title: The In Vivo Pattern of Binding of RAG1 and RAG2 to Antigen Receptor Loci

status: Public on Apr 20 2010

city: bethesda

first: Seolkyoung

last: Jung

address: 10 Center Dr

department: NIAMS

institute: NIH

summary: The critical initial step in V(D)J recombination, binding of RAG1 and RAG2 to recombination signal sequences flanking antigen receptor V, D, and J gene segments, has not previously been characterized in vivo. Here we demonstrate that RAG protein binding occurs in a highly focal manner to a small region of active chromatin encompassing Igκ and Tcrα J gene segments and Igh and Tcrβ J and J-proximal D gene segments. Formation of these small RAG-bound regions, which we refer to as recombination centers, occurs in a developmental stage- and lineage-specific manner. Each RAG protein is independently capable of specific binding within recombination centers. While RAG1 binding is restricted to regions containing recombination signal sequences, RAG2 binds extremely broadly in a pattern that mirrors that of trimethylated lysine 4 of histone 3. We propose that recombination centers coordinate V(D)J recombination by providing discrete sites within which gene segments are captured for recombination.

overall_design: RAG2 binding was analyzed in wild type, RAG2-/-β, and D708A-RAG1-/-β thymocytes. Histone modification H3K4me3 was analyzed in D708A-RAG1-/-β and wild type thymocytes.

first: Yanhong

last: Ji

first: Wolfgang

last: Resch

first: Elizabeth

last: Corbett

first: Arito

last: Yamane

first: Rafael

last: Casellas

first: David

last: Schatz


title: Developmental Regulation and Individual Differences of Neuronal Epigenomes in the Prefrontal Cortex

city: Boston

first: Hennady

last: Shulha

state: MA

address: 44 Cummington st

department: BME

country: USA

institute: Boston University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report global distribution of trimethylated Histone H3 Lysine 4 (H3K4me3) in human prefrontal cortex neurons at different ages

overall_design: Neuronal nuclei from human prefrontal cortex were isolated by FACS. Regions marked by H3K4me3 were identified by chromatin immunoprecipiation followed by deep sequencing.

first: Schahram

last: Akbarian

first: Zhiping

last: Weng


title: Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis

status: Public on Apr 16 2010

city: Duarte

first: Dustin

middle: E

last: Schones

state: CA

address: 1500 E Duarte Rd.

institute: City of Hope

type: Expression profiling by high throughput sequencing

summary:
We use male gonads isolated from a Drosophila strain that allows us to obtain enough cells at their primitive status as the starting material to study the endogenous chromatin structure of undifferentiated cells using ChIP-seq. We integrate the ChIP-seq data with RNA-seq data that measures the transcriptome in a digital manner. Our genome-wide analyses indicate that the majority of differentiation genes in undifferentiated cells lack an active chromatin mark and paused Pol II; instead, they are associated with either the repressive H3K27me3 mark or no detectable mark. In order to address the possibility that distinct techniques are responsible for such a difference, we also use the Drosophila S2 cells to perform ChIP-seq and RNA-seq and compare the results directly with published work using ChIP-chip and microarray on S2 cells.
For the S2 cell ChIP-chip data, we used data from the following paper:
Muse GW, Gilchrist DA, Nechaev S, Shah R, Parker JS, Grissom SF, Zeitlinger J, Adelman K: RNA polymerase is poised for activation across the genome. /Nat Genet /2007, 39(12):1507-1511. The accession number for this data is: GSE6714.

overall_design:
ChIP-seq: Profiling chromatin modifications using antibodies against 3 histone modifications and RNA Pol II in S2 cells
Profiling chromatin structure in bam testis using antibodies against 3 histone modifications and RNA Pol II

RNA-seq: Profiling transcriptome of S2 cells using RNA-seq

first: Qiang

last: Gan

first: SukHo

last: Eun

first: Gang

last: Wei

first: Kairong

last: Cui

first: Keji

last: Zhao

first: Xin

last: Chen


title: RNA-Seq on libraries made from serial dilutions of Drosophila melanogaster S2 cell mRNA and ERCC external RNA controls

status: Public on Apr 19 2010

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary:
RNA-Seq on libraries made from serial dilutions of mRNA from Drosophila melanogaster S2 cell and the External RNA Controls Consortium (ERCC)  external RNA controls.

We evaluated performance of RNA-Seq by serially diluting a complex pool of known synthetic PolyA+ mRNAs from the External RNA Controls Consortium (ERCC) and PolyA+ mRNA from Drosophila S2 cells.  ERCC mRNAs were obtained under Phase V testing from the National Institutes of Standards and Technology (NIST).  The ERCC pool contained 96 species of mRNA of various lengths and GC content covering a 2^20 concentration range.  Libraries were constructed with 100ng to 10pg of input mRNA.  Our data shows an outstanding linear fit between RNA-Seq read density and known input amounts.

sample_organism:
Drosophila melanogaster
synthetic construct

overall_design: We performed RNA-Seq from libraries made with 0.01ng to 100ng mRNA (mixture of mRNA from Drosophila melanogaster S2 cells and ERCC RNA controls). One RNA-Seq library was prepared with 100ng mRNA and six libraries were made with serial dilutions of mRNA using a modified protocol (see Sample 'extraction protocol'). One lane was sequenced for each library and all seven libraries were run on the same flow cell.

first: Yu

last: Zhang

first: Lichun

last: Jiang


title: Genome-wide maps of CFP1, RNA Polymerase II and H3K4me3 in mouse brain.

status: Public on Apr 15 2010

city: Edinburgh

first: Adrian

middle: P

last: Bird

state: Midlothian

address: Mayfield Road

department: WTCCB

country: United Kingdom

institute: The University of Edinburgh

summary: We report the application of single molecule-based sequencing technology for high-throughput mapping of CFP1, RNA polymerase II and H3K4me3 in mouse brain. By obtaining sequence from chromatin immunoprecipitated DNA, we generated genome-wide binding / chromatin-state maps for mouse brain. We find a good correlation between CFP1 binding and H3K4me3 consistent with it presence in the SetD1 histone methylatransferase complex. Mapped RNA polymerase II colocalised with the majority of CFP1 / H3K4me3 positive CpG islands but not all. This study provides a comprehensive characterisation of the genome wide distribution of a previously uncharacaterised DNA binding factor and suggests a link between DNA base composition and chromatin state.

overall_design: Examination of H3K4me3, RNA PolymeraseII and CFP1 in mouse brain.

first: John

last: Thomson

first: Pete

middle: J

last: Skene

first: Jim

last: Selfridge

first: Jacky

last: Guy

first: Aimée

last: Deaton

first: Alastair

last: Kerr

first: Shaun

last: Webb

first: Rob

last: Andrews

first: Keith

middle: D

last: James

first: Daniel

last: Turner

first: Stuart

last: McLaren

first: Robert

middle: S

last: Illingworth


title: Diverse Targets of the Transcription Factor STAT3 Contribute to T Cell Pathogenicity and Homeostasis [ChIP-seq]

status: Public on May 30 2010

first: Golnaz

last: Vahedi

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

institute: National Institutes of Health

summary: STAT3, an essential transcription factor with pleiotropic functions, plays critical roles in the pathogenesis of autoimmunity. Despite recent data linking STAT3 with inflammatory bowel disease, exactly how it contributes to chronic intestinal inflammation is not known. Using a T cell transfer model of colitis we found that STAT3 expression in T cells was essential for the induction of both colitis and systemic inflammation. STAT3 was critical in modulating the balance of T helper 17 (Th17) and regulatory T (Treg) cells, as well as in promoting CD4+ T cell proliferation. We used chromatin immunoprecipitation and massive parallel sequencing (ChIP-Seq) to define the genome-wide targets of STAT3 in CD4+ T cells. We found that STAT3 bound to multiple genes involved in Th17 cell differentiation, cell activation, proliferation and survival, regulating both expression and epigenetic modifications.  Thus, STAT3 orchestrates multiple critical aspects of T cell function in inflammation and homeostasis.

overall_design: Examination of gene expression profiles and histone modification (H3K4me3) in wild type and STAT3-deficient T cells. Also Examination of STAT3 binding in wild type T cells.

first: Lydia

last: Durant

first: Wendy

middle: T

last: Watford

first: Haydeé

middle: L

last: Ramos

first: Arian

last: Laurence

first: Lai

last: Wei

first: Hayato

last: Takahashi

first: Hong-Wei

last: Sun

first: Yuka

last: Kanno

first: Fiona

last: Powrie

last: O’Shea


title: Cell-Specific Determinants of PPARg Function in Adipocytes and Macrophages

status: Public on Apr 14 2010

city: philadelphia

first: Mitchell

middle: A.

last: Lazar

state: PA

address: 700 CRB, 415 Curie Blvd.

department: Institute for Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

summary: The nuclear receptor Peroxisome Proliferator Activator Receptor   (PPAR ) is the target of antidiabetic thiazolidinedione drugs, which improve insulin resistance but have side-effects that limit widespread use. PPAR  is required for adipocyte differentiation, but is also expressed in other cell types, notably macrophages, where it influences atherosclerosis, insulin resistance, and inflammation. A central question is whether PPAR  binding in macrophages occurs at the same or different genomic locations compared to adipocytes. Here, utilizing chromatin immunoprecipitation and high throughput sequencing (ChIP-seq), we demonstrate that PPAR  cistromes in adipocytes and macrophages are predominantly cell type specific. In macrophages, PPAR  colocalizes with the hematopoietic transcription factor PU.1 in areas of open chromatin and histone acetylation, near a distinct set of immune genes in addition to a number of metabolic genes shared with adipocytes. In adipocytes, the macrophage-unique binding regions are marked with repressive histone modifications, typically associated with local chromatin compaction and gene silencing. PPAR , when introduced into cells that are neither macrophages nor adipocytes, bound only to regions depleted of repressive histone modifications, where it increased DNA accessibility, enhanced histone acetylation, and induced gene expression. Thus, the cell-specificity of PPAR  function is regulated by cell-specific chromatin accessibility, histone marks, and transcription factors.

overall_design:
Genomic occupancy profiled by high throughput sequencing (ChIP-seq) from mouse macrophages for PPARgamma, PU.1, C/EBPbeta, H3K9Ace; and from 3T3-L1 adipocytes for PPARgamma and H3K9Ace

Masking file used to subtract input bias areas prior to generating final peak lists is linked below.

first: Martina

middle: I

last: Lefterova

middle: A


title: Genome-wide evolutionary analysis of eukaryotic DNA methylation

city: Berkeley

first: Toshiro

last: Nishimura

address: 211 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

type: Methylation profiling by high throughput sequencing

summary:
Eukaryotic cytosine methylation represses transposable elements, but also occurs in bodies of active genes. The extent to which these processes are conserved is unclear, and little is known about methylation outside of mammals, Arabidopsis thaliana, and Neurospora crassa. Utilizing deep bisulfite sequencing, we have quantified DNA methylation in five plant, seven animal, and five fungal genomes. We find that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons has evolved independently in the vertebrate lineage. We show that methylation of plant transposons in the CHG context extends to green algae, and present evidence for RNA-directed DNA methylation of fungal genes. We also show that antagonism between DNA methylation and histone H2A.Z is conserved between plants and animals. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes.

Keywords: Epigenetics

sample_organism:
Volvox carteri
Physcomitrium patens
Oryza sativa
Phycomyces blakesleeanus
Coprinopsis cinerea
Tribolium castaneum
Bombyx mori
Drosophila melanogaster
Apis mellifera
Ciona intestinalis
Laccaria bicolor
Uncinocarpus reesii
Nematostella vectensis
Selaginella moellendorffii
Tetraodon nigroviridis
Rhodonia placenta
Chlorella variabilis

overall_design: Examination of DNA methylation and transcription in plant, animal, and fungal genomes, and examination of how H2A.Z deposition relates to both methylation and transcription in puffer fish. Descriptions of the Samples' raw and processed data (provided as supplementary files) can be found in GSE19824_README.txt at the foot of this record.

first: Assaf

last: Zemach

first: Ivy

last: McDaniel

first: Pedro

last: Silva

last: Zilberman


title: Arabidopsis lyrata flowering tissues small RNAs

status: Public on Apr 22 2010

city: University Park

first: Michael

last: Axtell

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNA sequences from Arabidopsis lyrata flowering tissues, as isolated from flowering tissues of two biological replicates.  These data were analyzed to 1) discover new micoRNAs in A. lyrata 2) examine microRNA processing accuary in A. lyrata and 3) to examine patterns of 24nt siRNA accumulation in A. lyrata.

overall_design: Two small RNA libraries from flowering tissues of two biological replicates were analyzed using an Applied Biosystems SOLiD™ System

first: Zhaorong

last: Ma

first: Ceyda

last: Coruh


title: Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs

status: Public on May 01 2010

city: Cambridge

last: Guttman

address: 7 Cambridge Center

institute: Broad Institute

summary: RNA-Seq provides an unbiased way to study a transcriptome, including both coding and non-coding genes. To date, most RNA-Seq studies have critically depended on existing annotations, and thus focused on studying expression levels and variation in known transcripts. Here, we present Scripture, a method to reconstruct the transcriptome of a mammalian cell using only RNA-Seq reads and the genome sequence. We apply this approach to mouse embryonic stem cells, neuronal precursor cells, and lung fibroblasts to accurately reconstruct the full-length gene structures for the vast majority of known genes. We identify novel biological variation in protein-coding genes, including thousands of novel 5'-start sites, 3'-ends, and internal coding exons. We then determine the gene structures of over a thousand lincRNA loci. Our results open the way to direct experimental manipulation of thousands of non-coding RNAs, and demonstrate the power of ab initio reconstruction to provide a comprehensive picture of mammalian transcriptomes.

overall_design: RNA-Seq experiments of poly-A selected total RNA from embryonic stem cells, lung fibroblasts, and neural progenitor cells.

first: Manuel

last: Garber

first: Eric

last: Lander

first: Aviv

last: Regev


title: Human embryonic stem cells HELP-tagging cytosine methylation data (Albert Einstein College of Medicine)

status: Public on Apr 12 2010

city: Bronx

first: John

last: Greally

state: NY

address: 1301 Morris Park Avenue

department: Genetics

institute: Albert Einstein College of Medicine

summary: Background: To perform epigenome-wide association studies in human disease, assays need to be comprehensive and quantitative while remaining cost-effective.  We explored how the strengths of prior tag-based cytosine methylation assays based on massively-parallel sequencing can be maximised analytically.  Results:  We find that the use of the EcoP15I restriction enzyme to generate long tags and the normalisation of methylation-sensitive by methylation-insensitive restriction enzyme representations greatly improve assay performance.  When exploring sources of bias, we find that the length of the restriction fragment has moderate effects on EcoP15I digestion, while base composition exerts minimal effects.  We detail the analytical workflow that maximises the quantitative capabilities of this modified assay.  Also revealed are polymorphic sequences in the genome that could confound microarray, bisulphite sequencing or mass spectrometry-based assays, and a position effect causing hypomethylation of transposable elements near gene promoters.  Conclusions:  The new combined assay, referred to as HELP-tagging, interrogates over 1.8 million loci in the human genome quantitatively with a single lane of Illumina sequencing.  When the goal is to study not only CG-dense sequence but also the CG-depleted majority of the genome, this assay system should be suitable.

overall_design: Three MspI reference, one HpaII test

middle: M

first: Masako

last: Suzuki


title: MicroRNA-Directed siRNA Biogenesis in Caenorhabditis elegans

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

summary: C.elegans small RNAs from HA::ALG-1, HA::ALG-2 and HA::RDE-1 IP and rde-1 mutants

overall_design: Small RNAs were cloned from transgenic or mutant C. elegans adults. Sequencing was performed using 454 and Illumina platforms.


title: Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors.

first: Andrew

last: Oler

address: 31 Center Drive, Room 3B62E

department: Bioinformatics and Computational Biosciences Branch (BCBB)

institute: NIAID/NIH

summary: RNA polymerase (Pol) III transcribes many noncoding RNAs (for example, transfer RNAs) important for translational capacity and other functions. We localized Pol III, alternative TFIIIB complexes (BRF1 or BRF2) and TFIIIC in HeLa cells to determine the Pol III transcriptome, define gene classes and reveal 'TFIIIC-only' sites. Pol III localization in other transformed and primary cell lines reveals previously uncharacterized and cell type–specific Pol III loci as well as one microRNA. Notably, only a fraction of the in silico–predicted Pol III loci are occupied. Many occupied Pol III genes reside within an annotated Pol II promoter. Outside of Pol II promoters, occupied Pol III genes overlap with enhancer-like chromatin and enhancer-binding proteins such as ETS1 and STAT1. Moreover, Pol III occupancy scales with the levels of nearby Pol II, active chromatin and CpG content. These results suggest that active chromatin gates Pol III accessibility to the genome.

overall_design: Use of ChIP-seq to identify genomic regions bound by RNA Polymerase III machinery in multiple cell types as well as RNA-seq in HeLa for gene expression analysis.  See GSE20609 for whole human genome raw Pol III ChIP-array data.  See link below for supplementary methods and analysis.

first: Ravi

middle: K

last: Alla

first: Douglas

middle: N

last: Roberts

first: Alexander

last: Wong

first: Peter

middle: C

last: Hollenhorst

first: Katherine

last: Chandler

first: Patrick

last: Cassiday

first: Cassie

last: Nelson

first: Curt

middle: H

last: Hagedorn

first: Barbara

last: Graves

first: Bradley

middle: R

last: Cairns


title: Structural and Functional Analysis of Viral siRNAs using Solexa sequencing

city: Norwich

first: Simon

last: Moxon

state: Norfolk

address: University of East Anglia

institute: University of East Anglia

summary:
We profiled vsiRNAs using two different high-throughput sequencing platforms and also developed a hybridisation-based array approach. The profiles obtained through the Solexa platform and by hybridisation were very similar to each other but different from the 454 profile. Both deep sequencing techniques revealed a strong bias in vsiRNAs for the positive strand of the virus and identified regions on the viral genome that produced vsiRNA in much higher abundance than other regions. The hybridisation approach also showed that the position of highly abundant vsiRNAs were the same in different plant species and in the absence of RDR6. We used the TerminatorTM 5'-Phosphate-Dependent Exonuclease to study the 5' end of vsiRNAs and showed that a perfect control duplex was not digested by the enzyme without denaturation and that the efficiency of the Terminator was strongly affected by the concentration of the substrate. We found that most vsiRNAs have 5' monophosphates, which was also confirmed by profiling short RNA libraries following either direct ligation of adapters to the 5' end of short RNAs or after replacing any potential 5' ends with monophosphates. The Terminator experiments also showed that vsiRNAs were not perfect duplexes. Using a sensor construct we also found that regions from the viral genome that were not complementary to highly abundant vsiRNAs were targeted in planta just as efficiently as regions recognised by abundant vsiRNAs.

Different high-throughput sequencing techniques have different reproducible sequence bias and generate different profiles of short RNAs. The Terminator exonuclease does not process double-stranded RNA and because short RNAs can quickly re-anneal at high concentration, this assay can be misleading if the substrate is not denatured and not analysed in a dilution series. The sequence profiles and Terminator digests suggest that CymRSV siRNAs are produced from the structured positive strand rather than from perfect double-stranded RNA or by RNA-dependent RNA polymerase.

sample_organism:
Nicotiana benthamiana
Cymbidium ringspot virus

overall_design: Size-fractionated (19-24 nt) small RNA from early systemic leaves of CymRSV-infected Nicotiana benthamiana total RNA extracts was de-phosphorylated with Shrimp Alkaline Phosphatase and re-phosphorylated with T4 Polynucleotide Kinase. The resulting sRNAs were ligated to adaptors in the following reaction. The purified, adaptor ligated short RNAs were reverse transcribed. After PCR amplification, the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.

first: Gyorgy

last: Szittya

first: Vitantonio

last: Pantaleo

first: Gabor

last: Toth

first: Rachel

last: Rusholme-Pilcher

first: Jozsef

last: Burgyan

first: Tamas

last: Dalmay


title: CpG islands recruit a histone H3 lysine 36 demethylase [Illumina sequencing data]

status: Public on Apr 27 2010

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

summary: Eukaryotic gene expression profiles are largely defined by transcription factors that recognize specific DNA sequences in gene regulatory regions and impact RNA polymerase recruitment and transcription. In addition to specific core promoter regulatory elements, up to 70% of genes in higher eukaryotes are also characterized by an overrepresentation of cytosine/guanine base pairs (CpGs) surrounding promoters and gene regulatory units.  These features, called CpG islands, were identified over twenty years ago but there remains little mechanistic evidence to suggest how these enigmatic elements contribute to promoter function, with the exception that they are refractory to epigenetic silencing by DNA methylation. Here we uncover a role for CpG islands in buffering gene regulatory elements from repressive histone H3 lysine 36 methylation by directly recruiting the H3K36 specific lysine demethylase enzyme KDM2A. KDM2A is recruited to CpG islands by a zinc finger CxxC (ZF-CxxC) domain that specifically recognizes CpG DNA and is blocked by DNA methylation. This capacity to sense the epigenetic methylation state of DNA constrains KDM2A to non-methylated CpG islands. Importantly, these observations suggest CpG islands may function to delineate gene regulatory elements from bulk chromatin by recruiting factors that create unique chromatin architecture.

overall_design: This study provides information about binding of lysine demethylase enzyme KDM2A in mouse embryonic stem cells.

first: Neil

last: Blackledge

first: Jin

last: Zhou

first: Michael

middle: Y

last: Tolstorukov

first: Robert

last: Klose


title: Characterization of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training

status: Public on Apr 09 2010

city: Belfield

first: Paul

last: McGettigan

state: Co Dublin

address: Veterinary Sciences Centre, UCD

department: School of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

summary: Digital gene expression profiling was used to characterize the assembly of genes expressed in equine skeletal muscle and to identify the subset of genes that were differentially expressed following a ten month period of exercise training. The study cohort comprised 7 thoroughbred racehorses from a single training yard. Skeletal muscle biopsies were collected at rest from the gluteus medius at two time points: T1 (unconditioned), (9 +/- 0.5 months old) and T2 (conditioned) (20 +/- 0.7 months old). The most highly abundant genes in the muscle transcriptome were those involved in muscle contraction, aerobic respiration and mitochondrial function. A previously unreported over-representation of genes relating to RNA processing, the stress response and proteolysis was observed. Following training 92 tags were differentially expressed of which 74 were annotated. Sixteen genes showed increased expression, including the mitochondrial genes, ACADVL, MRPS21 and SLC25A29. Among the 58 genes with deceased expression MSTN, a negative regulator of muscle growth had the greatest decrease. Functional analysis of all expressed genes using FatiScan revealed an asymmetric distribution of 482 Gene Ontology groups and 18 KEGG pathways. Functional groups with highly significantly (P < 0.0001) increased expression included mitochondrion, oxidative phosphorylation and fatty acid metabolism while functional groups with decreased expression were mainly associated with structural genes and included the sarcoplasm, laminin complex and cytoskeleton.

overall_design: Examination of muscle expression changes in 7 thoroughbred horses following 10 months of exercise training using digital gene expression with NlaIII.

first: Beatrice

last: McGivney

first: John

last: Browne

first: Alexander

last: Evans

first: Rita

middle: G

last: Fonseca

first: Brendan

last: Loftus

first: Amanda

last: Lohan

first: David

middle: E

last: MacHugh

last: Murphy

first: Lisa

last: Katz

first: Emmeline

middle: W

last: Hill


title: Structural and Functional Analysis of Viral siRNAs

first: Simon

last: Moxon

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

platform_organism:
Nicotiana benthamiana
Cymbidium ringspot virus

overall_design: Refer to individual Series


title: Characterization of the RNA content of chromatin

status: Public on Apr 13 2010

city: Uppsala

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

country: Sweden

institute: Uppsala University

summary: We deep sequenced chromatin-associated RNAs (CARs) from human fibroblast (HF) cells. This resulted in the identification of 141 intronic regions and 74 intergenic regions harbouring CARS.

overall_design: We purified CARs from normal HFs by isolating soluble chromatin after MNase treatment, followed by separation of chromatin fragments of different lengths on a sucrose gradient. CARs were converted into double-stranded cDNAs and sequenced using the Illumina Genome Analyzer I.

first: Tanmoy

last: Mondal

first: Markus

last: Rasmussen

first: Gaurav

last: Pandey

first: Chandrasekhar

last: Kanduri


title: Small RNA Solexa sequencing of human liver samples

status: Public on Apr 10 2010

city: Hangzhou

first: Meng

last: Xia

address: 866 Yuhangtang Road

country: China

institute: Institute of Immunology, Zhejiang University School of Medicine

summary:
We applied small RNA Solexa sequencing technology to identify microRNA expression in human liver samples from surgically removed liver tissues including three normal liver tissues (distal normal liver tissue of liver hemangioma), an hepatitis B virus (HBV)-infected liver, a severe chronic hepatitis B liver, two HBV-related hepatocellular carcinoma (HCC), an hepatitis C virus (HCV)-related HCC, and an HCC without HBV or HCV infection. All samples were collected with the informed consent of the patients and the experiments were approved by the ethics committee of Second Military Medical University, Shanghai, China. We investigated the miRNome in human normal liver and suggested some deregulated abundantly expressed microRNAs in HCC.
center_name: National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai, China.

overall_design: Examination of miRNome in human liver samples from surgically removed liver tissues including three normal liver tissues (distal normal liver tissue of liver hemangioma), an hepatitis B virus (HBV)-infected liver tissue, a severe chronic hepatitis B liver tissue, an HBV-related hepatocellular carcinoma (HCC) tissue and adjacent liver tissues of different regions,an HBV-related HCC tissue and adjacent liver tissue, an hepatitis C virus (HCV)-related HCC tissue and adjacent liver tissue, and an HCC without HBV or HCV infection and adjacent liver tissue. All 15 human liver tissue samples.

first: Jin

last: Hou

first: Xuetao

last: Cao


title: Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with rice centromeres

city: Madison

first: Yufeng

last: Wu

state: WI

address: 1575 Linden Drive

institute: UW-Madison

summary: Specification and propagation of the centromeres of eukaryotic chromosomes is determined by epigenetic mechanisms. Unfortunately, the epigenetic characteristics of centromeric DNA and chromatin are difficult to define because the centromeres are composed of highly repetitive DNA sequences in most eukaryotic species. Several rice centromeres have been fully sequenced, making rice an excellent model for centromere research. We conducted genome-wide mapping of cytosine methylation using methylcytosine immunoprecipitation combined with Illumina sequencing. The DNA sequences in the core domains of rice Cen4, Cen5, and Cen8 showed elevated methylation levels compared to the sequences in the pericentromeric regions. In addition, elevated methylation levels were associated with the DNA sequences in the CENH3-binding subdomains compared to the sequences in the flanking H3 subdomains. In contrast, the centromeric domain of Cen11, which is composed exclusively of centromeric satellite DNA, is hypomethylated compared to the pericentromeric domains. Thus, the DNA sequences associated with functional centromeres can be either hypomethylated or hypermethylated. The methylation patterns of centromeric DNA appear to be correlated with the composition of the associated DNA sequences. We propose that both hypomethylation and hypermethylation of CENH3-associated DNA sequences can serve as epigenetic marks to distinguish where CENH3 deposition will occur within the surrounding H3 chromatin.

overall_design: mCIP-seq of one sample of rice seedling

first: Huihuang

last: Yan

first: Shinji

last: Kikuchi

first: Pavel

last: Neuman

first: Wenli

last: Zhang

first: Feng

last: Chen

first: Jiming

last: Jiang


title: Conservation and divergence of methylation patterning in plants and animals

city: Los Angeles

first: matteo

last: Pellegrini

address: 621 Charles Young Drive South

department: MCD Biology

institute: UCLA

summary: Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms. While DNA methylation likely has a conserved role in gene silencing, the levels and patterns of DNA methylation appear to vary drastically among different organisms. Here, we used shotgun genomic bisulfite sequencing (BS-Seq) to compare DNA methylation in eight diverse plant and animal genomes. We found that patterns of methylation are very similar in flowering plants with methylated cytosines detected in all sequence contexts, whereas CG methylation predominates in animals. Vertebrates have methylation throughout the genome except for CpG islands. Gene body methylation is conserved with clear preference for exons in most of the organisms. Furthermore, genes appear to be the major target of methylation in Ciona and honeybee. Among the eight organisms, the green alga Chlamydomonas has the most unusual pattern of methylation, having non-CG methylation enriched in exons of genes rather than in repeats and transposons. In addition, we demonstrate that the Dnmt1 cofactor Uhrf1 has a conserved function in maintaining CG methylation in both transposons and gene bodies in the mouse, Arabidopsis, and zebrafish genomes.

sample_organism:
Chlamydomonas reinhardtii
Populus trichocarpa
Arabidopsis thaliana
Oryza sativa
Apis mellifera
Ciona intestinalis
Danio rerio
Mus musculus

overall_design: Comparison of methylation across eight eukaryotic organisms

first: Suhua

last: Feng

first: Shawn

middle: J

last: Cokus

first: Xiaoyu

first: Pao-Yang

first: Magnolia

last: Bostick

first: Mary

last: Goll

first: Jonathan

last: Hetzel

first: Jayati

last: Jain

first: Steven

last: Strauss

first: Marnie

last: Halpern

first: Chinweike

last: Ukomadu

first: Kristen

last: Sadler

first: Sriharsa

last: Pradhan

first: Matteo

last: Jacobsen


title: mRNA-Seq of head tissue from Drosophila mojavensis

status: Public on Apr 11 2010

first: Brian

last: Oliver

address: 50 South Drive

institute: NIDDK, NIH

summary:
We sequenced mRNA from head tissue of females and male of Drosophila mojavensis to identify genes differentially expressed between the sexes and sex-specific alternative splicing events.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: Comparison of expresssion profiles in female and male head tissue from D. mojavensis

first: John

last: Malone


title: RNA-Seq of Drosophila cell line Dmel2

city: Heidelberg

first: Michael

last: Boutros

address: Im Neuenheimer Feld 580

department: Signaling and Functional Genomics

country: Germany

institute: German Cancer Research Center (DKFZ)

summary: Deep Sequencing of mRNA from the Drosophila melanogaster cell line D.Mel-2

overall_design: Analysis of poly(A)+ RNA of D.Mel-2 cell line

first: Thomas

last: Sandmann

last: Horn


title: RNA-Seq on libraries made from ERCC external RNA controls, and a mixture of D. melanogaster S2 cell mRNA and ERCC mRNAs

summary:
RNA-Seq on libraries made from External RNA Controls Consortium (ERCC) external RNA controls, and a mixture of mRNA from Drosophila melanogaster S2 cell and ERCC mRNAs.

We evaluated performance of RNA-Seq on known synthetic PolyA+ mRNAs from the External RNA Controls Consortium (ERCC) alone and in mixtures with PolyA+ mRNA from Drosophila S2 cells. ERCC mRNAs were obtained under Phase V testing from the National Institutes of Standards and Technology (NIST).  The ERCC pool contained 96 species of mRNA of various lengths and GC content covering a 2^20 concentration range.  Libraries were constructed using 100ng S2 mRNA with 5ng, 2.5ng, or 1ng ERCC mRNAs, and using 50ng ERCC mRNA without S2 cell mRNA. Our data shows an outstanding linear fit between RNA-Seq read density and known input amounts.

platform_organism:
Drosophila melanogaster
synthetic construct

overall_design: We made libraries with 100ng S2 mRNA with 5ng, 2.5ng or 1ng ERCC mRNAs and with 50ng ERCC mRNAs only. For each library, one lane was sequenced for a 36bp run and around 15 million reads were obtained for each lane.

first: Yu

last: Zhang

first: Lichun

last: Jiang


title: KLF1/EKLF regulatory networks in primary erythroid cells

status: Public on Apr 08 2010

city: The University of Queensland, St Lucia, Brisbane

first: Andrew

last: Perkins

state: QLD

address: Institute for Molecular Bioscience

department: Institute for Molecular Bioscience

country: Australia

institute: The University of Queensland

summary: KLF1 (EKLF) regulates a diverse suite of genes to direct erythroid cell differentiation from bi-potent progenitors. To determine the local cis-regulatory contexts and transcription factor networks in which KLF1 operates, we performed KLF1 ChIP-seq in the mouse. We found at least 945 sites in the genome of E14.5 fetal liver erythroid cells which are occupied by endogenous KLF1. Many of these recovered sites reside in erythroid gene promoters such as β-globin, but the majority are distant to any known gene. Our data suggests KLF1 directly regulates most aspects of terminal erythroid differentiation including production of α and β-globin protein chains, heme biosynthesis, co-ordination of proliferation and anti-apoptotic pathways, and construction of the red cell membrane and cytoskeleton by functioning primarily as a transcriptional activator. Additionally, we suggest new mechanisms for KLF1 co-operation with other transcription factors, in particular the erythroid transcription factor GATA1, to maintain homeostasis in the erythroid compartment.

overall_design: Examination of KLF1 occupancy in primary erythroid cells. KLF1-ChIP and input samples were run on AB SOLiD Systems 2.0 and 3.0. The genomic alignment files (*sorted.txt) and peak file (*bed) contain the combined System 2.0 and 3.0 data.

last: Tallack

first: Tom

last: Whitington

first: Wai

middle: S

last: Yuen

first: Elanor

last: Wainwright

first: Janelle

last: Keys

first: Brooke

middle: B

last: Gardiner

first: Ehsan

last: Nourbakhsh

first: Nicole

last: Cloonan

first: Sean

last: Grimmond

first: Timothy

last: Bailey


title: OCT4, NANOG and CTCF in human embryonic stem cells

status: Public on Apr 05 2010

city: Singapore

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

state: Singapore

address: 60, Biopolis street

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore


title: Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms

first: Cole

last: Trapnell

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: We introduce an approach to transcript discovery coupled with a statistical model for RNA-Seq experiments that produces estimates of transcript abundances. Our algorithms are implemented in an open source software program called Cufflinks. To test Cufflinks, we sequenced and analyzed more than 430 million paired 75bp RNA-Seq reads from a mouse myoblast cell line representing a differentiation timeseries.  We detected 13,689 known transcripts and 3,724 previously unannotated ones, 62% of which are supported by independent expression data or by homologous genes in other species.  Analysis of transcript expression over the timeseries revealed complete switches in the dominant transcription start site (TSS) or splice-isoform in 330 genes, along with more subtle shifts in a further 1,304 genes. These dynamics suggest substantial regulatory flexibility and complexity in this well-studied model of muscle development.

overall_design: Timeseries of C2C12 myoblast RNA-Seq

first: Brian

last: Williams

first: Geo

last: Pertea

first: Ali

last: Mortazavi

first: Gordon

last: Kwan

first: Marijke

last: van Baren

first: Steven

middle: L

last: Salzberg

first: Barbara

last: Wold

first: Lior

last: Pachter


title: Single-Base Resolution Methylomes of Silkworms and Functional Importance of Gene Methylation in Insects Revealed by Ultra-High-Throughput Sequencing

city: Kunming

first: Hui

last: Xiang

state: Yunnan Province

address: 32 East Jiaochang Road

institute: Kunming Insititute of Zoology

summary: Single-base resolution DNA methylomes have been accomplished for both Arabidopsis and human cells which have high genome methylation levels by Illumina ultra-high-throughput bisulfite sequencing technology (MethylC-Seq). Here by combining MethylC-Seq and biological replicate strategies we generated single-base resolution methylome for the silkworm which has low genome methylation levels like other insects. Our conservative estimation showed that methylcytosines (mCs) accout for about 0.11% of genomic cytosines, exclusively in CG context. The CG methylation is significantly enriched in gene bodies and positively correlated with gene expression levels, suggesting its positive role in gene transcription in silkworms. However, the well-documented functions of methylation on promoters and rDNAs in plants and mammals do not seem to have effects in insects. Methylated genes are enriched in functions involved in cellular metabolism and biosynthesis. Small RNA (smRNA) loci are also significantly enriched in gene bodies, and moreover, the smRNA loci and the predicted target sites of microRNA have high level of CG methylation, indicating functional involvement of smRNAs in the genic methylation This first methylome for silkworms provides a foundation for further studies on the epigenetic gene regulation of silkworms’ or even insects’ gene methylation.

overall_design: Each silk gland of 5th instar larvae of two individuals (called Biological Replicate 1 and 2, respectively) of the silkworm (Bombyx mori) strain Dazao was ground into powder in liquid nitrogen. Half of the powder from each silk gland was used to extract total DNAs using DNeasy Blood & Tissue Kit (Qiagen) and another half was used to extract total RNAs using RNeasy Mini Kit (Qiagen). We sequenced bisulfite-treated total DNA extracted from the silk glands of the two individuals, using Illumina Ultra-High-Throughput Sequencing, generating the Single-Base Resolution Methylomes. To reveal functional consequences of gene body methylation, we generated expression profiles for the two individuals’ silk glands using Digital Gene Expression tag profiling (DGE) technology, which combines classic SAGE (Serial Analysis of Gene Expression) and Illumina ultra-high-throughput sequencing technology.

first: Jingde

last: Zhu

first: Quan

last: Chen

first: Fangyin

last: Dai

first: Xin

last: Li

first: Muwang

first: Hongyu

last: Zhang

first: Guojie

first: Dong

first: Yang

last: Dong

first: Li

last: Zhao

first: Yin

last: Lin

first: Daojun

last: Cheng

first: Jian

last: Yu

first: Jingfeng

last: Sun

first: Xiaoyu

last: Zhou

first: Kelong

last: Ma

first: Yinghua

last: He

first: Yangxing

first: Shicheng

last: Guo

first: Mingzhi

last: Ye

first: Guangwu

first: Yingrui

first: Xiuqing

first: Lijia

first: Karsten

last: Kristiansen

first: Qiuhong

first: Jianhao

last: Jiang

first: Stephan

last: Beck

first: Qingyong

last: Xia

first: Wen

last: Wang

first: Jun


title: Next generation sequencing of human brain tissues transcriptome

city: Stanford

first: Kin Fai

last: Au

address: 390 Serra Mall, Stanford University

department: Statistics

institute: Stanford University

summary: Apply the Illumina next generaton sequencing technology to obtain 22 millions of 50-bp paired-end reads

overall_design: High-throughput RNA-seq in human brain tissues. Mapping results on human genome (hg18) by SeqMap.

first: Shujun

last: Luo

first: Gary

last: Schroth


title: Genome-wide Differential DNA Methylation in the Wild and Domestic Chicken

status: Public on Apr 02 2010

city: beijing

first: qinghe

last: li

address: no2, yuanmingyuan west road

institute: China Agricultural university


title: DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing

city: Mainz

first: John

last: Castle

address: Langenbeckstr. 1

department: Genomics

institute: Institute for Translational Oncology and Immunology

type: Genome variation profiling by high throughput sequencing

summary: DNA copy number variations occur within populations and aberrations can cause disease.  We sought to develop an improved lab-automatable, cost-efficient, accurate platform to profile DNA copy number. We developed a sequencing-based assay of nuclear, mitochondrial, and telomeric DNA copy number that draws on the unbiased nature of next-generation sequencing and incorporates techniques developed for RNA expression profiling.  To demonstrate this platform, we assayed UMC-11 cells using 5 million 33 nt reads and found tremendous copy number variation, including regions of single and homogeneous deletions and amplifications to 29 copies; 5 times more mitochondria and 4 times less telomeric sequence than a pool of non-diseased, blood-derived DNA; and that UMC-11 was derived from a male individual. The described assay outputs absolute copy number, outputs an error estimate (p-value), and is more accurate than array-based platforms at high copy number.  The platform enables profiling of mitochondrial levels and telomeric length.  The assay is lab-automatable and has a genomic resolution and cost that are tunable based on the number of sequence reads.

overall_design: DNA genome sequencing at roughly 0.03 coverage to identify genomic copy number variations

first: Ronghua

last: Chen


title: Examination of whole genome gene expression profiles of two chicken breeds

summary: We report the genome-wide DNA methylation mapping of chicken by methylated DNA immunoprecipitation following by highthroughput sequencing, and the gene expression profile of chicken by RNA-seq. For meDIP-seq, about 17,202,074 to 27,501,760 reads were generated for the tissue and liver tissues of the red jungle fowl and the avian broiler each.  We found that compared with the red jungle fowl, DNA methylation in muscle tissue of the avian broiler, showed dramatically decline on a genome-wide scale. Furthermore, the length of the highly methylated regions (HMRs) has become shorter in the avian broiler, which has suffered intense artificial selection. In addition to the global changes in DNA methylation, transcriptome-wide analysis of the two breeds of chicken revealed that the patterns of gene expression in the domestic chicken have undergone a specific bias towards a pattern that is more suited to human-made environments with variable expression in certain gene functions, such as immune response and fatty acid metabolism. Our results demonstrated a potential role of epigenetic modification in animal domestication besides the genetic variations.

overall_design: Examination of whole genome gene expression profiles in liver and muscle tissues of two chicken breeds.

first: Qinghe

last: Li

first: Ning


title: Natural selection on cis and trans regulation in yeasts

city: Taichung

first: Li-Ching

last: Hsieh

address: 145 Xingda Rd.

department: Graduate Institute of Genomics and Bioinformatics

country: Taiwan

institute: National Chung Hsing University

summary: Gene expression is regulated both by cis elements, which are DNA segments closely linked to the genes they regulate, and by trans activating factors, which are usually proteins capable of diffusing to unlinked genes. Understanding the patterns and sources of regulatory variation is crucial for understanding phenotypic and genome evolution. Here, we investigate the global patterns of gene expression evolution in Saccharomyces cerivisiae. We report statistical methods useful in quantifying cis and trans regulation using next generation sequencing data. Using these methods,  measured genome-wide allele-specific expression by deep sequencing to investigate the genetic architecture of gene regulatory variation between two strains of Saccharomyces cerevisiae. We find that expression polymorphism in yeast is common for both cis and trans regulation, though trans variation is more common. Our detailed analyses of the effects of functional constraint on expression variation as indicated by measures such as protein connectivity, gene essentiality, and the ratio of nonsynonymous substitutions to synonymous substitutions clearly reveal that both classes of variation are under purifying selection, but trans variation is more sensitive to selective constraint. Comparing interspecific expression divergence between S. cerevisiae and S. paradoxus to our intraspecific variation suggests that natural selection strongly influences the patterns of variation we observe. Further analyses revealed that cis divergence is more frequently mediated by positive Darwinian selection than trans divergence, which is compatible with neutral evolution.

overall_design: Study the gene expression patterns in two strains of yeast (BY and RM)

first: Wen-Hsiung

first: James

last: Emerson

first: Huang-Mo

last: Sung

first: Tzi-Yuan

first: Chih-Jen

last: Huang

first: Henry

last: Lu

first: Mei-Yeh

first: Shu-Hsing

last: Wu


title: Comparison of small RNA levels in Dicer helicase mutants

status: Public on Apr 01 2010

city: Salt Lake City

first: Noah

last: Welker

state: UT

address: 15 N Medical Drive E. Rm. 4800

department: Biochemistry

institute: University of Utah

summary: Years after the discovery that Dicer is a key enzyme in gene-silencing, the role of its helicase domain remains enigmatic. Here we show that this domain is critical for accumulation of certain endogenous small interfering RNAs (endo-siRNAs) in C. elegans. The domain is required for the production of the direct products of Dicer, or primary endo-siRNAs, and consequently, affects levels of downstream intermediates, the secondary endo-siRNAs. Consistent with the role of endo-siRNAs in silencing, their loss correlates with an increase in cognate mRNA levels. We find that the helicase domain of Dicer is not required for microRNA (miRNA) processing, or RNA interference following exposure to exogenous double-stranded RNA. Comparisons of wildtype and helicase-defective strains using deep-sequencing analyses show that the helicase domain is required by a subset of annotated endo-siRNAs, in particular, those associated with the slightly longer 26 nucleotide small RNA species containing a 5’ guanosine.

overall_design: We reintroduced either wildtype Dicer, or Dicer harboring a mutation (K39A) in it's helicase domain, into dcr-1(ok247) mutant worms via transgene rescue. We then used high-throughput sequencing to compare levels of small RNAs present in each of these strains.

first: Derek

last: Pavelec

first: David

last: Nix

first: Thomas

middle: F

last: Duchaine

first: Scott

last: Kennedy

first: Brenda

last: Bass


title: Examination of whole genome DNA methylation status of two chicken breeds

first: qinghe

overall_design: Examination of whole genome DNA methylation status in liver and muscle of two chicken breeds.

first: Qinghe


title: Promoter proximal pausing and its regulation by c-Myc in embryonic stem cells: ChIP-Seq

city: Cambridge

first: Charles

last: Lin

address: 9 Cambridge Center

institute: Massachusetts Institute of Technology

summary: Recruitment of the RNA Polymerase II (Pol II) transcription initiation apparatus to promoters by specific DNA binding transcription factors is well recognized as a key regulatory step in gene expression.  We describe here evidence that promoter-proximal pausing is a general feature of transcription by Pol II in embryonic stem (ES) cells, and thus an additional step where regulation of gene expression may occur.  We report here that c-Myc, which occupies a third of actively transcribed genes in ES cells and is a key regulator of cellular proliferation, binds P-TEFb and contributes to release of promoter-proximal paused Pol II at these genes.

overall_design: ChIP-seq data for Pol II and additional factors controlling pause release in mouse ES cells.

first: Peter

last: Rahl

first: Amy

last: Seila

first: Ryan

middle: A

last: Flynn

last: McCuine

first: Christopher

last: Burge

first: Philip

last: Sharp

first: Richard

last: Young


title: Deep sequencing of small RNAs in the trasngenic wild type plant and the IWR1-type transcription factor mutant, dms4

status: Public on Mar 31 2010

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary:
Full title: Deep sequencing of small RNAs in the trasngenic wild type plant (contains trigger and silencer transgenes) and the IWR1-type transcription factor mutant, dms4

RNA-directed DNA methylation (RdDM) in plants requires two RNA polymerase II (PolII)-related RNA polymerases named PolIV and PolV. A genetic screen designed to reveal factors important for RdDM in a developmental context in Arabidopsis identified DEFECTIVE IN MERISTEM SILENCING 4 (DMS4). Unlike other mutants defective in RdDM, dms4 mutants have a pleiotropic developmental phenotype.DMS4 is similar to yeast IWR1, a conserved putative transcription factor that interacts with PolII subunits. In the transgenic system studied, mutations in DMS4 directly or indirectly affect PolIV-dependent secondary siRNAs, PolV-mediated RdDM, PolV-dependent synthesis of intergenic noncoding RNA, and expression of many PolII-driven genes. These data suggest that DMS4 may be a regulatory factor for multiple RNA polymerases, thus explaining its diverse roles in the plant.

overall_design: Examination of siRNA abundance in the trasngenic wild type plant (contains trigger and silencer transgenes) and the dms4 mutant.

first: Lucia

last: Daxinger

first: Marjori

last: Matzke

first: Stacey

last: Simon


title: mRNA-Seq of head tissue from Drosophila melanogaster

city: Bethesda

first: Brian

last: Oliver

department: LBG

summary:
We sequenced mRNA from head tissue of females and male of Drosophila melanogaster to identify genes differentially expressed between the sexes and sex-specific alternative splicing events.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: Comparison of expresssion profiles in female and male head tissue from D. melanogaster

first: John

last: Malone


title: Genome-wide assessment of differential roles for p300 and CBP in transcription regulation

status: Public on Mar 30 2010

city: Leiden

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

institute: Leiden University Medical Center

summary: Through ChIP-Seq analysis with the Illumina Whole Genome Analyzer, we identify binding sites for P300 (EP300) and CBP (CREBBP) in Human glioblastoma T98G cells that were cell cycle synchronized before and after stimulation. In our analysis, we focused on the identification of genes differentially bound by P300 and CBP.

overall_design: ChIP-seq with P300 and CBP antibodies over 2 timepoints

first: Matthew

last: Hestand

first: Yolande

last: Ramos


title: Human variation in PolII and NF-KappaB binding (RNA-seq study with TNF-alpha induced)

status: Public on Mar 22 2010

city: New Haven

first: Flora

last: Vaccarino

state: CT

address: 230 South Frontage Road

department: Child Study Center

institute: Yale University

summary: We examined genome-wide variation in transcription factor binding in different individuals and a chimpanzee using chromatin immunoprecipitation followed by massively-parallel sequencing (ChIP-Seq). The binding sites of RNA Polymerase II (Pol II) as well as a key regulator of immune responses, NFkB, were mapped in ten HapMap lymphoblastoid cell lines derived from individuals of African, European, and Asian ancestry, including a parent-offspring trio. We also mapped gene expression in all ten human cell lines for two treatment conditions: a) no treatment and b) following induction by TNF-alpha.

overall_design: Genome-wide comparison of Pol II and NF-KappaB binding in ten individuals. RNA-seq study with TNF-alpha treatment.

first: Maya

last: Kasowski

first: Fabian

last: Grubert

last: Heffelfinger

first: Manoj

last: Hariharan

first: Akwasi

last: Asabere

first: Sebastian

middle: M

last: Waszak

first: Lukas

last: Habegger

first: Joel

last: Rozowsky

first: Minyi

last: Shi

first: Alexander

last: Urban

first: Mi-Young

last: Hong

first: Sherman

last: Weissman

first: Mark

last: Gerstein

first: Jan

middle: O

last: Korbel

first: Michael

last: Snyder


title: Metagenomic, metatranscriptomic and metaproteomic study of enrichment culture of M. oxyfera (denitrifying methanotroph)

status: Public on Mar 25 2010

city: Bremen

first: Marc

last: Strous

address: Celciusstrasse 1

department: Microbial Fitness Group

institute: MPI Bremen

summary: DNA, RNA and protein were extracted from the culture and subjected to massive parallel sequencing and nano-LC-MS-MS respectively

overall_design: Combination of these methods enabled the reconstruction of the complete genome sequence of M oxyfera from the metagenome and identification of the functionally relevant enzymes and genes

first: Kees-Jan

last: Francois

first: Henk

last: Stunnenberg


title: small RNA sequencing of two developmental stages of Ciona intestinalis

status: Public on Mar 27 2010

city: Corvallis

first: David

middle: Anthony

last: Hendrix

state: OR

address: 2011 Ag & Life Sciences Bldg

department: Biochemistry and Biophysics/EECS

institute: Oregon State University

summary: We report the comprehensive sequencing of small RNA libraries created from different developmental stages (larva and gastrula) of the basal chordate, Ciona intestinalis. These libraries were used for the identification of microRNAs in this organism.

overall_design: Sequencing of small RNA libraries from 2 stages of Ciona intestinalis.

first: Weiyang

last: Levine


title: Metatranscriptomic analysis of an anaerobic ammonium oxidizing community dominated by Kuenenia stuttgartiensis

summary: We compiled a metatranscriptome by extracting total RNA (including ribosomes), reverse transcription and solexa sequencing. We obtained quantitative data on the transcription of each orf to assess the importance of each orf to the metabolism of Kuenenia stuttgartiensis

overall_design: The transcriptomic data are combined with proteomic data and physiological/biochemical experiments

last: Stunneberg

first: Kees

last: Francoijs

first: Eva

last: Janssen-Megens


title: Characterization of the melanoma miRNAome by deep sequencing

city: Brisbane

first: Mitchell

last: Stark

address: 300 Herston Rd Herston

institute: QIMR

summary: MicroRNAs are 18-23 nucleotide non-coding RNAs that regulate gene expression in a sequence specific manner. Little is known about the repertoire and function of miRNAs in melanoma or the melanocytic lineage. We therefore undertook a comprehensive analysis of the miRNAome in a diverse range of pigment cells including: melanoblasts, melanocytes, congenital nevocytes, acral, mucosal, cutaneous and uveal melanoma cells. We sequenced 12 small RNA libraries using Illumina's GAII platform. This massively parallel sequencing approach revealed a total of 539 known mature and mature-star sequences, along with the prediction of 389 novel miRNA candidates. Using the relative proportion of the total unique read counts against total number of reads, hierarchal clustering of all novel candidates plus known miRNAs gave good separation of the different histological subtypes. Some of the novel miRNAs may be specific to the melanocytic lineage and as such could be used as biomarkers to assist in the early detection of distant metastasises by measuring the circulating levels in blood. Follow up studies of the functional roles of these pigment cell miRNAs and the identification of their targets should shed further light on their role in the development and progression of melanoma.

overall_design: Illumina GAII deep sequencing of 12 melanoma and pigment cell lines

first: Nicholas

middle: K

last: Hayward


title: Human variation in PolII and NF-KappaB binding (RNA-seq study uninduced by TNF-alpha)

first: Flora

last: Vaccarino

overall_design: Genome-wide comparison of Pol II and NF-KappaB binding in ten individuals. RNA-seq study with no treatment.

first: Maya

last: Kasowski

first: Fabian

last: Grubert

first: Christopher

last: Heffelfinger

first: Manoj

last: Hariharan

first: Akwasi

last: Asabere

first: Sebastian

last: Waszak

first: Lukas

last: Habegger

first: Joel

last: Rozowsky

last: Shi


title: Human variation in PolII and NF-KappaB binding (ChIP-seq study with NF-KappaB)

overall_design: Genome-wide comparison of Pol II and NF-KappaB binding in ten individuals. ChIP-seq with NF-KappaB.

first: Minyi

first: Alexander

last: Urban

first: Mi-Young

last: Hong

first: Sherman

last: Weissman

first: Mark

last: Gerstein

first: Jan

last: Korbel

first: Michael

last: Snyder


title: MCM KC-167 ChIP-Seq experiment

status: Public on Mar 16 2010

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_2783
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes.  These experiments will be conducted in multiple cell types and developmental tissues.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: CHIP-seq

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female;  EXPERIMENTAL FACTORS: Antibody Pan MCM2-7 Antibody

first: David

last: MacAlpine

first: Heather

first: Matthew

last: Eaton

first: Joseph

last: Prinz


title: Human variation in PolII and NF-KappaB binding

first: Flora

last: Vaccarino

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

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: Refer to individual Series


title: ORC2 KC-167 ChIP-Seq experiment

summary:
modENCODE_submission_2755
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes.  These experiments will be conducted in multiple cell types and developmental tissues.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: CHIP-seq

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female;  EXPERIMENTAL FACTORS: Antibody dORC2


title: ORC2 ML-DmBG3-c2 ChIP-Seq experiment

summary:
modENCODE_submission_2754
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes.  These experiments will be conducted in multiple cell types and developmental tissues.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: CHIP-seq

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: ML-DmBG3-c2; Tissue: CNS-derived cell-line; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Unknown;  EXPERIMENTAL FACTORS: Antibody dORC2


title: DNA Methylation Mediated by a MicroRNA Pathway

status: Public on Mar 12 2010

city: Beijing

first: Yijun

last: Qi

address: No.7 Science Park Road,Zhongguancun Life Science Park

institute: National Institute of Biological Sciences, Beijing

summary: In plants, the known microRNAs (miRNAs) are produced as ~21 nucleotide (nt) duplexes from their precursors by Dicer like 1 (DCL1). They are incorporated into Argonaute 1 (AGO1) protein to regulate target gene expression primarily through mRNA cleavage. We report here the discovery of a new class of miRNAs in the model monocot rice (Oryza sativa). These are 24 nt in length and require another member of the Dicer family, DCL3, for their biogenesis. The 24 nt long miRNAs (lmiRNAs) are loaded into AGO4 clade proteins according to hierarchical rules, depending on the upstream biogenesis machinery and the 5’ terminal nucleotide.  We demonstrated that lmiRNAs direct DNA methylation at loci from which they are produced as well as in trans at their target genes and play roles in gene regulation. Considered together, our findings define a novel miRNA pathway that mediates DNA methylation.

overall_design: Small RNAs were prepared from Rice total extract in wide type, dcl1, dcl3, rdr2 dbsRNA mutant and AGO4a, AGO4b, and AGO16 complexes, ligated to a 3' adaptor and a 5' acceptor sequentially, and then RT-PCR amplified. PCR products were reamplified using a pair of solexa cloning primers and then provided for sequencing. For technical details, see Wu, L., Zhang, Q., Zhou, H.,  Ni, F., Wu, X., and Qi, Y. (2009). Rice microRNA effector complexes and targets. The Plant Cell, 21: 3421-3435.

first: Liang

last: Wu

first: Huanyu

last: Zhou

first: Qingqing

last: Zhang


title: Promoter proximal pausing and its regulation by c-Myc in embryonic stem cells

first: Charles

last: Lin

state: MA

department: Biology

type: Genome binding/occupancy profiling by genome tiling array

first: Peter

last: Rahl

first: Amy

middle: C

last: Seila

first: Ryan

last: Flynn

first: Scott

last: McCuine

first: Christopher

last: Burge

first: Philip

last: Sharp

first: Richard

last: Young


title: BRD7 is a candidate tumour suppressor gene required for p53 function

status: Public on Mar 14 2010

city: Amsterdam

first: Jarno

last: Drost

address: Plesmanlaan 121

department: Gene Regulation

institute: The Netherlands Cancer Institute

summary: Oncogene-induced senescence (OIS) is a p53-dependent defence mechanism against uncontrolled proliferation. Consequently, many human tumours harbour p53 mutations while others show a dysfunctional p53 pathway, frequently by unknown mechanisms. We identified BRD7, a bromodomain-containing protein whose inhibition allows full neoplastic transformation in the presence of wild-type p53. Intriguingly, in human breast tumours harbouring wild-type, but not mutant p53, the BRD7 gene locus was frequently deleted and low BRD7 expression was found in a subgroup of tumours. Functionally, BRD7 is required for efficient p53-mediated transcription of a subset of target genes. BRD7 interacts with p53 and p300, and is recruited to target gene promoters, affecting histone acetylation, p53 acetylation, and promoter activity. Thus, BRD7 suppresses tumourigenicity by serving as a p53 cofactor required for efficient induction of p53-dependent OIS.

overall_design: We recorded mRNA expression profiles of BJ primary fibroblasts expressing the oncogene RasV12 and either control vector, one of two BRD7 knockdown vectors, or p53 knockdown vector. In addition, we profiled genome-wide protein DNA interactions for p53 and BRD7 using ChIP-Seq. p53- and BRD7-binding sites were recorded in RasV12-expressing BJ cells; as a control we used knockdown of the gene of interest (BRD7 or p53).

first: Fiamma

last: Mantovani

first: Francesca

last: Tocco


title: Complex patterns of accessibility discriminate sites of PcG repression, H4K16 acetylation and replication initiation

city: Vienna

first: Michaela

last: Schwaiger

address: Althanstr. 14

country: Austria

institute: University of Vienna

type: Methylation profiling by genome tiling array

summary:
Full title: Complex patterns of genome accessibility discriminate sites of PcG repression, H4K16 acetylation and replication initiation

Histone modifications have been proposed to regulate gene expression in part by modulating DNA accessibility and higher-order chromatin structure. However, there is limited direct evidence to support structural differences between euchromatic and heterochromatic fibers in the nucleus. To ask how histone modifications relate to chromatin compaction, we measured DNA accessibility throughout the genome by combining M.SssI methylase footprinting with methylated DNA immunoprecipitation (MeDIP-footprint). In the Drosophila genome, we find that accessibility to DNA methylase is variable in a manner that relates to the differential distribution of active and repressive histone modifications. Active promoters are highly permissive to M.SssI activity, yet inactive chromosomal domains decorated with H3 lysine 27 trimethylation are least accessible providing in vivo evidence for Polycomb-mediated chromatin compaction. Conversely, DNA accessibility is increased at active chromosomal regions marked with H4 lysine 16 acetylation and at the dosage-compensated male X chromosome suggesting that Drosophila transcriptional dosage compensation is facilitated by more permissive chromatin structure. Interestingly early replicating chromosomal regions and sites of replication initiation show also higher accessibility linking temporal and spatial control of genome duplication to the structural organization of chromatin. In conclusion, using a novel protocol we generated a comprehensive view of DNA accessibility and uncover different levels of chromatin organization, which are delineated by distinct patterns of posttranslational histone modifications and replication.

Keywords: cell type comparison, ChIP-chip, MeDIP-footprint, RNA-seq, ChIP-seq

overall_design:
MeDIP-footprint and ChIP-chip: ChIP-chip was performed for H3K4me3, H3K36me2, H3K36me3, H3K27me3, and H3K9me2 in Kc cells. We measured DNA accessibility throughout the genome by combining M.SssI methylase footprinting with methylated DNA immunoprecipitation (MeDIP-footprint) in Kc and S2 cells.

RNA-seq: cDNA from RNA from Drosophila Kc cells was sequenced using Illumina deep sequencing. Reads were mapped and the abundance of all transcripts was determined.

ChIP-seq: PSC ChIP from Drosophila Kc cells was sequenced using Illumina deep sequencing in three lanes. Reads were mapped and the binding profile of PSC was determined.

first: Oliver

last: Bell

first: Edward

last: Oakeley

first: Florian

last: Lienert

first: Christian

last: Beisel

first: Michael

last: Stadler

first: Dirk

last: Schübeler


title: Individual-specific and allele-specific chromatin signatures in diverse human populations

status: Public on Mar 15 2010

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary:
This dataset contains DNase-seq data and CTCF ChIP-seq data for 6 lymphoblastoid cell lines. There are 3 cell lines from a YRI trio and 3 lines from a CEU trio (HapMap GM19238, GM19239, GM 19240, GM12891, GM12892, GM12878).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022  and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: DNase-seq and ChIP-seq data from each of the 6 cell lines.

first: V

middle: R

first: G

last: Crawford


title: Molecular Basis of Infrared Detection by Snakes

city: Berkeley

first: Nicholas

middle: T

last: Ingolia

email: ingolia@berkeley.edu, nick@ingolia.org

state: CA

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: Snakes possess a unique sensory system for detecting infrared radiation, enabling them to generate a ‘thermal image’ of predators or prey. Infrared signals are initially received by the pit organ, a highly specialized facial structure that is innervated by nerve fibers of the somatosensory system. How this organ detects and transduces infrared signals into nerve impulses is not known. Here we use an unbiased transcriptional profiling approach to identify TRPA1 as the infrared receptor on sensory neurons that innervate the pit organ. TRPA1 from pit bearing snakes (rattlesnakes and pythons) are the most heat sensitive vertebrate ion channels thus far identified, consistent with their role as primary transducers of infrared stimuli in these animals. Thus, snakes detect infrared signals through a mechanism involving radiant heating of the pit organ, rather than photochemical transduction. These findings illustrate the broad evolutionary tuning of TRP channels as thermosensors in the vertebrate nervous system.

sample_organism:
Crotalus atrox
Python regius
Pantherophis obsoletus lindheimeri
Masticophis flagellum testaceus
Corallus hortulana

overall_design: Gene expression measurements implicate TRPA1 as the heat-sensitive channel in diverse pit snakes

first: Elena

last: Gracheva

first: Yvonne

last: Kelly

first: Julio

last: Cordero- Morales

first: Gunther

last: Hollopeter

first: Alexander

last: Chesler

first: Elda

last: Sánchez

first: John

last: Perez

first: Jonathan

last: Weissman

first: David

last: Julius


title: ORC precisely positions nucleosomes at origins of replication

status: Public on Mar 19 2010

city: Durham

first: Matthew

middle: Lucas

last: Eaton

state: NC

address: LSRC Room C315, Research Dr

department: Pharmacology & Cancer Biology

institute: Duke University

summary: The budding yeast genome is marked by 250-350 origins of DNA replication. These origins are bound by the origin recognition complex (ORC) throughout the cell cycle. ORC has known DNA binding sequence preferences which, though necessary for binding, are not sufficient to fully specify a genomic locus as being bound by ORC, indicating that the cell must use additional chromosomal cues to specify ORC binding sites and origins of replication. Using high-throughput sequencing to precisely locate both ORC binding sites and nucleosome locations genome-wide, we find that a nucleosome depleted region (NDR) and precisely positioned nucleosomes are a ubiquitous feature of yeast replication origins. The ARS consensus sequence (ACS) and adjacent sequences are sufficient to maintain the nucleosome-free properties of the NDR.  We use a temperature sensitive ORC1 mutant to demonstrate that ORC is required to maintain precisely positioned nucleosomes at origins of replication. These findings demonstrate the importance of local nucleosome positioning at replication origins, and that chromatin organization is an important determinant of origin selection.

overall_design: Examination of nucleosome positioning in wild-type and orc1-161ts mutant S. cerevisiae at room temperature and heatshock temperatures. Examination of ORC binding locations by ChIP-seq. All reported coordinates are based on the SGD genome build released 12/16/2005.

first: Kyriaki

last: Galani

first: Sukhyun

last: Kang

first: Stephen

middle: P

last: Bell

last: MacAlpine


title: Genome-wide maps of H3K4me2/3 in prostate cancer cell line LNCaP

status: Public on Mar 09 2010

first: Housheng

middle: Hansen

last: He

address: 101 College Street, PMCRT 11-305

department: Medical Biophysics

institute: UNIVERSITY HEALTH NETWORK

summary: We report the high-throughput profiling of histone modifications in prostate cancer cells. By obtaining over 1 billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of prostate cancer cells. we found androgen treatment dismisses a nucleosome over AR binding sites that are flanked by a pair of H3K4me2 marked nucleosomes. A novel quantitative model built on the behavior of such nucleosome pairs correctly identified regions bound by the regulators of the immediate androgen response including AR and FoxA1. More importantly this model also correctly predicted novel binding sites for other transcription factors present following prolonged androgen stimulation including Oct1 and NKX3.1. Thus quantitative modeling of enhancer structure provides a powerful predictive method to infer the identity of transcription factors involved in cellular responses to specific stimuli.

overall_design: Examination of 2 different histone modifications in prostate cancer cells with and without androgen (dihydrotestosterone, DHT) treatment.

middle: H

first: Cliff

last: Meyer

first: Myles

last: Brown

first: Xiaole

last: Liu


title: Genome-wide mapping of H3K4me3 and of PHF8 and ZNF711 binding sites in SH-SY5Y cells

status: Public on Mar 08 2010

city: Copenhagen

first: Daniela

last: Kleine-Kohlbrecher

address: Ole Maaløes vej 5

department: University of Copenhagen

country: Denmark

institute: BRIC

summary: We analyzed the genome wide binding sites for the potential XLMR genes PHF8 and ZNF711 in  the neuroblastoma cell line SH-SY5Y using antibodies specific for PHF8 and ZNF711 and correlated this with binding pattern of H3K4me3.  The total number of peaks detected for PHF8 based on 9.8 million sequence reads, 9.6 million sequence reads for ZNF711 and 9.1 million sequence reads for H3K4me3 after IgG normalization were 17075, 1875 and 19534, respectively. Annotation of the peaks to genes using the hg18 genome database revealed 10039 genes positive for H3K4me3, 7682 were bound by PHF8 and 1103 genes were bound by ZNF711 within +/-1000bp from TSS. As former genome wide analysis of H3K4me3 revealed is this histone mark preferentially associated with transcription start sites. The analysis revealed that 82% of H3K4me3 positive genes are also positive for PHF8. In general, PHF8 either co-localizes or partly overlaps with regions positive for H3K4me3 and covers the putative TSS of the target genes.

overall_design: Examination of two different proteins and one histone modification in a human neuroblastoma cell line

first: Jesper

last: Christensen

first: Mads

last: Bak

first: Kristian

last: Helin


title: Neuronal MeCP2 is expressed at near histone-octamer levels and globally alters the chromatin state

status: Public on Mar 04 2010

city: Edinburgh

first: Adrian

last: Bird

state: Midlothian

address: Mayfield Road

department: WTCCB

institute: The University of Edinburgh

summary: We report the application of single molecule-based sequencing technology for high-throughput genom-wide mapping of MeCP2 binding and DNA methylation in mouse brain and cerebellum respectively. We find a good correlation between MeCP2 occupancy and methyl-CpG density and depletion of MeCP2 binding at CpG Islands, the majority of which are constitutively hypomethylated. This study provides a comprehensive characterisation of the genome wide distribution of MeCP2.

overall_design: Examination of MeCP2 occupancy in mouse brain and the distribution of methylation in mouse cerebellum.

first: Pete

middle: J

last: Skene

first: Robert

middle: S

last: Illingworth

first: Shaun

last: Webb

first: Alastair

last: Kerr

first: Keith

middle: D

last: James

first: Daniel

last: Turner

first: Rob

last: Andrews


title: ORC2 S2-DSRC ChIP-Seq experiment

first: DCC

last: modENCODE

summary:
modENCODE_submission_2753
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes.  These experiments will be conducted in multiple cell types and developmental tissues.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: CHIP-seq

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  EXPERIMENTAL FACTORS: Antibody dORC2

first: David

last: MacAlpine

first: Heather

first: Matthew

last: Eaton

first: Joseph

last: Prinz


first: Lukas

last: Habegger

address: 266 Whitney Ave

summary:
Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short long, and paired-end sequencing
In order to examine the fundamental mechanisms governing neural differentiation, we analyzed the transcriptome changes that occur during the differentiation of human embryonic stem cells (hESCs) into the neural lineage. Undifferentiated hESCs as well as cells at three stages of early neural differentiation, N1 (early initiation), N2 (neural progenitor), and N3 (early glial-like) were analyzed using a combination of single read, paired-end read, and long read RNA sequencing. The results revealed enormous complexity in gene transcription and splicing dynamics during neural cell differentiation. We found previously unannotated transcripts and spliced isoforms specific for each stage of differentiation. Interestingly, splicing isoform diversity is highest in undifferentiated hESCs and decreases upon differentiation, a phenomenon we call “isoform specialization.” During neural differentiation, we observed differential expression of many types of genes including those involved in key signaling pathways, and a large number of extracellular receptors exhibit stage-specific regulation. These results provide a valuable resource for studying neural differentiation and reveal insights into the mechanisms underlying in vitro neural differentiation of hESCs, such as neural fate specification, NPC identity maintenance and the transition from a predominantly neuronal state into one with increased gliogenic potential

overall_design:
Characterization of changes in the transcriptome profiles during early stages of human neural differentiation from H1 !Series_overall_design=hESCs.

454 SFF files are missing.

hESC_B_s9.fastq--> SRR037192
hESC_B_s8.fastq--> SRR037191
hESC_B_s7.fastq--> SRR037190
hESC_B_s6.fastq--> SRR037189
hESC_B_s5.fastq--> SRR037188
hESC_B_s4.fastq--> SRR037187
hESC_B_s3.fastq--> SRR037186
hESC_B_s2.fastq--> SRR037185
hESC_B_s16.fastq--> SRR037184
hESC_B_s15.fastq--> SRR037183
hESC_B_s14.fastq--> SRR037182
hESC_B_s13.fastq--> SRR037181
hESC_B_s12.fastq--> SRR037180
hESC_B_s11.fastq--> SRR037179
hESC_B_s10.fastq--> SRR037178
hESC_B_s1.fastq--> SRR037177
hESC_B_p6_2.fastq--> SRR037176
hESC_B_p6_1.fastq--> SRR037176
hESC_B_p5_2.fastq--> SRR037175
hESC_B_p5_1.fastq--> SRR037175
hESC_B_p4_2.fastq--> SRR037174
hESC_B_p4_1.fastq--> SRR037174
hESC_B_p3_2.fastq--> SRR037173
hESC_B_p3_1.fastq--> SRR037173
hESC_B_p2_2.fastq--> SRR037172
hESC_B_p2_1.fastq--> SRR037172
hESC_B_p1_2.fastq--> SRR037171
hESC_B_p1_1.fastq--> SRR037171
hESC_A_s3.fastq--> SRR037170
hESC_A_s2.fastq--> SRR037169
hESC_A_s1.fastq--> SRR037168
hESC_A_p3_2.fastq--> SRR037167
hESC_A_p3_1.fastq--> SRR037167
hESC_A_p2_2.fastq--> SRR037166
hESC_A_p2_1.fastq--> SRR037166
hESC_A_p1_2.fastq--> SRR037165
hESC_A_p1_1.fastq--> SRR037165
N3_A_s4.fastq--> SRR037226
N3_A_s3.fastq--> SRR037225
N3_A_s2.fastq--> SRR037224
N3_A_s1.fastq--> SRR037223
N3_A_p3_2.fastq--> SRR037222
N3_A_p3_1.fastq--> SRR037222
N3_A_p2_2.fastq--> SRR037221
N3_A_p2_1.fastq--> SRR037221
N3_A_p1_2.fastq--> SRR037220
N3_A_p1_1.fastq--> SRR037220
N2_B_s8.fastq--> SRR037219
N2_B_s7.fastq--> SRR037218
N2_B_s6.fastq--> SRR037217
N2_B_s5.fastq--> SRR037216
N2_B_s4.fastq--> SRR037215
N2_B_s3.fastq--> SRR037214
N2_B_s2.fastq--> SRR037213
N2_B_s1.fastq--> SRR037212
N2_B_p6_2.fastq--> SRR037211
N2_B_p6_1.fastq--> SRR037211
N2_B_p5_2.fastq--> SRR037210
N2_B_p5_1.fastq--> SRR037210
N2_B_p4_2.fastq--> SRR037209
N2_B_p4_1.fastq--> SRR037209
N2_B_p3_2.fastq--> SRR037208
N2_B_p3_1.fastq--> SRR037208
N2_B_p2_2.fastq--> SRR037207
N2_B_p2_1.fastq--> SRR037207
N2_B_p1_2.fastq--> SRR037206
N2_B_p1_1.fastq--> SRR037206
N2_A_s4.fastq--> SRR037205
N2_A_s3.fastq--> SRR037204
N2_A_s2.fastq--> SRR037203
N2_A_s1.fastq--> SRR037202
N2_A_p3_2.fastq--> SRR037201
N2_A_p3_1.fastq--> SRR037201
N2_A_p2_2.fastq--> SRR037200
N2_A_p2_1.fastq--> SRR037200
N2_A_p1_2.fastq--> SRR037199
N2_A_p1_1.fastq--> SRR037199
N1_A_s3.fastq--> SRR037198
N1_A_s2.fastq--> SRR037197
N1_A_s1.fastq--> SRR037196
N1_A_p3_2.fastq--> SRR037195
N1_A_p3_1.fastq--> SRR037195
N1_A_p2_2.fastq--> SRR037194
N1_A_p2_1.fastq--> SRR037194
N1_A_p1_2.fastq--> SRR037193
N1_A_p1_1.fastq--> SRR037193

first: Jia

middle: Q

last: Wu

first: Michael

last: Snyder


title: Transcriptome conservation of the D. discoideum and D. purpureum developmental programs revealed through RNA-sequencing

city: Houston

first: Anup

last: Parikh

address: One Baylor Plaza

department: Molecular & Human Genetics

institute: Baylor College of Medicine

summary:
Cross species comparison of genomes and transcriptomes is a powerful tool for understanding underlying biological processes, accurate functional classification of genes, and discovery of novel elements. The shift to next-generation sequencing platforms has tremendously accelerated the analysis of genomes and transcriptomes. The use of this technology for transcriptome analysis has many advantages over hybridization based technologies, including higher sensitivity and specificity, and eliminates the need for probe design. Using Illumina sequencing of mRNAs, we have captured the global transcriptional profiles of the developmental cycles of D. discoideum and D. purpureum. The morphology and transcriptional profiles in these two species have been largely conserved even after greater than 300 million years of divergence. We also captured the transcriptional profiles of prespore and prestalk cells from both species. The RNA-seq results correlate well with previously known markers and reveal many new transcripts with unique developmental regulation and cell type enrichment.    Our analysis provides the first complete picture of the transcriptional landscape in both D. discoideum and D. purpureum. Transcriptional abundance of over 13,900 genome elements from seven time points of development, and prespore/prestalk cell types will be available through a graphical, highly-interactive, explorative web interface at: http://www.ailab.si/dictyexpress , which currently displays all of our published microarray data. Sequence coverage at a single nucleotide resolution will also be available through an interactive genome browser. These data, from morphology to genome to transcriptome, provide a global picture of the developmental cycles of D. discoideum and D. purpureum and will facilitate the functional classification of genes, as well as discovery of novel genes, splice variants, regulatory elements and non-coding RNAs.

Keywords: Transcriptome Analysis

sample_organism:
Dictyostelium purpureum
Dictyostelium discoideum

overall_design: Examination of 7 developmental time points in two cell types with 2 biological replicates for each sample.

first: Edward

last: Miranda

first: Mariko

last: Katoh

first: Danny

last: Fuller

first: Gregor

last: Rot

first: Lan

last: Zagar

first: Tomaz

last: Curk

first: Rui

last: Chen

first: Blaz

last: Zupan

first: William

middle: F

last: Loomis

first: Adam

last: Kuspa

first: Gad

last: Shaulsky


title: Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq

status: Public on Mar 02 2010

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

summary: The goal of the ChIP-seq study was to investigate the distribution of the TATA-binding protein (TBP) across the human genome. TBP is the DNA-binding subunit of the basal transcription factor TFIID for RNA polymerase II (pol II) and it also participates in other complexes for the other RNA polymerase. The BTAF1 ATPase forms a stable complex with TBP and regulates its activity in pol II transcription. BTAF1 is believed to mobilize TBP from promoter and non-promoter sites. To test this hypothesis, TBP ChIP samples were prepared from human HeLa cervix carcinoma cells after knock-down of BTAF1 expression and compared to HeLa cells with a control knock-down of GAPDH. GAPDH is a cytosolic enzyme that participates in glycolysis, and its inactivation is not expected to affect the genomic distribution of TBP, and acts as negative control. ChIP samples were sequenced using SOLiD technology along with the INPUT sample to normalize the distribution of background signals within each of the two chromatin samples.

overall_design: 2 ChIP samples + one input sample


title: Human variation in PolII and NF-KappaB binding (ChIP-seq study with Pol II)

first: Flora

last: Vaccarino

address: 230 South Frontage Road

summary: We examined genome-wide variation in transcription factor binding in different individuals and a chimpanzee using chromatin immunoprecipitation followed by massively-parallel sequencing (ChIP-Seq). The binding sites of RNA Polymerase II (Pol II) as well as a key regulator of immune responses, NFkB, were mapped in ten HapMap lymphoblastoid cell lines derived from individuals of African, European, and Asian ancestry, including a parent-offspring trio. We also mapped gene expression in all ten human cell lines for two treatment conditions: a) no treatment and b) following induction by TNF-alpha.

overall_design: Genome-wide comparison of Pol II and NF-KappaB binding in eleven individuals. ChIP-seq study with Pol II.

first: Maya

last: Kasowski

first: Fabian

last: Grubert

first: Christopher

last: Heffelfinger

first: Manoj

last: Hariharan

first: Akwasi

last: Asabere

first: Sebastian

last: Waszak

first: Joel

last: Rozowsky

first: Minyi

last: Shi

first: Alexander

middle: E

last: Urban

first: Mi-Young

last: Hong

first: Sherman

last: Weissman

first: Mark

middle: B

last: Gerstein

first: Jan

last: Korbel


title: Distinct factors control histone variant H3.3 localization at specific genomic regions

city: New York

first: Aaron

last: Goldberg

state: NY

address: 1230 York Avenue - Box 78

department: Laboratory of Chromatin Biology

institute: The Rockefeller University

summary: The incorporation of histone H3 variants has been implicated in the epigenetic memory of cellular state. Using genome editing with zinc finger nucleases to tag endogenous H3.3, we report genome-wide profiles of H3 variants in mammalian embryonic stem (ES) cells and neuronal precursor cells. Genome-wide patterns of H3.3 are dependent on amino acid sequence, and change with cellular differentiation at developmentally regulated loci. The H3.3 chaperone Hira is required for H3.3 enrichment at active and repressed genes. Strikingly, Hira is not essential for localization of H3.3 at telomeres and many transcription factor binding sites. Immunoaffinity purification and mass spectrometry reveal that the proteins Atrx and Daxx associate with H3.3 in a Hira-independent manner. Atrx is required for Hira-independent localization of H3.3 at telomeres, and for the repression of telomeric RNA. Our data demonstrate that multiple and distinct factors are responsible for H3.3 localization at specific genomic locations in mammalian cells.

overall_design: Crosslinking ChIP-seq:  Examination of 1 histone variant (H3.3), 2 histone modifications, and Serine-5 phosphorylated RNA polymerase in 2 different cell types (H3.3-HA ES samples 1-4, and H3.3-HA NPC samples 7-10).  Examination of 1 histone variant (H3.2), and one histone modification (H3K36me3) in 2 different cell types (H3.2-HA ES samples  5-6, and H3.2-HA NPC samples 11-12). Examination of 1 histone variant (H3.3), input control, and one histone modification (H3K36me3) in one cell type (H3.3-HA hybrid ES, samples 13-15).  Examination of 1 histone variant (H3.1S31), input control, and one histone modification (H3K36me3) in one cell type (H3.1S31-HA hybrid ES, samples 16-18).  Native ChIP-seq: Examination of 1 histone variant (H3.3), input control, and one histone modification (H3K4me3) in one cell type (H3.3-HA ES, samples 19-21). Examination of 1 histone variant (H3.2), input control, and two histone modifications (H3K4me3 and H3K27me3) in one cell type (H3.2-HA ES, samples 22-25).  Examination of 1 histone variant (H3.3), input control, and two histone modifications (H3K4me1 and H3K36me3) in one cell type (H3.3-EYFP ES, samples 26-29).  Examination of 1 histone variant (H3.3), input control, and two histone modifications (H3K4me1 and H3K36me3) in one cell type (Hira -/- H3.3-EYFP ES, samples 30-33).  Examination of 1 histone variant (H3.3) and input control in one cell type (Atrxflox H3.3-EYFP ES, samples 34-37).  Examination of HA antibody background in one cell type (wild-type ES, sample 38).

first: Scott

last: Dewell

first: Deyou

last: Zheng

first: C

last: Allis


title: Genome-wide nucleosome occupancy profiling by high throughput sequencing, and microarray analysis of RNA abundance

city: Chapel Hill

first: Jason

last: Lieb

address: 408 Fordham Hall, CB# 3280

institute: University of North Carolina at Chapel Hill

summary:
We profiled nucleosome occupancy of different developmental stages in C. elegans. Mononucleosomal DNA was sequenced by Illumina paired-end sequencing. We used embryos, germlineless adults, germ line containing adults, and XO hermaphrodites at L3 larval stage. RNA abundance is determined by microarray analysis. We also digested naked DNA with MNase.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: After MNase digestion of chromatin, we purified mononucleosomal DNA and used Illumina paired-end sequencing. Mapping was done in embryo (strain N2), germlineless adults (strain JK1107), germ line containing adults (strain DH245),and XO hermaphrodites (strain TY2205) at L3 larval stage. For each experimental replicate RNA abundance is determined by microarray analysis. We also digested naked DNA with MNase.

first: Sevinc

last: Ercan

first: Yaniv

last: Lubling

first: Eran

last: Segal


title: Genome-wide mapping of OCT4, NANOG and CTCF in human embryonic stem cells

status: Public on Mar 06 2010

city: Singapore

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

address: 60, Biopolis street

department: Computational and Systems Biology

institute: Genome Institute of Singapore

summary: Transcription factors and their specific interactions with targets are crucial in specifying gene expression programs. To gain insights into the transcriptional regulatory networks in embryonic stem cells, we used chromatin immunoprecipitation coupled to ultra-high-throughput DNA sequencing (ChIP-seq) to map the locations of OCT4, NANOG and CTCF.

overall_design: ChIP-enriched DNA from pooled ChIP samples were analyzed by Solexa sequencing.

first: G

last: Bourque

first: Huck-Hui

last: Ng


title: Phenotypic plasticity in the pea aphid Acyrthosiphon pisum: miRNA sequencing

status: Public on Mar 01 2010

city: Rennes

first: Stephanie

last: Jaubert

address: domaine de la Motte

country: France

institute: INRA

summary:
Bioinformatic prediction, deep sequencing of microRNA and expression analysis during phenotypic plasticity in the pea aphid acyrthosiphon pisum
We developed high throughput Solexa sequencing and bioinformatic analyses of the genome of the pea aphid Acyrthosiphon pisum in order to identify the first miRNAs from a hemipteran insect. By combining these methods we identified 155 miRNAs including 56 conserved and 99 new miRNAs. Moreover, we investigated the regulation of these miRNAs in different alternative morphs of the pea aphid by analysing the expression of miRNAs across the switch of reproduction mode.

overall_design: deep sequencing of small RNAs from parthenogenetic Acyrthosiphon pisum

first: Tom

last: Walsh

first: Owain

last: Edwards

first: Shuji

last: Shigenobu


title: NAP provides neuroprotection against kainic acid-induced cell death

city: Tel Aviv

first: Illana

last: Gozes

address: Einstein

country: Israel

institute: Tel Aviv University

summary:
NAP - neuroprotective peptide demonstrates increase in neuronal survival when injected into the hippocampus of rats in the model of epilepsy
Microarray analysis was used to understand the expression of genes following KA treatment and the changes in gene expression following KA+NAP treatment
Keywords: stress response

overall_design: KA was injected into the hippocampus of Sprague-Dawley rats. The other group of rats was injected with KA and NAP(10-13M). The third group was injected with NAP only and the last group was injected with PBS as a vehicle. CA3 area of hippocampus was removed 24h later and RNA extraction was done. The samples were subjected to microarray analysis.

first: Ilona

last: Zemlyak


title: Comparison of nucleosome positioning among two yeast species and their hybrid for wild-type and deletion mutant strains

city: Rehovot

first: Itay

last: Tirosh

address: herzl

department: Molecular genetics

institute: Weizmann Institute of Science

summary: To study the evolution of nucleosome positioning we mapped nucleosome positioning in two species of yeasts. Identified differences in nucleosome positioning were classified into cis-based changes or trans-bseed changes based on the pattern of nucleosomes in the hybrid. This analysis was performed for wild-type strains as well as for strains deleted of 5 chromatin regulatoirs allolwing us to examine their roles in determining nucleosome positioning.

sample_organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

overall_design: Illumina sequencing of mono-nucleosome fragments isolated by MNase digestion. Samples include pooled DNA fragments of S. cerevisiae and S. paradoxus or DNA fragments of the interspecific hybrid. Experiments were performed for WT strains as well as strains deleted of 5 chromatin regulators.