jim

last: Rosinski


title: RNAseq data from in vitro-stimulated (6 and 24 hours) murine relafl/flCD19-Cre and CD19-Cre splenic B cells purified by magnetic cell separation

first: Ulf

last: Klein

address: 1130 St. Nicholas Avenue

department: Herbert Irving Comprehensive Cancer Center

institute: Columbia University


title: RNAseq data from in vitro-stimulated (6 hours) murine relafl/flCD19-Cre and CD19-Cre splenic B cells purified by magnetic cell separation (RELA)

summary: RNAseq analysis of CD40 + IgM in vitro-stimulated (6 hours) murine relafl/flCD19-Cre (furtheron designated as RELA) and CD19-Cre (furtheron designated as WT) splenic B cells identifies genes regulated by the transcription factor RELA in activated B cells.

overall_design: Splenic B cells from 12-week old relafl/flCD19-Cre and CD19-Cre littermate mice were isolated by magnetic cell separation from splenic mononuclear cells and stimulated in vitro for 6 hours with anti-CD40 and anti-IgM. RNA was isolated and submitted for RNA-sequencing on an Illumina HiSeq2000 instrument for 30 million single-ended reads.

first: Nilushi

last: De Silva


title: Whole-transcriptome high-throughput RNA sequencing of blood leukocytes from Parkinson's disease human patients pre- and post-deep brain stimulation

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

institute: UCL

summary: The given data set is the first deep sequencing transcriptome-wide data set of human Parkinson's disease (PD) patients RNA. The data set was produced from blood leukocytes of PD patients, from the same patients following deep brain stimulation (DBS), and from matched healthy control volunteers. Post-DBS samples were taken from the patients while being on electrical stimulation (ON-Stim), and following one hour off of electrical stimulation (OFF-Stim state). We have previously shown that gene expression changes, and in particular, alternative splicing changes, are observed in blood leukocytes and may contribute to PD and being subjected to regulation following DBS. Here, SOLiD RNA-Seq was applied to study the transcriptome of PD patients. Exon- and junction-level analyses revealed deep insight into both differential expression and alternative splicing regulation in PD blood leukocytes prior to and following DBS both on and off electrical stimulation. This transcriptome genome-wide data obtained through high-throughput sequencing of RNA produced from human Parkinson's disease (PD) patients blood leukocytes prior to treatment and following deep brain stimulation (DBS) neurosurgical treatment may yield insights into the molecular mechanisms that underlie the pathogenesis of PD and treatment efficacy. It may further enable the development of future diagnostics and therapeutics for PD.

overall_design: Blood leukocyte RNA was analyzed from 3 healthy control volunteers, and from 3 PD patients pre-DBS, ON-Stim, and OFF-Stim.

first: Hagai

last: Bergman

first: Zvi

last: Israel

first: Hermona


title: Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: RNAseq data from in vitro-stimulated (6 hours) murine relfl/flCD19-Cre and CD19-Cre splenic B cells purified by magnetic cell separation (REL6)

summary: RNAseq analysis of CD40 + IgM in vitro-stimulated (6 hours) murine relfl/flCD19-Cre (furtheron designated as REL) and CD19-Cre (furtheron designated as WT) splenic B cells identifies genes regulated by the transcription factor c-REL in activated B cells.

overall_design: Splenic B cells from 12-week old relfl/flCD19-Cre and CD19-Cre littermate mice were isolated by magnetic cell separation from splenic mononuclear cells and stimulated in vitro for 6 hours with anti-CD40 and anti-IgM. RNA was isolated and submitted for RNA-sequencing on an Illumina HiSeq2000 instrument for 30 million single-ended reads.


title: Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

summary:
Purpose: The goals of this study are to compare transcriptomes using RNA-seq of mouse myoblasts (C2C12 cell line) in undifferentiated and differentiated states and with siRNA-mediated knock down of the RNA binding proteins, Rbfox1 (only expressed in differentiated state) and Rbfox2 (expressed in both undifferentiated and differentiated states).
Methods: Differentiated and undifferentiated C2C12 cultures treated with Rbfox1 (differentiated only) or Rbfox2 siRNAs or a mock siRNA transfection were used for RNA-Seq analysis using Illumina HiSeq2000. 101x2 paired-end RNA-seq reads were first uniquely aligned to the mouse genome (mm9) using TopHat 1.4.1. RSEM was used to count the number of reads mapped to genes using UCSC database, followed by edgeR to call differentially expressed genes with false discovery rate less than 0.01. Cufflinks was used to reconstruct isoforms and analyze alternative splicing and percent spliced in (PSI) was calculated. PSI values were validated by RT-PCR.
Results: 58-88% of the RNA-seq reads from technical and biological replicates mapped uniquely to the mouse genome. Analysis of gene expression and alternative splicing changes are published in Singh et al. Molecular Cell (2014).
Conclusions: Our study has identified gene expression and alternative splicing transitions that occur during myoblast differentiation, demonstrate that 30% of the splicing transitions are regulated by Rbfox2, demonstrated that Rbfox2 is required for a late step of myoblast differentiation and identified two Rbfox2-regulated splicing transitions that are required for differentiation.

overall_design: Undifferentiated and differentiated C2C12 cultures with Rbfox2 depletion or Rbfox1 depletion (differentiated only) in at least duplicate samples analyzed by deep sequencing on Illumina HiSeq2000.

first: Ravi

middle: K

last: Singh

first: Chris

last: Bland

first: Auinash

last: Kalsotra

first: Marissa

last: Ruddy

first: Tomaz

last: Curk

first: Jernej

last: Ule

first: Wei

last: Li

first: Thomas

last: Cooper


title: Co-transcriptional histone H2B monoubiquitylation is tightly coupled with RNA polymerase II elongation rate

city: Tel Aviv

first: Dror

last: Hollander

address: Ramat Aviv

department: Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine

institute: Tel Aviv University

summary: Various histone modifications decorate nucleosomes within transcribed genes. Among these, monoubiquitylation of histone H2B (H2Bub1) and methylation of histone H3 on lysines 36 (H3K36me2/3) and 79 (H3K79me2/3) correlate positively with gene expression. By measuring the progression of the transcriptional machinery along genes within live cells, we now report that H2B monoubiquitylation occurs co-transcriptionally and accurately reflects the advance of RNA polymerase II (Pol II). In contrast, H3K36me3 and H3K79me2 are less dynamic and represent Pol II movement less faithfully. High resolution ChIP-seq reveals that H2Bub1 levels are selectively reduced at exons, and decrease in an exon-dependent stepwise manner towards the 3' end of genes. Exonic depletion of H2Bub1 in gene bodies is highly correlated with Pol II pausing at exons, suggesting elongation rate changes associated with intron-exon structure. Overall, our data shed light on the organization of H2Bub1 within transcribed genes, and single out H2Bub1 as a reliable marker for ongoing transcription elongation.

overall_design: H2Bub1 and H2B ChIP-seq in NT2 cells

first: Gilad

last: Fuchs

first: Gil

last: Ast

first: Moshe

last: Oren


title: Trans-generationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing [ChIP-seq]

status: Public on Jul 26 2014

city: Pasadena

first: Adrien

last: Le Thomas

state: CA - California

address: 231 South Hudson Avenue

department: Biology and Biological Engineering

institute: California Institute of Technology

summary: Small non-coding RNAs that associate with Piwi proteins, called piRNAs, serve as guides for repression of diverse transposable elements in germ cells of Metazoa. In Drosophila, the genomic regions that give rise to piRNAs, the so-called piRNA clusters, are transcribed to generate long precursor molecules that are processed into mature piRNAs. How genomic regions that give rise to piRNA precursor transcripts are differentiated from the rest of the genome and how these transcripts are specifically channeled into the piRNA biogenesis pathway are not known. We found that trans-generationally inherited piRNAs provide the critical trigger for piRNA production from homologous genomic regions in the next generation by two different mechanisms. First, inherited piRNAs enhance processing of homologous transcripts into mature piRNAs by initiating the ping-pong cycle in the cytoplasm.  Second, inherited piRNAs induce installment of the H3K9me3 mark on genomic piRNA cluster sequences. The HP1 homolog Rhino binds to the H3K9me3 mark through its chromodomain and is enriched over piRNA clusters. Rhino recruits the piRNA biogenesis factor Cutoff to piRNA clusters and is required for efficient transcription of piRNA precursors. We propose that trans-generationally inherited piRNAs act as an epigenetic memory for identification of substrates for piRNA biogenesis on two levels, by inducing a permissive chromatin environment for piRNA precursor synthesis and by enhancing processing of these precursors.

overall_design:
ChIPseq of Rhino and Cutoff in Drosophila melanogaster ovaries
The Rhino-BioTAP flies were made by fusing the BioTAP tag (Alekseyenko et al. 2014 )to the C-terminal region of the Rhino gene under the UASp promoter.
The Cutoff-EGFP fly line (Nanos-GAL4/UASp-Cutoff-GFP), Cuff^wm25 and Cuff^qq37 were a generous gift from T. Schupbach.


title: Characterization of the small RNA content of Trypanosoma cruzi extracellular vesicles

city: Sao Paulo

first: Ethel

last: Bayer-Santos

state: SP

address: 862 Botucatu

department: Microbiologia, Imunologia e Parasitologia

country: Brazil

institute: Universidade Federal de Sao Paulo

summary: A growing body of evidence in mammalian cells indicates that secreted vesicles can be used to mediate intercellular communication processes by transferring various bioactive molecules, including mRNAs and microRNAs. Based on these findings, we decided to analyze whether T. cruzi-derived extracellular vesicles contain RNA molecules and performed a deep sequencing and genome-wide analysis of a size-fractioned cDNA library (16–40 nt) from extracellular vesicles secreted by noninfective epimastigote and infective metacyclic trypomastigote forms. Our data show that the small RNAs contained in these extracellular vesicles originate from multiple sources, including tRNAs. In addition, our results reveal that the variety and expression of small RNAs are different between parasite stages, suggesting diverse functions. Taken together, these observations call attention to the potential regulatory functions that these RNAs might play once transferred between parasites and/or to mammalian host cells.

overall_design: Small RNAs profiles (16-40 nt) of epimastigote-derived extracellular vesicles, metacyclic trypomastigote-derived extracellular vesicles and metacyclic trypomastigote parental cells.

first: Fabio

last: Lima

first: Jeronimo

last: Ruiz

first: Igor

last: Almeida

first: Jose-Franco

last: Da Silveira


title: The human skeletal muscle transcriptome – sex differences, alternative splicing and tissue homogeneity assessed with RNA sequencing

city: Solna

first: Joakim

last: Lundeberg

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH-Science for Life Laboratory

summary: The amount of RNA sequencing data on skeletal muscle is very limited. We have analyzed a large set of human muscle biopsy samples and provide extensive information on the baseline skeletal muscle transcriptome, including completely novel protein-coding transcripts.

overall_design: Analyze of transcriptome in 23 skeletal muscle biopsy samples from six individuals. Four biopsies from each subject, two biopsies from each leg (except subject 6 which has only three biopsies in total).

first: Maléne

last: Lindholm

first: Mikael

last: Huss

first: Beata

last: Solnestam

first: Sanela

last: Kjellkvist

first: Carl

middle: J

last: Sundberg


title: Promoter-specific recruitment of PPARG in adipocytes depends on GPS2-dependent stabilization of histone demethylase KDM4A/JMJD2

status: Public on Jul 14 2014

city: Boston

first: Valentina

last: Perissi

state: MA

address: 72 E. Concord St

department: Department of Biochemistry

institute: Boston University School of Medicine

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

overall_design: Refer to individual Series


title: Promoter-specific recruitment of PPARG in adipocytes depends on GPS2-dependent stabilization of histone demethylase KDM4A/JMJD2 [KDM4A]

summary: Timely and selective recruitment of transcription factors to their appropriate DNA-binding sites represents a critical step in regulating gene activation; however the regulatory strategies underlying each factor’s effective recruitment to specific promoter and/or enhancer regions are not fully understood. Here, we identify an unexpected regulatory mechanism by which promoter-specific binding, and therefore function, of PPARG in adipocytes requires G protein Suppressor 2 (GPS2) to prime the local chromatin environment via inhibition of the ubiquitin ligase RNF8 and stabilization of the H3K9 histone demethylase KDM4A/JMJD2. Integration of genome-wide profiling data indicates that the pioneering activity of GPS2/KDM4A is required for PPARG mediated regulation of a specific transcriptional program, including the lipolytic enzymes ATGL and HSL. Hence, our findings reveal that GPS2 exerts a biologically important function in adipose tissue lipid mobilization by directly regulating ubiquitin signaling and indirectly modulating chromatin remodeling to prime selected genes for activation.

overall_design: KDM4A ChIP-seq in control 3T3-L1 cells (CTL) and after siRNA-mediated  knockdown of GPS2 (siGPS2)

first: M

middle: D

last: Cardamone

first: Bogdan

last: Tanasa

first: Michael

last: Rosenfeld


title: Promoter-specific recruitment of PPARG in adipocytes depends on GPS2-dependent stabilization of histone demethylase KDM4A/JMJD2 [GPS2]

overall_design: GPS2 ChIP-seq at day 0 and day 6 of induced adipogenesis of 3T3-L1 cells


title: Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

city: Stockholm

first: Rickard

last: Sandberg

address: Berzelius vag 35

department: Department of Cell and Molecular Biology

institute: Karolinska Institutet

summary: Massively parallel DNA sequencing of thousands of samples in a single machine-run is now possible, but the preparation of the individual sequencing libraries is expensive and time-consuming. Tagmentation-based library construction, using the Tn5 transposase, is efficient for generating sequencing libraries but currently relies on undisclosed reagents, which severely limits development of novel applications and the execution of large scale projects. Here, we present simple and robust procedures for Tn5 transposase production and optimized reaction conditions for tagmentation-based sequencing library construction. We further show how molecular crowding agents both modulate library lengths and enable efficient tagmentation from sub-picogram amounts of cDNA. Comparison of single-cell RNA-sequencing libraries generated using produced and commercial Tn5 demonstrated equal performances in terms of gene detection and library characteristics. Finally, as naked Tn5 can be annealed to any oligonucleotide of choice, for example molecular barcodes in single-cell assays or methylated oligonucleotides for bisulfite sequencing, custom Tn5 production and tagmentation enables innovation in sequencing-based applications.

sample_organism:
Homo sapiens
Mus musculus
synthetic construct

overall_design: Sequencing libraries from cDNA was generated using in-house produced or commercial Tn5 and in a variety of tagmentation buffers and conditions.

first: Simone

last: Picelli

first: Åsa

last: Björklund

first: Björn

last: Reinius

first: Gösta

last: Winberg


title: Genome-wide mapping of Myc, AP4, and phosphorylated RNA polymerase II binding in activated CD8 T cells by ChIP sequencing

status: Public on Jul 13 2014

city: Saint Louis

first: Takeshi

last: Egawa

state: MO

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: The trasncription factor cMyc is an essential transcription factor that establishes a metabolically active and proliferative state in T cells after antigen priming. However, its expression is transient. To date, it remains unknown how T cell activation is maintained after cMyc down-regulation. Here, we identify AP4, encoded by the gene Tfap4, as the transcription factor that is induced by cMyc and sustains activation of antigen-specific CD8+ T cells. Despite normal priming, Tfap4–/– CD8+ T cells fail to continue transcription of a broad range of cMyc gene targets necessary for sustained proliferation. Genome-wide analysis suggests that many activation-induced metabolic genes are shared targets of cMyc and AP4. Thus, AP4 maintains Myc-initiated cellular activation programs in CD8+ T cells to control microbial infections.

overall_design: Naive CD8+ T cells from C57BL6 mice were activated with anti-CD3 and anti-CD28 stimulation in vitro for two days and genome-wide occupancy of Myc, AP4 and Ser2 or Ser5 phipsphorylated RNA polymerase II was profiled by chromatin immunoprecipitation and high-throughput sequencing.

first: Chun

last: Chou


title: Short RNAs expression profiling of two Italian Large White pig backfat

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

country: Italy

institute: University of Padova

summary: We report the application of Illumina short RNA sequencing for characterization and discovery of miRNAs and moRNAs in two Italian Large White pig backfat tissue.

overall_design: Short RNAs sequencing for miRNA quantification, discovery and characterisation. Sequenced reads from the two samples were pooled together for the bioinformatic analysis.

first: Enrico

last: Gaffo

first: Andrea

last: Bisognin

first: Paolo

last: Zambonelli

first: Roberta

last: Davoli


title: RNAseq data from in vitro-stimulated (24 hours) murine relfl/flCD19-Cre and CD19-Cre splenic B cells purified by magnetic cell separation.

first: Ulf

last: Klein

summary: RNAseq analysis of CD40 + IgM in vitro-stimulated (24 hours) murine relfl/flCD19-Cre (furtheron designated as REL) and CD19-Cre (furtheron designated as WT) splenic B cells identifies genes regulated by the transcription factor c-REL in activated B cells.

overall_design: Splenic B cells from 12-week old relfl/flCD19-Cre and CD19-Cre littermate mice were isolated by magnetic cell separation from splenic mononuclear cells and stimulated in vitro for 24 hours with anti-CD40 and anti-IgM. RNA was isolated and submitted for RNA-sequencing on an Illumina HiSeq2000 instrument for 30 million single-ended reads.

first: Nilushi

last: De Silva


title: Analysis of gene expression in CD8+ T cells activated in vitro or in vivo


title: Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells [mouse]

city: Rehovot

first: Amos

last: Tanay

state: ISR

address: 234 Herzl St.

institute: Weizmann Institute of Science

summary: Stable maintenance of gene regulatory programs is essential for normal function in multi-cellular organisms. Epigenetic mechanisms, and DNA methylation in particular, are hypothesized to facilitate such maintenance by creating cellular memory that can be written during embryonic development and then guide cell-type specific gene expression. Here we use new methods to study distributions of DNA methylation patterns within cell populations to show that embryonic stem cells preserve their epigenetic state by balancing antagonistic processes that add and remove methylation marks rather than by copying epigenetic information from mother to daughter cells. Quantitative tuning of this equilibrium leads to convergence into a binary epigenetic configuration maintaining a sharp distinction between methylated and unmethylated regions. In contrast, somatic cells transmit considerable epigenetic information from mother to daughter cell. Paradoxically, the persistence of the somatic epigenome makes it more vulnerable to noise, since random epi-mutations can be preserved and accumulate to massively perturb the binary epigenomic ground state. Epigenetic perturbation is not observed in the pluripotent state, since the rapid turnover-based equilibrium continuously reinforces the canonical state. This dynamic epigenetic equilibrium also explains how the somatic epigenome can be reprogrammed quickly and accurately following induced pluripotency.

overall_design: Comparison of single cell clonal population DNA methylation variation to the original population in primary CD8

first: Zohar

last: Shipony


title: RNAseq analysis of mouse lung transcriptome from allergic and non-allergic mice prior to and following lung Klebsiella pneumoniae infection

city: Nashville

first: Daniel

middle: E

last: Dulek

state: TN

address: D-7235 Medical Center North, 1161 21st Avenue South

department: Pediatrics

institute: Vanderbilt University Medical Center

summary: We have demonstrated that allergic airway inflammation (induced by an ovalbumin sensitization and aerosol challenge protocol) decreases lung bacterial burden following lung infection with Klebsiella pneumoniae.  The goals of this study are to indentify novel targets that are expressed during allergic airway inflammation in this model that contribute to enhanced lung bacterial immunity.

overall_design: We isolated total RNA from the lungs of 4 groups of mice at both 0 hours (pre-infection) and 6 hours post-infection.  WT and STAT6KO (BALB/c) mice were intraperitoneally sensitzed with alum or ovalbumin (OVA)-alum on day -18.  Alum injected mice were not subsequently exposed to OVA aerosol.  OVA-alum injected mice underwent aerosol sensitization on days -4, -3, -2, and -1.  On day 0, four groups of mice were harvested (pre-infection).  These included WT-ALUM, WT-OVA, STAT6KO-ALUM, and STAT6KO-OVA.  On day 0, four groups of mice were infected with 10^4cfu of Klebsiella and then lungs were removed at 6 hours post-infection.  These groups included WT-ALUM-KP, WT-OVA-KP, STAT6KO-ALUM-KP, and STAT6KO-OVA-KP.  The right lung was removed for RNA isolation.  Each group contained between 4 and 5 mice.

first: Kasia

last: Goleniewska

first: Stokes

last: Peebles


title: Transcriptome analysis of Germinal Center and naïve B cells from miR-217TG and control mice by RNAseq

city: Madrid

first: Almudena

last: Ramiro

address: Melchor Fernandez Almagro 3

department: Vascular Biology and Inflammation

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares

summary: microRNAs (miRNAs) regulate virtually all biological processes, but little is known of their role in germinal center (GC) B cells. While the GC reaction is crucial to ensure a competent immune response, GC B cells are also the origin of most human lymphomas. Here we report that miR-217 is specifically upregulated in GC B cells. Gain- and loss-of-function mouse models reveal that miR-217 functions as a positive modulator of the GC response through the regulation of a DNA repair gene network. Moreover, we show that miR-217 overexpression promotes mature B cell lymphomagenesis. Therefore miR-217 provides a novel molecular link between the normal GC response and B cell transformation

overall_design: 4 samples were analyzed by RNAseq: 1) naïve (CD19+Fas-GL7-) B cells from miR-217TG,  2) GC (CD19+Fas+GL7+) B cells from miR-217TG, 3) naïve (CD19+Fas-GL7-) B cells from  littermate controls and 4) GC (CD19+Fas+GL7+) B cells from littermate controls.  Samples were isolated by cell sorting from pooled Peyer’s patches (4-6 animals per genotype). Two independent experiments were performed.

first: Virginia

last: de Yébenes

first: Nahikari

last: Bartolomé-Izquierdo

first: Rubén

last: Nogales-Cadenas

first: Pablo

last: Pérez-Durán

first: Nerea

last: Martínez

first: Davide

last: Robbiani

first: Marta

last: Cañamero

first: Miguel

last: Piris

first: Alberto

last: Pascual-Montano


title: RNA-Seq of ex vivo culture of circulating breast tumor cells

status: Public on Jul 11 2014

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary: Analyses of circulating tumor cells (CTC) cultured from blood of patients with cancer may allow individualized testing for susceptibility to therapeutic regimens.  We established ex vivo cultures of CTCs from six patients with metastatic estrogen receptor-positive breast cancer and performed RNA-Seq on those cultures.

overall_design: One sample each from six metastatic estrogen receptor positive breast cancer patients

first: Min

last: Yu

first: Aditya

last: Bardia

first: Nicola

last: Aceto

first: Marissa

middle: W

last: Madden

first: Maria

last: Donaldson

first: Rushil

last: Desai

first: Huili

last: Zhu

first: Francesca

last: Bersani

first: Valentine

last: Comaills

first: Zongli

last: Zheng

first: Petar

last: Stojanov

first: Elena

last: Brachtel

first: Dennis

last: Sgroi

first: Ravi

last: Kapur

first: Toshi

last: Shioda

first: David

last: Ting

first: Sridhar

last: Ramasswamy

first: Gad

last: Getz

first: A

last: Iafrate

first: Cyril

last: Benes

first: Mehmet

last: Toner

first: Shyamala

last: Maheswaran

last: Haber


title: Probing the effect of promoters on noise in gene expression using thousands of designed sequences

status: Public on Jul 12 2014

first: Eilon

last: Sharon

summary: Genetically identical cells exhibit large variability (noise) in gene expression, with important consequences for cellular function. Although the amount of noise decreases with and is thus partly determined by the mean expression level, the extent to which different promoter sequences can deviate away from this trend is not known. Here, we study how different noise levels are encoded by the promoter sequence using massively parallel noise measurements of thousands of synthetically designed promoters. We find that the noise levels of promoters with similar mean expression levels can vary over more than one order of magnitude, with nucleosome-disfavoring sequences resulting in lower noise and more transcription factor binding sites resulting in higher noise. We devised a computational model that can accurately predict the mean-independent component of the noise from DNA sequence alone. Our model suggests that the effect of promoters on noise is partly mediated by the combination of non-specific DNA binding and one-dimensional sliding along the DNA that occurs when transcription factors search for their target sites. Overall, our results demonstrate that small changes in the DNA sequence of promoters can allow tuning of noise levels in a manner that is largely predictable and partly decoupled from effects on the mean expression levels. These insights may assist in designing promoters with desired noise levels.

overall_design: Expression measurements of a collection of synthetic promoters collection that was published in Sharon et al. Nature Biotechnology 2012(doi: 10.1038/nbt.2205).  Two replicates of the promoter library integrated into a plasmid in yeast were measured in SC-Glu-URA medium. The promoter library was measured as described in Sharon et. al.(Sharon et al. 2012), except for the differences below. Briefly, a large collection of synthetic promoter reporter gene strains was generated by a pooled ligation of 6500 fully designed DNA oligos (obtained by synthesis on a microarray(LeProust et al. 2010) by Agilent Technologies, Santa Clara, California). The oligos were ligated upstream to a yellow fluorescent protein (YFP) gene with a short (100 bp) core promoter sequence taken from HIS3 gene promoter and into a low copy plasmid which also contains a TEF2 promoter deriving red fluorescent protein (mCherry). The resulting plasmids were then transformation into yeast (S. cerevisiae). Next, the pool of cells was grown in amino acid starvation condition (SCD without amino acid except Histidine), and sorted according to their YFP expression level into 32 expression bins (mCherry was used for gating one plasmid copy cells and for normalization). The DNA of the promoters in each bin were then amplified and sent to multiplexed parallel sequencing. Each sequencing result was mapped to a specific promoter and expression bin, resulting in a distribution of cells that contain each promoter across all expression bins. The following differences were applied relative to the description in Sharon et. al.(Sharon et al. 2012). The medium used both for growing the cells and for their sorting was SC-Glu-URA (synthetic complete media with 2% glucose and without uracil) medium without amino acids, except for Histidine. In order to achieve expression distributions with high resolution that would allow good assessment of expression noise, the library cells were sorted into 32 bins according to their ratio of YFP and mCherry expression level, thereby normalizing for extrinsic noise effects. Each of the two extreme expression bins contained 2% of the library cells and each of the remaining 30 bins contained 3.2%. We collected a total of 10,000,000 cells. As previously described, the mapping of cells to bins involves parallel sequencing of the amplified promoter regions. For this purpose, Illumina Hi-Seq 2000 was used to obtain >30,000,000 mapped reads. The two replicates were separately generated from the ssDNA oligo library and separately measured as described above.

last: van Dijk

first: Yael

last: Kalma

first: Leeat

last: Keren

first: Ohad

last: Manor

first: Zohar

last: Yakhini

first: Eran

last: Segal


title: Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells [human]

first: Amos

last: Tanay

overall_design: Comparison of single cell clonal population DNA methylation variation to the original population in 6 cell lines and 1 primary

last: Shipony


title: Multicilin drives centriole biogenesis via E2f proteins

status: Public on Jul 10 2014

city: La Jolla

first: Ian

last: Quigley

address: 10010 North Torrey Pines Road

department: Molecular Neurobiology Lab

institute: Salk Institute

summary: Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify multiciliated cells in vertebrates. Here, we performed RNAseq on Xenopus laevis ectoderm in the presence of multicilin alone or multicilin and a dominant-negative e2f4 construct. We also performed ChIPseq on e2f4 in the presence or absence of multicilin. Taken together, these data demonstrate how multicilin affects e2f4 genomic targets and their downstream transcription.

overall_design:
RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates.
ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced;  2 biological replicates. Background was input prior to IP.

first: Lina

last: Ma

first: Chris

last: Kintner


title: Deep sequencing and analysis of small RNAs from the flowers of four Rosa

city: Daejeon

first: Jungeun

last: Kim

country: South Korea

institute: KRIBB

summary: High-throughput sequencing was employed to identify conserved and variable microRNAs among 4 Rosa

sample_organism:
Rosa rugosa
Rosa hybrid cultivar

platform_organism:
Rosa rugosa
Rosa hybrid cultivar

overall_design: floral sRNA profiles generated from Rosa (Vital, Marrussia, Simpas, Haedang)


title: next generation sequencing facilitates quantitative analysis of control and TKO liver transcriptomes

city: Stanford

first: Julien

last: Sage

address: 265 Campus Drive, SIM1 G2078

institute: Stanford University

summary: We used RNAseq to analyse the transcriptomes of cycling and quiescent livers from cTKO (Rblox/lox;p130lox/lox;p107/) and control mice.

overall_design: mRNA profiles of cycling and quiescent control and TKO liver tissue were generated by deep sequencing in duplicate

first: Ursula

last: Ehmer

first: Dedeepya

last: Vaka


title: RNA-seq analysis in Cornea epithelial cells (CECs), skin epithelial cells (SECs), LSCs after knocking down PAX6 (3-D shPAX6 LSCs) and SESCs transduced with PAX6(3-D PAX6+ SESCs) upon 3-D differentiation

first: Hai-Ri

last: Li

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

summary:
Purpose: We find that Wnt7a-PAX6 axis determine corneal epithelial cell fate. To obtain global evidence for successful cell fate conversion, we performed gene expression profiling by RNA-seq on CECs, SECs, and LSCs after knocking down PAX6 and on SESCs transduced with PAX6 upon 3-D differentiation.
Methods: Under 3-D culture condition, limbal stem cell (LSCs) can be differentiated to Cornea epithelial cells (CECs), and skin epithelial stem cells (SESCs) can be differentiated to skin epithelial cells (SECs). Total RNA was isolated from CECs, SECs, and LSCs after knocking down PAX6 (3-D shPAX6 LSCs) and on SESCs transduced with PAX6 (3-D PAX6+ SESCs) upon 3-D differentiation. Libraries were prepared following published standard protocol (Fox-Walsh K et al., 2011, genomics, 266-71). mRNA profiles were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000.
Results: Following optimized decoding and mapping workfollow, we mapped about 5 million sequence reads to the human genome and identified more than 23659 transcripts per sample.
Conclusions: Hierarchical clustering analysis of differentially expressed gene signatures revealed that the gene expression pattern of SESCs with PAX6 transduction was strikingly similar to that of CECs, whereas the profile of LSCs with PAX6 knockdown was highly related to that in SECs upon differentiation. These data therefore provided global evidence for a decisive role of the WNT7A/PAX6 axis in cell fate conversion from SESCs to CECs.

overall_design: RNA-seq on CECs, SECs, and LSCs after knocking down PAX6 and on SESCs transduced with PAX6 upon 3-D differentiation, using Illumina HiSeq 2000

first: Yuanchao

last: Xue

first: Hairi


title: Genome-wide transcriptome analysis of the dietary chemopreventive phytochemical sulforaphane on normal and prostate cancer cells.

city: Corvallis

first: Laura

last: Beaver

state: OR

address: 103 Milam, Oregon State University

department: BPHS

institute: Oregon State University

summary: Epidemiological studies provide strong evidence that consumption of cruciferous vegetables, such as broccoli, can significantly reduce the risk of developing cancers. Sulforaphane (SFN), a phytochemical derived from cruciferous vegetables, induces anti-proliferative and pro-apoptotic responses in prostate cancer cells, but not in normal prostate cells. The mechanisms responsible for these specific chemopreventive properties remain unclear. We utilized RNA sequencing to test the hypothesis that SFN modifies the expression of genes that are critical in prostate cancer progression. Normal prostate epithelial cells, and androgen-dependent and androgen-independent prostate cancer cells were treated with 15 µM SFN and the transcriptome was determined at 6 and 24 hour time points. SFN altered the expression of ~3,000 genes in each cell line and the response was highly dynamic over time. SFN influenced the expression of genes in functional groups and pathways that are critical in cancer including cell cycle, apoptosis and angiogenesis, but the specific effects of SFN differed depending on the state of cancer progression. Network analysis suggested that a transcription factor that is overexpressed in many cancers, Specificity protein 1 (Sp1), is a major mediator of SFN-induced changes in gene expression. Nuclear Sp1 protein was significantly decreased by 24 hour SFN treatment in prostate cancer cells, while a related transcription factor, Sp3 protein was only modestly decreased in androgen-independent prostate cancer cells.  Overall, the data show that SFN significantly affects gene expression in normal and cancer cells, with key targets in chemopreventive processes, making it a promising dietary anti-cancer agent.

overall_design: Examination of how the transcriptome of normal and prostate cancer cells is altered by treatment with sulforaphane

first: Alex

last: Buchanan

first: Emily

last: Ho


title: Direct Induction of Hematoendothelial Program in Human Pluripotent Stem Cells by Transcriptional Regulators

city: Madison

first: Scott

last: Swanson

state: WI

address: 330 N. Orchard St

institute: Morgridge Institute for Research

summary: Advancing pluripotent stem cell technologies for modeling hematopoietic stem cell development and therapies requires identifying key regulators of hematopoietic commitment from human pluripotent stem cells (hPSCs). Here, by screening the effect of 27 candidate factors, we identified two groups of transcriptional regulators capable of inducing distinct hematopoietic programs from hPSCs: pan-myeloid (GATA2 and ETV2) and erythro-megakaryocytic (GATA2 and TAL1). In both cases, these transcription factors directly converted hPSCs to endothelium, which subsequently transformed into blood cells with pan-myeloid or eryhtro-megakaryocytic potential. These data demonstrate that two distinct genetic programs regulate the hematopoietic development from hPSCs and that both of these programs specify hPSCs directly to hemogenic endothelial cells. Additionally, this study provides a novel method for efficient induction of blood and endothelial cells from hPSCs via overexpression of modified mRNA for selected transcription factors.

overall_design: mRNA profiles of 54 samples, including 4 samples in duplicate and 6 control samples were generated by deep sequencing, using Illumina HiSeq 2500.

first: Irina

last: Elcheva

first: Vera

middle: B

last: Volchanskaya

first: Ron

last: Stewart

first: James

last: Thomson

first: Igor

last: Slukvin


title: Site- and allele-specific de-silencing of polycomb repressive activity by insertional oncogenesis: a new recurrent mechanism of TAL1 activation in T-ALL

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

country: France

institute: CNRS

summary: T-cell acute lymphoblastic leukemia’s (T-ALL) are malignant proliferations of thymocytes occurring through a large diversity of genomic and epigenetic alteration.  TAL1 is amongst the most frequently deregulated oncogenes. Known TAL1 dysregulation mechanisms consist of t(1;14) translocations and SIL-TAL deletions. Yet, over half of TAL1+ cases lack TAL1 lesions, pointing to unrecognized (epi)genetic deregulation mechanisms. In such “unresolved cases”, TAL1 expression can be mono-allelic, compatible with a direct alteration in cis within or around the TAL1 gene, or bi-allelic, likely reflecting indirect deregulation in trans. Using ChIP-seq, we show that TAL1 is normally silenced in the T-cell lineage, and that the polycomb H3K27me3 repressive mark is focally diminished in TAL1+ T-ALLs. Sequencing revealed that >20% of mono-allelic TAL1+ patients without previously known alterations display micro-insertions or RAG1/2-mediated episomal reintegration in a single site 5’ to TAL1. Using “allelic-ChIP” and CrispR assays, we demonstrate that such insertions induce selective switch from H3K27me3 to H3K27ac at the inserted but not the germline allele. We also show that, despite a considerable mechanistic diversity, the mode of oncogenic TAL1 activation, rather than expression levels, impact on clinical outcome. Altogether, these studies reveal a new adverse mechanism of mono-allelic oncogenic activation through site-specific epigenetic de-silencing.

overall_design: ChIP-seq experiments were designed to asses the dynamic enrichment of H3K27me3 and H3K27ac marks on the genome and understand the mechanisms underlying the TAL1 expression cys-regulation.

first: Jean-Marc

last: Navarro

first: Aurore

last: Touzart

first: Lydie

last: Pradel

first: Marie

last: Loosveld

first: Myriam

last: Koubi

first: Sandrine

last: Le Noir

first: Muhammad

last: Ahmad Maqbool

first: Ester

last: Morgado

first: Claude

last: Gregoire

first: Sebastien

last: Jaeger

first: Emilie

last: Mamessier

first: Charles

last: Pignon

first: Salima

last: Hacein-Bey

first: Bernard

last: Malissen

first: Marta

last: Gut

first: Ivo

middle: G

first: Hervé

last: Dombret

first: Elizabeth

last: Macintyre

first: Steve

last: Howe

first: Adrian

last: Thrasher

first: Norbert

last: Ifrah

first: Dominique

last: Payet-Bornet

first: Estelle

last: Duprez

first: Jean-Christophe

last: Andrau

first: Vahid

last: Asnafi

first: Bertrand

last: Nadel


title: Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells

first: Amos

last: Tanay

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

overall_design: Refer to individual Series


title: RNA-sequencing experiment: Treatment of MCF-7 breast cancer cells with the novel small molecule ZNA

city: Oklahoma City

first: Bryan

last: Welm

state: Oklahoma

address: 825 Northeast 13th Street

department: Immunobiology and Cancer

institute: Oklahoma Medical Research Foundation

summary:
MCF-7 cells were treated with either ZNA (30 uM) or a vehice control for 3 or 12 hours.  Following RNA sequencing, the control-normalized data was used to analyze genes altered by ZNA treatment.
Following RNA sequencing, the control-normalized data was used to analyze genes altered by ZNA treatment.

first: Rachel

last: Vaden


title: Comparing Reference-Based RNA-Seq Mapping Methods for Non-Human Primate Data

city: Durham

first: Geoffrey

middle: S

last: Ginsburg

state: NC

address: 101 Science Drive

department: Clinical Genomics Studies Unit

institute: Duke University

summary: We present a comparison of four reference-based mapping methods for mapping non-human primate data to a human reference sequence. We utilize TopHat2 and GSNAP for mapping to the human genome, and Bowtie2 and Stampy for mapping to the human genome and transcriptome for a total of six mapping approaches

overall_design: Comparison of reference-based mapping methods for 12 yellow baboons

first: Ashlee

last: Benjamin


title: Investigation into human Tra2 protein-dependent splicing in MDA-MB-231 cells using iCLIP and RNA-seq

city: Newcastle upon Tyne

first: David

last: Elliott

address: 1 Central parkway

department: Institute of Genetic Medcine

institute: Newcastle University

summary: Alternative splicing—the production of multiple mRNA isoforms from a single gene—is regulated in part by RNA-binding proteins (RBPs). While the RBPs Tra2α and Tra2β have both been implicated in the regulation of alternative splicing, their relative contribution to this process are not well understood. Here we use iCLIP to identify Tra2β target exons in MDA-MB-231 cells. We find that simultaneous—but not individual—depletion of Tra2α and Tra2β induces substantial shifts in the splicing pattern of endogenous Tra2β target exons identified by iCLIP. We next use RNA-seq following joint Tra2 protein depletion to comprehensively identify Tra2 protein-dependent exons in MDA-MB-231 cells.

overall_design: Endogenous Tra2β binding sites were mapped across the MDA-MB-231 cell transcriptome in biological triplicate iCLIP experiments. RNA-seq was performed using three biological replicates of negative control siRNA treated MDA-MB-231 cells and three biological replicates of TRA2A and TRA2B siRNA treated MDA-MB-231 cells.

first: Andrew

last: Best

first: Katherine

last: James

first: Caroline

last: Dalgliesh

first: Elaine

last: Hong

first: Mahsa

last: Kheirolahi-Kouhestani

first: Tomaz

last: Curk

first: Yaobo

last: Xu

first: Marina

last: Danilenko

first: Rafiq

last: Hussain

first: Bernard

last: Keavney

first: Anil

last: Wipat

first: Roscoe

last: Klinck

first: Ian

last: Cowell

first: Ka

last: Lee

last: Austin

first: Julian

middle: P

last: Venables

first: Benoit

last: Chabot

first: Mauro

last: Santibanez Koref

first: Alison

last: Tyson-Capper


title: A Novel HDAC Complex in the Control of Transcription and Genome Stability

city: San Diego

first: Nicola

last: Zilio

address: 10550 N Torrey Pines Road

institute: The Scripps Research Institute

summary: The acetylation state of histones, controlled by histone acetyltransferases and deacetylases, profoundly affects DNA transcription and repair by modulating chromatin accessibility to the cellular machinery. The Schizosaccharomyces pombe HDAC Clr6 (human HDAC1) binds to different sets of proteins that define functionally distinct complexes: I, I’ and II. Here we determine the composition, architecture and functions of a new Clr6 HDAC complex, I'', delineated by the novel proteins Nts1, Mug165 and Png3. Deletion of nts1 causes increased sensitivity to genotoxins and deregulated expression of Tf2 elements, long non-coding RNA, subtelomeric and stress-related genes. Similar, but more pervasive, phenotypes are observed upon Clr6 inactivation, supporting the designation of complex I'' as a mediator of a key subset of Clr6 functions. We also reveal that with the exception of Tf2 elements, Clr6 I''-regulated loci and its genome-wide loading sites do not correlate. Instead, Nts1 loads at genes that are expressed in mid-meiosis, following oxidative stress, or are periodically expressed. Collective data suggest that Clr6 I'' has (i) indirect effects on gene expression, conceivably by mediating higher-order chromatin organization of sub-telomeres and Tf2 elements, and (ii) direct effects on the transcription of specific genes in response to certain cellular or environmental stimuli.

overall_design: Identification of the genome binindg sites for Nts1 (SPCC24B10.19C) in Schizosaccharomyces pombe

first: Michael

middle: N

last: Boddy


title: RNA-seq in response to antibiotic stress (Acinetobacter baumannii 1207552)

city: Baltimore

first: David

middle: A

last: Rasko

state: MD

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

summary: Identification of transcriptional pathways associated with antibiotic stress

overall_design: 20 samples


title: RNA-seq in response to antibiotic stress (Acinetobacter baumannii 1428368)


title: RNA-seq in response to antibiotic stress (Acinetobacter baumannii 1592897)


title: RNA-seq in response to antibiotic stress (Acinetobacter baumannii 983759)


title: RNA-seq in response to antibiotic stress (Acinetobacter baumannii 478810)


title: RNA-seq in response to antibiotic stress (Acinetobacter baumannii 1000160)


title: Genotyping of E14 mouse embryonic stem cells by sequencing

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

institute: University of Torino

summary: More than 2x10E9 sequences made on Illumina platform derived from the genome of E14 embryonic stem cells cultured in our laboratory were used to build a database of about 2.7x10E6 single nucleotide variant. The database was validated using other two sequencing datasets from other laboratory and high overlap was observed. The identified variant are enriched on intergenic regions, but several thousands reside on gene exons and regulatory regions, such as promoters, enhancers, splicing site and untranslated regions of RNA, thus indicating high probability of an important functional impact on the molecular biology of this cells. We created a new E14 genome assembly including the new identified variants and used it to map reads from next generation sequencing data generated in our laboratory or in others on E14 cell line. We observed an increase in the number of mapped reads of about 5%. CpG dinucleotide showed the higher variation frequency, probably because of it could be target of DNA methylation. We performed a reduced representation bisulfite sequencing on E14 cell line to test our new genome assembly with respect to the mm9 genome reference. After mapping and methylation status calling, we obtained an increase of about 120,000 called CpG and we avoided about 20,000 wrong CpG calling.

overall_design: genotyping of E14 embryonic stem cells (ESCs) and Reduced representation Bisulfite Sequencing (RRBS) of E14 ESCs.

first: Danny

last: Incarnato


title: Bromodomain protein BRD4 is required for estrogen receptor-dependent transcription and enhancer activation [RNA-Seq]

city: Göttingen

first: Steven

last: Johnsen

state: Niedersachsen

address: Robert-Koch-Straße 40

department: Department of General, Visceral and Pediatric Surgery

institute: University Medical Center Göttingen

summary: The estrogen receptor-α (ERα) is a transcription factor which plays a critical role in controlling cell proliferation and tumorigenesis by recruiting various cofactors to estrogen response elements (EREs) to induce or repress gene transcription. A deeper understanding of these transcriptional mechanisms may uncover novel therapeutic targets for ERα-dependent cancers. Here we show for the first time that BRD4 regulates ERα−induced gene expression by affecting elongation-associated phosphorylation of RNA Polymerase II (RNAPII P-Ser2) and histone H2B monoubiquitination (H2Bub1). Consistently, BRD4 activity is required for estrogen-induced proliferation of ER+ breast and endometrial cancer cells and uterine growth in mice. Genome-wide occupancy studies revealed an enrichment of BRD4 on transcriptional start sites as well as EREs enriched for H3K27ac and demonstrate a requirement for BRD4 for H2B monoubiquitination in the transcribed region of estrogen-responsive genes. Importantly, we further demonstrate that BRD4 occupancy correlates with active mRNA transcription and is required for the production of ERα-dependent enhancer RNAs (eRNAs). These results uncover BRD4 as a central regulator of ERα function and potential therapeutic target.

overall_design: mRNA expression profiles of MCF7 cells treated with +/- estrogen treatment under negative control siRNA, BRD4 siRNA or JQ1 treatment, in duplicates.

first: Sankari

last: Nagarajan

first: Malik

last: Alawi


title: Bromodomain protein BRD4 is required for estrogen receptor-dependent transcription and enhancer activation


title: Bromodomain protein BRD4 is required for estrogen receptor-dependent transcription and enhancer activation [ChIP-seq]

overall_design: ChIP-sequencing  of BRD4, ERα and H2Bub1 in MCF7 cells treated with +/- estrogen treatment and or +/- JQ1 treatment in triplicates.


title: MethylC-Seq of idm2 single mutant and idm1idm2 double mutant

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

summary: Using MethylC-Seq to provide single-base resolution of DNA methylation status in idm2 single mutant and idm1idm2 double mutant

overall_design: MethylC-Seq: 2 mutants examined, idm2 single mutant (two biological replicates) and idm1idm2 double mutant

first: Weiqiang

last: Qian

first: Kai

last: Tang


title: Examination of the transcirptional response of Acinetobacter baumannii to antibiotics

summary: This SuperSeries is composed of the SubSeries listed below. Strains of A. baumannii were exposed to sub-MIC doses of clinically relevant antibiotics to determine the transcriptional response

relation:
SuperSeries of: GSE56218
SuperSeries of: GSE56219
SuperSeries of: GSE56220
SuperSeries of: GSE56221
SuperSeries of: GSE56222
SuperSeries of: GSE56223
SuperSeries of: GSE56224
SuperSeries of: GSE56225
SuperSeries of: GSE56226

sample_organism:
Acinetobacter baumannii 34654
Acinetobacter sp. 983759
Acinetobacter sp. 1592897
Acinetobacter baumannii 1457504
Acinetobacter sp. 478810
Acinetobacter sp. 1564232
Acinetobacter baumannii 1207552
Acinetobacter baumannii 1428368
Acinetobacter sp. 1000160

overall_design: Refer to individual Series. Duplicate RNA samples were sequenced using the Illumina HiSeq.

first: Tracy

middle: H

last: Hazen

first: J

last: Johnson

first: Anthony

last: Harris


title: RNA-seq analysis of FSS1-dependent genes in Fusarium graminearum Z-3639

status: Public on Jul 09 2014

city: Seoul

first: Hokyoung

last: Son

address: Daehak-dong, Gwanak-gu

department: Center for Food and Bioconvergence

institute: Seoul National University

summary: Fusarium graminearum (teleomorph Gibberella zeae) is a prominent pathogen that infects major cereal crops, such as wheat, barley, and maize. FSS1 contains a Zn(II)2Cys6 fungal-type DNA-binding domain and localized exclusively to nuclei responding to sodium, suggesting that FSS1 is a TF required for sodium tolerance. By RNA-seq and genetic studies, we found a P-type ATPase pump (FgENA5) that is under control of FSS1 and is responsible for phenotypic defects of fss1 mutants. The wild-type, fss1 deletion, fss1 overexpression mutant strains were incubated in potato dextrose broth (PDB) with or without 1 M NaCl supplementation for an hour.

overall_design: 6 samples examined: 1 h after inoculation of Fusarium graminearum wild-type, Δfss1(Δfss1::gen), and fss1 overexpression mutant (fss1::gen-Pef1a-fss1) strains in potato dextrose broth with or without 1 M NaCl supplementation

first: Jae

middle: Y

last: Lim

first: Yin-Won

last: Lee


title: High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm

status: Public on Jul 08 2014

city: Worcester

first: Benjamin

last: Carone

state: Massachusetts

address: 364 Plantation St

department: BMP

institute: UMass Medical School

summary: Mammalian embryonic stem (ES) cells and sperm exhibit unusual chromatin packaging that plays important roles in cellular function. Here, we extend a recently developed technique, based on deep paired-end sequencing of lightly digested chromatin, to assess footprints of nucleosomes and other DNA-binding proteins genome-wide in murine ES cells and sperm. In ES cells, we recover well-characterized features of chromatin such as promoter nucleosome depletion, and further identify widespread footprints of sequence-specific DNA-binding proteins such as CTCF, which we validate in knockdown studies. We document global differences in nuclease accessibility between ES cells and sperm, finding that the majority of histone retention in sperm preferentially occurs in large gene-poor genomic regions, with only a small subset of nucleosomes being retained over promoters of developmental regulators. Finally, we describe evidence that CTCF remains associated with the genome in mature sperm, where it could play a role in organizing the sperm genome.

overall_design: We use Micrococcal Nuclease (MNase) to map chromatin structure in mouse ES cells and sperm. Specifically, we generate paired-end deep-sequencing libraries that are able to distinguish DNA digestion products by size, thus allowing us to simultaneously map nucleosomes as well as other DNA-binding proteins such as transcription factors.

first: Oliver

last: Rando

first: Jui

last: Hung


title: Activation and repression by oncogenic Myc shapes tumour-specific gene expression profiles

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

summary: In mammalian cells, the Myc oncoprotein binds to thousands of promoters. During mitogenic stimulation of primary lymphocytes, Myc promotes an increase in expression of virtually all genes. In contrast, Myc-driven tumour cells differ from normal cells in expression of specific sets of up- and downregulated genes that have significant prognostic value. To understand this discrepancy, we studied the consequences of inducible expression and depletion of Myc in human cells and murine tumour models. Changes in Myc levels activate and repress specific sets of direct target genes that are characteristic of Myc-transformed tumour cells. Three factors account for this specificity: First, the magnitude of response parallels the change in occupancy by Myc at each promoter. Functionally distinct classes of target genes differ in the E-box sequence bound by Myc, arguing that different cellular responses to physiological and oncogenic Myc levels are controlled by promoter affinity. Secondly, Myc both positively and negatively affects transcription initiation independent of its effect on transcriptional elongation. Third, complex formation with Miz1 mediates repression of multiple target genes by Myc and the ratio of Myc and Miz1 bound to each promoter correlates with the direction of response.

overall_design: Myc, Miz1 and RNA polymerase II ChIPseq as well as RNAseq experiments in two human cancer cell lines and murine carcinoma cells as well as fibroblasts from Miz1∆POZ mice. All sequencing experiment were performed on an Illumina Genome Analyzer IIx.

first: Susanne

last: Walz

first: Francesca

last: Lorenzin

first: Jennifer

last: Morton

first: Katrin

last: Wiese

first: Björn

last: von Eyss

first: Steffi

last: Herold

first: Lukas

last: Ryzak

first: Hélène

last: Dumay-Odelot

first: Saadia

last: Karim

first: Marek

last: Bartkuhn

first: Frederik

last: Roels

first: Torsten

last: Wuestefeld

first: Matthias

last: Fischer

last: Teichmann

first: Lars

last: Zender

first: Chia-Lin

last: Wei

first: Owen

last: Samson

first: Elmar

last: Wolf


title: RNA-seq in response to antibiotic stress (Acinetobacter baumannii 1457504)

first: David

last: Rasko

overall_design: 22 samples


title: RNA-seq in response to antibiotic stress (Acinetobacter baumannii 1564232)


title: MethylPurify: tumor purity deconvolution and differential methylation detection from tumor DNA methylomes

city: Boston

first: Shirley

last: Liu

address: 450 Brookline Ave

department: Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute and Harvard School of Public Health

summary: We propose a statistical algorithm MethylPurify that uses regions with bisulfite reads showing discordant methylation levels to infer tumor purity from tumor samples alone. With purity estimate, MethylPurify can identify differentially methylated regions (DMRs) from individual tumor samples without genomic variation information or prior knowledge from other datasets. In simulations with mixed bisulfite reads from cancer and normal cell lines, MethylPurify correctly inferred tumor purity and identified over 96% of the DMRs. On real patient data where tumor to normal comparison were used as golden standard, MethylPurify called DMR from tumor samples alone at over 57% sensitivity and 91% specificity.

overall_design: Lung adenocarcinoma cancer and normal tissues from 5 patients were captured by Agilent SureSelect Methyl-Seq system, followed by bisulfite sequencing.

first: Xiaoqi

last: Zheng

first: Qian

last: Zhao


title: miR-7 blockade alters E12.5 mouse cortical mRNA levels

city: new york

first: Andrew

last: Pollock

state: New York

address: 1300 York Ave

department: Cell and Developmental Biology

institute: Weill Cornell Medical College

summary:
Purpose: To assess changes in mRNA levels due to in vivo blockade of microRNA miR-7 with a miR-7 sponge in the E12.5 mouse neocortex
Methods: total RNA was isolated and sequenced from the dorsal cortex of wild-type or Emx1-Cre:miR-7-sponge transgenic mice in triplicate using an Illumina high-seq 1000.  Raw data was analyzed using Gobyweb v1.7.  Genes were considered changed which demonstrated expression level>1RPKM, fold-change>1.25, and FDR-qvalue <0.25.  Changed genes were then filtered by prediction of miR-7 targeting to reveal predicted miR-7 targets which were altered in vivo due to miR-7 sponge expression.
Results: 419 cortically expressed genes were significantly increased in expression level due to miR-7 sponge expression.  Of these, 162 are predicted to be targets of miR-7.

first: Shan

last: Bian

first: Zhengming

last: Chen

first: Chao

last: Zhang

first: Tao

last: Sun


title: Global Analysis of DNA Methylation by Methyl-Capture Sequencing Reveals Epigenetic change of pancreatic cancer

first: Shicheng

last: Guo

state: CA

address: 8730 Costa Verde

institute: MCRI, SHSCI, GHH, UCSD

summary:
Purpose: To establish pancreatic cancer-related aberrnat DNA methylation patterns, especially in CGI, CGI shore, orphan CGI and non-CGI promoter region and provide diagnosis or prognosis biomarker for pancreatic cancer dignosis or prognosis prediction
Methods:MBD methylCap/seq was carried out to screen differentially methylated CpG islands in 3 libraries which includes 1 pancreatic cancer mix library, 1 adjacent normal tissue mix library and 1 normal pancreas tissue. MSP and multiplex-BSP validation was performed in independent tumor and adjacent tissues.
Results: 66807 Hypermethylation DMR and 46815 Hypomethylation DMR were discovered in whole pancreatic cancer genome. 5280 Hypermethylation and 3488 Hypomethylation CpGI region were related gene promoter or gene body. Gene expression of 10 aberrant DMR were related with their methylation status validated by MSRE-qPCR and RT-PCR in 5-aza’ treated pancreatic cancer cell line. 40 DMR were validated in pancreatic cancer and adjacent tissues with MSP and gene ontology analysis showed seven of them were related with regulation of transcription(GO:0006355) which included DLX4,ELAVL2,IRX1,PITX2,SIM2,TBX5,TFAP2C.
Conclusions: Methylcap-seq identified hundreds of DMR genes and regions which might involve with gene expression regulation and could be used as biological markers of pancreatic cancer therapy target or diagnosis.

overall_design: Global Analysis of DNA Methylation by Methyl-CaptureSequencing Reveals Epigenetic change of pancreatic cancer

first: Jian

last: Yu

first: Yangxing

first: Hongyu


title: RNA-seq in response to antibiotic stress (Acinetobacter baumannii 34654)


title: Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting: small RNA-seq  profiling in Arabidopsis thaliana Col, Ler, and Cvi parental and reciprocal F1 hybrid seeds

city: Cambridge

first: Mary

last: Gehring

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Imprinted gene expression occurs during seed development in plants and is associated with differential DNA methylation of parental alleles, particularly at proximal transposable elements (TEs). Imprinting variability could contribute to observed parent-of-origin effects on seed development. We investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three Arabidopsis strains with diverse seed phenotypes. The majority of imprinted genes were parentally biased in the same manner among all strains. However, we identified several examples of allele-specific imprinting correlated with intraspecific epigenetic variation at a TE. We successfully predicted imprinting in additional strains based on methylation variability. We conclude that there is standing variation in imprinting even in recently diverged genotypes due to intraspecific epiallelic variation. These data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds.

overall_design: Sequencing of 12 small RNA samples from whole seeds 6 days after pollination.

first: Robert

middle: M

last: Erdmann

first: George

last: Bell


title: Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting

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

overall_design: Refer to individual Series


title: Epigenetic and transcriptional aberrations in human pluripotent stem cells reflect differences in reprogramming mechanisms

city: La Jolla

last: Morey

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

type: Methylation profiling by genome tiling array


title: VIB1, a link between glucose signaling and carbon catabolite repression, is essential for plant cell wall degradation by Neurospora crassa

city: Berkeley

first: N. Louise

last: Glass

address: 341 Koshland Hall, Univerisity of California

department: Plant and Microbial Biology

institute: UC Berkeley

summary: Purpose: To explore the function of VIB1 in regulating cellulase production in Neurospora crassa. Method: mRNA from vib-1 mutants were collected after a culture shift from sucrose to Avicel (crystaline cellulose) or carbon-free media. Expression profiles of vib-1 mutants were compared with published profiles of wild type created under the same conditions. Results: We found that many genes that specifically upregulated in wild type upon exposure to Avicel were expressed at low levels in ∆vib-1 and many other genes involved in metabolism and energy were expressed at high levels compared to wild type. Conclusions: Our study shows that VIB1 is required for suppression of glucose response and carbon catabolite repression to allow proper expression of clr-2 and subsequent cellulase production in response to cellulosic induction.

overall_design: Biological triplicates of liquid culture N. crassa were harvested at 4 hours after a switch from sucrose media to media of interest. Global mRNA abundances were measured by sequencing on the Illumina Genome Analyzer Iix and HiSeq2000 platforms.

first: Yi

last: Xiong

first: Jianping

first: N

middle: L


title: Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting: allele specific mRNA-seq expression profiling in Arabidopsis thaliana Col, Ler, and Cvi parental and reciprocal F1 hybrid embryo and endosperm

summary: Imprinted gene expression occurs during seed development in plants and is closely tied to differential DNA methylation of maternal and paternal alleles, particularly at proximal transposable elements (TEs). Since the epigenetic modification of TEs can vary within species, we investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three strains of Arabidopsis that display diverse seed size phenotypes. Unexpectedly we found that one strain, Cvi, is globally CG hypomethylated. We discovered three examples of strain-specific imprinting caused by epigenetic variation at a TE. Our data allowed us to predict and experimentally validate an instances of allele-specific imprinting in additional strains based only on methylation patterns. We conclude that numerous differences in imprinting can evolve in highly similar, recently diverged genotypes due to epiallelic variation present within the species. Our data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds.

overall_design: Examination of parent-of-origin specific and total gene expression in embryo, endosperm, and whole seeds. Samples with the same heading are biological replicates (e.g. CVN1, CVN2, and CVN3). High throughput Illumina sequencing of poly-A selected RNA from Arabidopsis Col, Ler and Cvi reciprocal F1 hybrid embryo and endosperm tissue isolated at 6 days after pollination to identify imprinted genes.

first: Elias

last: Scheer

first: Daniela

last: Pignatta


title: Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting: BS-seq of Arabidopsis thaliana Col, Ler, and Cvi parental and reciprocal F1 hybrid embryo and endosperm

overall_design: Whole genome bisulfite sequencing of embryo and endosperm (14 samples).


title: RNA sequencing of mice spermatozoa

city: shanghai

first: Zhongdong

last: Qiao

address: NO.800 Dongchuan Road

institute: Shanghai Jiao Tong University

summary: We reported RNA profiles of mice spermatozoa, a total of 35,288,825 reads matching 33,039 transcripts, including 27,310 coding transcripts, were obtained.

overall_design: RNA profiles of the spermatozoa of 9-10 weeks adult mice were sequenced by RNA-seq,using Illumina GAIIx.

first: Peng

last: Fang


title: Unexpected complexity of the Escherichia coli K-12 transcriptome architecture revealed by single nucleotide resolution RNA sequencing

city: Norman

first: James

last: Creecy

address: 770 Van Vleet Oval

department: Microbiology

institute: University of Oklahoma

summary: To investigate the architecture of the E. coli K-12 transcriptome, we used two RNA-Seq technologies to analyze strand-specific transcription at single-nucleotide resolution. We analyzed the data by using an organizational schema to annotate the promoters and terminators that define transcription units across the genome.  Our results showed that most (ca. two-thirds) operons have a single promoter and terminator, whereas one-third of operons contain multiple transcription units. We found substantial evidence for differential gene expression within complex operons, which we categorized based on operon architecture.

overall_design: E. coli K-12 strain MG1655 substrain BW38028 and isogenic rpoS mutant were cultured in minimal glucose media and the total transcriptome of log and stationary phase samples was sequenced.

first: Tyrrell

last: Conway

first: Joe

last: Grissom

first: Barry

last: Wanner

first: Phillip

last: Miguel