title: Developmental transcriptomics of the model caterpillar fungus Cordyceps militaris

status: Public on Nov 08 2011

city: Shanghai

first: Chengshu

last: Wang

address: 300 Fenglin Road

department: Institute of Plant Physiology and Ecology

institute: Shanghai Institutes for Biological Sciences, CAS

summary: The RNA-Seq technique was used to investigate the differentially transcribed genes of the caterpillar fungus Cordyces militaris. It was calculated that >63% of total annotated genes were expressed, including >55% of putative pathogen-host interaction genes. Overall, the fruiting-body development and mycelium growth by C. militaris activated high expression levels of genes in association with translation and post-translational modifications. Otherwise, there were many differentially expressed genes when the fungus was grown on insect pupae to different stages or in liquid medium. In general, the transcriptional profiles were more similar with each other during fungal fruiting-body developmental stages than during growth in a liquid culture.

overall_design: Examination of differential gene expressions by Cordyceps militaris during fruiting-body developments on silkmoth pupae and growth in a liquid medium.

first: Peng

last: Zheng


title: Genome-wide reductions in active chromatin, paused RNA Polymerase II and nucleosome turnover during heat shock

status: Public on Nov 15 2011

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

country: USA

institute: Fred Hutchinson Cancer Research Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Heat shock rapidly induces expression of a small set of genes while globally repressing transcription, making it an attractive system for studying alterations in the chromatin landscape that accompany changes in gene regulation. We have characterized these changes using low-salt extraction of intact micrococcal nuclease (MNase)-treated Drosophila S2 cell nuclei to determine the active nucleosomal and subnucleosomal chromatin landscapes. The low-salt-soluble fraction corresponds to classical "active" chromatin and includes distinct size fractions of MNase-protected particles that can be precisely mapped by paired-end sequencing. After heat shock, the distribution of low-salt-soluble nucleosomes showed an overall reduction over gene bodies, consistent with down-regulation of transcription. No global changes were detected in the subnucleosomal landscape upstream of transcriptional start sites, however, we observed a genome-wide reduction of paused RNA Polymerase II from the active chromatin fraction. Furthermore, nucleosome turnover decreased within gene bodies in a pattern similar to that observed when transcription elongation was artificially inhibited. These observations suggest that reduced Pol II affinity and processivity is the dominant nuclear mechanism for genome-wide repression during heat shock. Our ability to precisely map both nucleosomal and subnucleosomal particles directly from classical active chromatin extracts to assay changes in the chromatin landscape provides a simple general strategy for epigenome characterization.

overall_design:
High-throughput sequencing (Illumina HiSeq 2000)
We have characterized changes to the active nucleosomal and subnucleosomal landscape during the heat shock response in Drosophila cells by genome-wide profiling of low-salt extracted micrococcal nuclease-treated nuclei, paused RNA Polymerase II and CATCH-IT nucleosome turnover.

first: Teves

last: Sheila

middle: G

first: Steven


title: RNA-seq and expression profile of WT and ZFP57 KO ES cells

status: Public on Nov 07 2011

city: Lausanne

first: Simon

last: Quenneville

address: station 15

country: Switzerland

institute: EPFL SV

type: Expression profiling by high throughput sequencing

overall_design: RNA was extracted from both cell lines, PolyA RNA were extracted and RNA-seq was performed

first: Adamandia

last: Kapopoulou

first: Didier

last: Trono


title: ZFP57/KAP1 recognize a methylated hexanucleotide to affect the chromatin and DNA methylation of imprinting control regions in embryonic stem cells

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

overall_design: Refer to individual Series


title: RNA Subcellular Localization by Paired End diTag Sequencing from ENCODE/GIS

status: Public on Nov 10 2011

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Yijun Ruan mailto:ruanyj@gis.a-star.edu.sg). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

This track is produced as part of the ENCODE Transcriptome Project. It shows the starts and ends of full length mRNA transcripts determined by GIS paired-end ditag (PET) sequencing using RNA extracts (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=rnaExtract) from different sub-cellular localizations (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=localization) in different cell lines (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=cellType). The RNA-PET information provided in this track is composed of two different PET length versions based on how the PETs were extracted. The cloning-based PET (18 bp and 16 bp) is an earlier version and detailed information can be found from reference (Ng et al. 2006). The cloning-free PET (25 bp and 25 bp) is a recently modified version which uses Type II enzyme EcoP15I to generate a longer length of PET (unpublished), which results in a significant enhancement in both library construction and mapping efficiency. Both versions of PET templates were sequenced by Illumina platform at 2 x 36 bp Paired End sequencing. See the Methods and References sections below for more details.

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:
Cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell). Two different GIS RNA-PET protocols were used to generate the full length transcriptome PETs: one is based on a cloning-free RNA-PET library construction and sequencing strategy (unpublished), and the other is a cloning-based library construction (Ng et al. 2005) and recent Illumina paired end sequencing.
Cloning-free RNA-PET (50 bp reads, 25 bp and 25 bp tag for each of the 5' and 3' ends)--Method: The cloning-free RNA-PET libraries were generated from polyA mRNA samples and constructed using a recently modified GIS protocol (unpublished). Total RNA in good quality was used as starting material and purified through MACs polyT column to obtain full length polyA mRNAs. Approximately 5 micrograms of enriched polyA mRNA were used for reverse transcription to convert polyA mRNA to full length cDNA. The obtained full length cDNA was modified and ligated with specific linker sequences, followed by circularization through ligation to generate circular cDNA molecules. The 25 bp tag from each end of the full length cDNA was extracted by type II enzyme EcoP15I digestion. The resulting PETs were ligated with sequencing adaptors at the both ends, amplified by PCR, and further purified as complex templates for paired end (PE) sequencing using Illumina platforms. Data: The sequenced RNA-PETs are unified in 25/25 bp length from each end of a cDNA. After filtering out redundant and noise tags, the unique PETs will proceed to analysis pipeline. Initially, the orientation of each tag will be screened out by the barcode built in the sequencing-template, then paired into a given orientation-PET. The orientation-determined RNA-PET is mapped onto reference genome allowing up to two mismatches. Majority of PETs are mapped on the known transcripts, or splice variants. A small portion of misaligned PETs, defined as discordant PETs, are mapped either too far from each tag, have wrong orientations, or mapped in different chromosomes, indicating exist some transcription variations which could be caused by genome structure variations: such as fusion, deletion, insertion, inversion, tandem repeat and translocation; or RNA trans-splicing etc.
Cloning-based RNA-PET (34 bp reads, 18 bp and 16 bp tag for each of the 5' and 3' ends)--Method: The cloning-based RNA-PET (GIS-PET) libraries were generated from polyA RNA samples and constructed using the protocol described by Ng et al. (2005). Total RNA in good quality was used as starting material and further purified through MACs polyT column to enrich polyA mRNA and remove any contaminants (e.g., rRNA, tRNA, DNA, protein etc). Approximately 10 micrograms of polyA mRNA were then used for reverse transcription to convert polyA mRNA into full length cDNA. The obtained full length cDNA was modified with specific linker sequences, then, ligated to a GIS-developed (pGIS4) vector to form a complex full length cDNA library, which was cloned into E. coli. The plasmid DNA was then isolated from the library, followed by MmeI (a type II enzyme) digestion to generate a final length of 18 bp/16 bp ditags from each end of the full length cDNA. The single ditag (or called PET) was then ligated to form a diPET structure (a concatemer with two unrelated PET linked by a linker sequence) to facilitate Illuminaa Paired End sequencing. Data: The cloning-based RNA-PETs are unified in 18 bp and 16 bp length, respectively extracted from 5' and 3' end of each cDNA. The redundant reads were filtered out initially and unique ones were included for analysis. PET sequences were then mapped to (GRCh37, hg19, excluding mitochondirion, haplotypes, randoms and chromosome Y) reference genome using the following specific criteria (Ruan et al. 2007):
A minimal continuous 16 bp match must exist for the 5' signature; the 3' signature must have a minimal continuous 14 bp match. Both 5' and 3' signatures must be present on the same chromosome. Their 5' to 3' orientation must be correct (5' signature followed by 3' signature). The maximal genomic span of a PET genomic alignment must be less than one million bp. PETs mapping to 2-10 locations are also included and may represent duplicated genes or pseudogenes in the genome. A majority of PETs mapped on the known transcripts or splice variants. A small portion of misaligned PETs, defined as discordant PETs, were mapped either too far from each other, mapped in the wrong orientation, or mapped to different chromosomes, indicating that some transcription variations exist which could be caused by genome structure variations: such as fusion, deletion, insertion, inversion, tandem repeat and translocation; or RNA trans-splicing etc.
Clusters: To cluster the PETs the following procedure was applied: the mapping location of the 5' and 3' tag of a given PET was extended by 100 bp in both directions creating 5' and 3' search windows. If the 5' and 3' tags of a second PET mapped within the 5' and 3' search window of the first PET then the two PETs were clustered and the search windows were adjusted so that they contained the tag extensions of the second PET. PETs which subsequently mapped with their 5' and 3' tags within the adjusted 5' and 3' search window, respectively, were also assigned to this cluster and search window readjusted. This iterative process continued till no new PET was found to fall within the search window, at which stage all the found PETs are classified as belonging to a single cluster. This process is repeated till all PETs are assigned to a cluster.
Verification: To assess overall PET quality and mapping specificity, the top ten most abundant PET clusters that mapped to well-characterized known genes were examined. Over 99% of the PETs represented full-length transcripts, and the majority fell within 10 bp of the known 5' and 3' boundaries of these transcripts. The PET mapping was further verified by confirming the existence of physical cDNA clones represented by the ditags. PCR primers were designed based on the PET sequences and amplified the corresponding cDNA inserts either from full length cDNA library (cloning-based PET) or from total RNA isolate (cloning-free PET) for sequencing confirmation.

first: Xiaoan

last: Ruan

first: Atif

last: Shahab

first: Chialin

last: Wei

first: Yijun


title: Histone Deacetylase 3 is an Epigenomic Brake in Macropahge Alternative Activation

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency


title: ChIP-Seq of HA tagged ZFP57 and KAP1 in mouse ES cells

summary: We have performed ChIP seq analysis to obtain the positions of KAP1 and ZFP57 binding sites in mouse ES cells.  By comparing the two lists, we were able to find bona fide sites.

first: Andrea

last: Corsinotti


title: RNA sequencing reveals differential expression of mitochondrial and oxidation reduction genes in the long-lived naked mole-rat when compared to mice.

city: Oxford

first: Yang

last: Li

address: 3 Fettlers House, Walton Wells Road

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

summary: The goal was to find genes which are differentially expressed between the naked mole-rat (Heterocephalus glaber) and the wild-type mice liver tissue. The genes which are most differentially expressed may provide a clue for the remarkable differences between naked mole-rat and mouse in terms of longevity, cancer resistance and adaptation to subterranean environments.

sample_organism:
Mus musculus
Heterocephalus glaber

platform_organism:
Mus musculus
Heterocephalus glaber

overall_design: Analysis of 2 mRNA samples, one pooled from 3 wild-type mice liver tissue and another pooled from 3 naked mole-rat liver tissue.

first: Chuanfei

last: Yu

first: Andrew

last: Holmes

first: Karol

last: Szafranski

first: Chris

last: Faulkes

first: Clive

middle: W

last: Coen

first: Rochelle

last: Buffenstein

first: Matthias

last: Platzer

first: JoÃ£o

middle: P

last: de MagalhÃ£es

first: George

middle: M

last: Church


title: Genome-wide binding map of the HIV Tat protein to the human genome

status: Public on Nov 06 2011

city: Los Angeles

first: Siavash

middle: K

last: Kurdistani

address: 615 Charles E. Young Dr. South, 337

department: Biological Chemistry

institute: University of California Los Angeles

type: Genome binding/occupancy profiling by genome tiling array


title: Nutrigenomics in honey bees: the impact of pollen nutrients on bee health

city: Avignon

first: Cédric

last: Alaux

address: Domaine Saint-Paul

department: UMR 406 Abeilles et Environnement

country: France

institute: INRA

summary: We studied the molecular mechanisms underlying the impact of pollen nutrients on honey bee (Apis mellifera) health and how those nutrients improve resistance to parasites. Using digital gene expression, we determined the changes in gene expression induced by pollen intake in worker bees parasitized or not by the mites Varroa destructor, known for suppressing immunity and decreasing lifespan of bees.

overall_design: bees with or without verroa, and fed or not fed pollen

first: Christelle

last: Dantec

first: Hughes

last: Parrinello

first: Yves

last: Le Conte


title: Genome-wide binding map of the HIV Tat protein to the human genome (ChIP-Seq)

summary: The HIV-1 Trans-Activator of Transcription (Tat) protein binds to multiple host cellular factors and greatly enhances the level of transcription of the HIV genome.  Here, we report the genome-wide binding map of Tat to the human genome in Jurkat T cells (Jurkat-Tat cells) using chromatin immunoprecipitation combined with next-generation sequencing.  cDNA microarray was used to monitor gene expression changes between Jurkat and Jurkat-Tat cells.  Additionally, we compared distribution of H3K9ac near gene promoters between Jurkat and Jurkat-Tat cells using ChIP-chip method and hybridized onto Agilent promoter array.  Our data reveal that Tatâs interaction with the host genome is more extensive than previously thought, with potentially important implications for the viral life cycle.

overall_design: Expression profiles on Jurkat-Tat cells versus Jurkat cells.   ChIP on chip for H3K9ac in Jurkat-Tat versus Jurkat cells.  ChIP-seq for HIV-1 Tat protein in Jurkat-Tat cells.

first: Celine

last: Marrban

first: Trent

last: Su


title: SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers

status: Public on Nov 05 2011

city: Strasbourg

first: Krishanpal

last: Karmodiya

email: krish@igbmc.fr, laszlo@igbmc.fr

address: 1 rue Laurent Fries / BP 10142

institute: Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)

summary: Metazoan SAGA and ATAC are distinct multi-subunits complexes that share the same catalytic HAT subunit (GCN5 or PCAF). Here we show that these human HAT complexes are targeted to different genomic loci representing functionally distinct regulatory elements both at broadly expressed and tissue specific genes. While SAGA can principally be found at promoters, ATAC is recruited to promoters and enhancers, yet only its enhancer binding is cell-type specific. Furthermore, we show that ATAC functions at a set of enhancers that are not bound by p300, revealing a new class of enhancers not yet identified. These findings demonstrate important functional differences between SAGA and ATAC coactivator complexes at the level of the genome and define a novel role for the ATAC complex in the regulation of a set of enhancers.

overall_design: Examination of SPT20 in two different cell types.

first: Krebs

last: Arnaud

first: Marianne

last: Lindahl-Allen

first: Kevin

last: Struhl

first: Laszlo

last: Tora


title: Mapping origins of replication in Arabidopsis thaliana: Examination of BrdU labeled DNA and unlabeled DNA in one cell type

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

summary: Genomic integrity requires faithful chromosome duplication. Origins of replication are the genomic sites where DNA replication initiates in every cell cycle. There are multiple origins scattered throughout the eukaryotic genome whose genome-wide identification has been a hard challenge, especially in multicellular organisms. Thus, very little is known on the distinctive features of origins in terms of DNA sequence and chromatin context at a genomic scale. Here we have profiled origins in Arabidopsis thaliana by high-throughput sequencing of purified nascent DNA strands. We have identified 1543 replication origins, which were uniformly distributed across the Arabidopsis genome and enriched in binding signals of two replication initiation proteins, CDC6 and ORC1. We have also analyzed novel epigenome maps of various histone modifications and found links between origins and epigenetic signatures, which differ from or have not been reported for other eukaryotic systems. Arabidopsis origins tend to be embedded in G+C-rich regions within the 5’ half of genes, enriched in histone H2A.Z, H3K4me2/3 and acetylated H3 and H4, and depleted of H3K4me1 and H3K9me2. Our data establish the basis for the understanding of the epigenetic specification of origins of replication in Arabidopsis and have implications for the mechanisms of origin specification in other eukaryotes.

overall_design: Examination of BrdU labelled DNA and unlabelled DNA in one cell type


title: Methanobrevibacter smithii expression profiling

city: St Louis

first: Federico

middle: E

last: Rey

state: MO

address: 4444 Forest Park Blvd

department: Pathology

institute: Washington University

sample_organism:
Methanobrevibacter smithii
Methanobrevibacter smithii ATCC 35061

platform_organism:
Bacteroides thetaiotaomicron
Phocaeicola vulgatus
Parabacteroides distasonis
Methanobrevibacter smithii
Lachnospira eligens
Agathobacter rectalis
Methanobrevibacter smithii ATCC 35061


title: DNA methylation profiling of flatfish dab (Limanda limanda)

status: Public on Nov 09 2011

city: Birmingham

first: Leda

last: Mirbahai

address: Edgbaston

department: Biosciences

institute: University of Birmingham

type: Methylation profiling by high throughput sequencing

summary: We report the application of DNA methylation immunoprecipitation coupled with de novo high throughput sequencing for profiling and identifying methylation alterations in liver tumours of un-sequenced flatfish dab (Limanda limanda).  We achieved approximately 90 million and 88 million paired-end reads for hepatocellular adenoma (HCA) and corresponding healthy surrounding tissue (S.T) respectively, of which 47,052,820 and 45,008,483 were uniquely mapped. By calculating the fold changes observed between HCA and S.T we identified 1693 CpG island containing regions  that are differentially methylated in HCA compared to S.T (fold change >1.5). The identified genes were further annotated for gene name and biological functions. Ingenuity Pathway Analysis demonstrated enrichment of networks and top functions, such as cell-to-cell signalling, cell cycle, DNA replication,   cellular assembly and organisation as well as canonical pathways including Wnt/Î²-catenin signalling, growth hormone signalling and apoptosis signalling associated with the differentially methylated genes in HCA compared to S.T. Finally, our data showed that MeDIP-HTP sequencing achieves substantial overlapping reads for construction of contigs and annotation of the based on closely related species for studying DNA methylation in un-sequenced species.

overall_design: Investigating alteration in methylation profile of heaptocellular adenoma compared to healthy surrounding tissue of flatfish dab.

first: Timothy

middle: D

last: Williams

first: James

last: Chipman

first: Guangliang

last: Yin

first: Ning

last: Li


title: Comprehensive assembly and spatio-temporal analysis of the C. elegans 3' UTRome through isolation and sequencing of 3'UTRs in germline-dereived cell types and somatic tissues.

status: Public on Nov 04 2011

city: Ann Arbor

first: Ryan

last: Mills

state: MI

address: 100 Washtenaw Ave

department: Computational Medicine and Bioinformatics

institute: University of Michigan

summary: Our computational analyses of sequencing depth and the discovery rates of sequence elements in the 3’UTR strongly demonstrate that interrogation of the 3’UTRome in specific tissues and cell types across development will greatly expand the identification of new 3’UTR isoforms and the sequence elements therein. Therefore, we will generate and sequence the 3’UTRs from the cell types isolated from the developing germline, mature germ cells, and early embryogenesis. In addition, we will identify the 3’UTRs for the transcripts isolated from the major somatic tissues during late- and post-embryonic development. Based on our sequencing estimates, we anticipate that the tissue-specific interrogation of the 3’UTRome will reveal a far greater diversity of novel 3’UTR isoform expression that is masked in the whole-worm 3’UTRome sequence data. Using the transgenic myo-3::PABP strain, we have generated polyA-captured libraries for late embryos and across the major stages of post-embryonic development for the muscle transcriptome. We propose to generate these polyA-captured libraries for transcripts expressed in the other major tissues across development. PolyA-captured libraries will be generated for deep sequencing following the tissue-specific isolation of mRNAs by PABP pulldowns (the PABP immunoprecipitations will take advantage of a FLAG epitope which is fused to PABP in all of the transgenic strains). We propose to validate the expression of tissue- specific transcripts by qPCR for select transcripts known to be expressed in those particular tissues. In addition, following the strategy we have employed for the large-scale polyA-captured libraries from muscle, we will perform quality checks for 3ʼ end capture by manually sequencing ~60 clones isolated from each library. Once we have obtained the deep sequencing data, we will analyze all of the sequence reads using the bioinformatics pipeline that we established for the whole-worm polyA- captured sequences (Mangone et al., 2010).

overall_design: Four samples representing gravid, L2, L3, and L4 developmental stages were analyzed.

first: John

last: Kim

first: Sang

middle: Y

last: Chun

first: Vishal

last: Khivansara

first: Arun

last: Manoharan


title: Interferon-alpha mediates the development of autoimmunity by direct tissue toxicity and through immune-cell recruitment mechanisms

status: Public on Nov 03 2011

city: New York

first: Weijia

last: Zhang

state: NY

address: 1425 Madison Avenue

department: Department of Medicine

institute: Mount Sinai School of Medicine

summary: Interferon-alpha is a major therapeutic agent for many diverse diseases.  However, the interferon-alpha mechanism of therapeutic action and associated side effects are not well understood. In particular, thyroiditis is a common unexplained complication.  We hypothesized that direct thyroid-toxic actions coupled with immune mechanisms play a major role in the thyroiditis etiology. To test this hypothesis, we investigated the actions of interferon-alpha on cultured thyrocytes in vitro, and in vivo by creating transgenic mice overexpressing interferon-alpha tissue specifically in thyrocytes. Interferon-alpha treatment of cultured PCCL3 rat thyrocytes increased markers of thyroid differentiation, levels of MHC class I, and expression of heat shock protein and CXCL10.  This was associated with markedly increased nonapoptotic thyroid cell death. Consistent with these in vitro findings, transgenic mice overexpressing interferon-alpha in the thyroid displayed striking thyroid cell death characteristic of nonimmune thyroid destruction that progressed to profound primary hypothyroidism. Moreover, genes linked to cell death pathways, granzyme B, or known to be associated with recruitment of a cytotoxic immune response, CXCL10, interleukin-23, and TRIM21 were increased in the transgenic thyroids. Taken together, the etiology of interferon-induced thyroiditis likely involves both a direct toxic action on thyrocytes, as well as provocation of a destructive immune response.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 1) Thyroid cells were incubated with interferon-alpha, and global gene expression was determined by RNA-seq. 2) Thyroid tissues were obtained from transgenic mice overexpressing interferon-alpha and from wild type mice, and global gene expression was analyzed using RNA-seq.

first: Nagako

last: Akeno

first: Eric

last: Smith

first: Amanda

last: Huber

first: Mihaela

last: Stefan

first: Mehdi

last: Keddache

first: Yaron

last: Tomer


title: Genome-wide Analysis of Nascent Transcription in Saccharomyces cerevisiae

status: Public on Nov 01 2011

first: Carlos

last: Araya

address: 1705 NE Pacific

department: Genome Sciences

institute: University of Washington

summary: We combined the nuclear run-on (NRO) assay which labels and captures nascent transcripts with high throughput DNA sequencing to examine transcriptional activity in Saccharomyces cerevisiae.

overall_design: Examination of nascent transcripts and steady-state transcripts in exponentially growing and heat-shock treated yeast.

middle: L

first: Anastasia

last: McKinlay

first: Stanley

last: Fields


title: Sequentially acting Sox transcription factors in neural lineage development [ChIP-seq]

city: Stockholm

first: Rickard

last: Sandberg

address: Berzelius vag 35

department: Department of Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

summary: We report sequential binding but unique functions of different Sox transcription factors during distinct stages of neural differentiation

overall_design: Examination of genome-wide Sox2, Sox3 and Sox11 transcription factor binding during different stages of neurogenesis.

first: Maria

last: Bergsland

first: Daniel

last: Ramsköld

first: Jonas

last: Muhr


title: Genes affected upon dsRNA knockdown treatment for nbr/CG9247 in Drosophila DL1 cells and small RNA profiling in Drosophila wild-type and nbr[f02257] mutants

city: Philadelphia

first: Bonini

last: Nancy

state: PA

address: 415 S University Ave

institute: University of Pennsylvania

type: Non-coding RNA profiling by high throughput sequencing

first: Masashi

last: Abe

first: Nancy

last: Bonini


title: Sequentially acting Sox transcription factors in neural lineage development


title: Genome-wide consequences of compromised NMD and their relavence for variable clinical phenotype of patients with UPF3B mutations

city: North Adelaide

first: Jozef

last: Gecz

state: South Australia

address: 72 King William Rd

department: Genetics Medicine

country: Australia

institute: SA Pathology


title: Genome-wide consequences of compromised NMD and their relavence for variable clinical phenotype of patients with UPF3B mutations [mRNA profiling]

summary:
Nonsense-mediated mRNA decay (NMD) surveillance pathways are best known to be involved in the degradation of mRNA with premature termination codons (PTCs). More recent studies demonstrate that the role of NMD pathways goes well beyond the degradation of PTC containing mRNA, into the regulation of cell function and thus normal development.
We have taken advantage of the availability of naturally occurring loss of function mutations in the UPF3B gene, a major component of the exon junction complex (EJC), to inquire about genome-wide consequences of compromised NMD. We identify that about 5% of the lymphoblastoid cell transcriptome is directly or indirectly impacted upon in patients with UPF3B mutations with minimal effect on alternative splicing. We identify UPF3A-NMD as a likely, major modifier of the UPF3B patient phenotype through variable UPF3A protein stabilisation. Among the most consistently deregulated direct targets of UPF3B-NMD we identify the ARHGAP24 as the most likely gene implicated in the neuronal phenotype of UPF3B patients.

overall_design: To assess the impact of UPF3B-NMD deficiency on human transcriptome, we sequenced polyA RNA extracted from lymphoblastoid cell lines of patients (n=4) and controls (n=2). We complemented the analysis using Affymetrix Human Exon 1.0 St array using total RNA of the same cell line from patients (n=5, 3 of whom were also sequenced) and controls (n=5). Moreover, we overlapped identified differently expressed genes with copy number variation data of the patients, obtained using Illumina Human Omniexpress chip, to exclude possible false positive.

first: Lam

middle: S

last: Nguyen

first: Lachlan

last: Jolly

first: Cheryl

last: Shoubridge

first: Wai-kin

last: Chan

first: Lulu

last: Huang

first: Frederic

last: Laumonnier

first: Martine

last: Raynaud

first: Michael

last: Field

first: Jayson

last: Rodriguez

first: Anand

last: Srivastava

first: Yohan

last: Lee

first: Anjene

last: Addinton

first: Judy

last: Rapoport

first: Suganthi

last: Suren

first: Chris

last: Hahn

first: Jennifer

last: Gamble

first: Miles

middle: F

last: Wilkinson

first: Mark

middle: A

last: Corbett


title: SRC-1 targets ADAM22: an ER-independent mechanism of tumour progression in endocrine resistance

city: Cork

first: Ailis

last: Fagan

address: University College Cork

country: Ireland

institute: University College Cork

summary: We profile the binding of Steroid Receptor Co-activator (SRC1) in LY2 cells, a tamoxifen-resistant cell line, in the presence and absence of tamoxifen using ChIP-sequencing technology. The development of breast cancer resistance to endocrine therapy results from an increase in cellular plasticity leading to the development of a steroid-independent tumour.  The p160 steroid coactivataor protein SRC-1, through interactions with developmental proteins and other non-steroidal transcription factors, drives this tumour adaptability.  Here, using discovery studies, we identify ADAM22, a non-protease member of the ADAMs family, as a direct, ER-independent target of SRC-1. Molecular, cellular and in vivo studies confirmed SRC-1 as a regulator of ADAM22. At a functional level, a role for ADAM22 in cellular migration and differentiation was observed. In vivo data from a mouse xenograft model indicated that ADAM22 expression was higher in 4-OHT-treated endocrine-resistant tumours than in tumours derived from isogenic, sensitive cells.  Furthermore, in breast cancer patients, ADAM22 expression is an independent predictor of poor disease free survival.  SRC-1 can function as a molecular switch which converts a steroid-responsive tumour to a steroid-resistant tumour.  The ER-independent SRC-1 target ADAM22 is a potential drug target and a companion predictive biomarker in the treatment of endocrine-resistant breast cancer.

overall_design: Examination of SRC-1 binding in LY2 cells in the presence or absence of tamoxifen treatment. 2 replicates each.


title: Sequentially acting Sox transcription factors in neural lineage development [RNA-seq]

first: Rickard

last: Sandberg

overall_design: Loss of function experiment for Sox2/Sox3 in neural progenitor cells and gene expression profile for Sox11 expressing (PSA NCAM sorted) early formed neurons.

first: Maria

last: Bergsland

first: Daniel

last: Ramsköld

first: Jonas

last: Muhr


title: Small RNA profiling in Drosophila wild-type and nbr[f02257] mutants

first: Bonini

last: Nancy

summary:
nbr/CG9247 gene regulates 3'end heterogeneity of a subset of miRNAs.
It is not clear how broad this effect is on small RNA population.
To address this, we compared small RNA population in wild-type and tmr[f02257]  mutants.
This approach identified more miRNAs whose 3'end heterogeneity was affected in nbr[f02257] mutants.

overall_design:
2-3 day old control (w homogeneous strain Bloomington stock center 5905) and nbr[f02257] null mutant flies were collected.
nbr[f02257] line was in the homogenous (Bloomington stock center stock 5905) background through a minimum of 5 backcrosses.
Total RNA from whole flies was extracted using TRIzol reagent (Invitrogen).
40ug of total RNA from each genotype was used for small RNA library preparation with Small RNA Sample Prep kit (v1.5) (Illumina).

first: Masashi

last: Abe

first: Nancy

last: Bonini


title: Transgenerational inheritance of an acquired small RNA-based antiviral response in C.elegans

status: Public on Oct 31 2011

first: Gregory

last: Minevich

address: 701 W 168th st HHSC 726

department: Biochemistry

institute: Columbia University

summary: Deep sequencing was used to detect Flock House Virus (FHV)-derived small RNAs (viRNAs) that were inherited over generations. Small RNA libraries were constructed from 4 different samples: (a) FR1gfp-transgenic worms that can mount an RNAi response and should contain viRNAs (positive control); (b) rde-4(-/-) mutants (negative control as no viRNAs are expected to be produced); (c) FR1gfp; rde-4(-/-) worms that are two generations away from their rde-4(+/-) grandparents, i.e. worms that can themselves not produce viRNAs, but may have inherited viRNA from their grandparents; and (d) the F3 progeny of wild-type animals that contained the FR1gfp transgene (and therefore produced viRNAs), but have lost this transgene through outcrossing with non-transgenic wild-type worms. This tests whether the silencing reagent can exist without its template. The Small RNA libraries were constructed using a protocol that enriches for Dicer products which harbor a single phosphate at the 5’ end of the RNA (Zamore et al., 2000), such as primary siRNAs, and unlike RdRP products that harbor tri-phosphate ends (Parameswaran et al., 2010). This was the protocol of choice because we were interested in identifying viRNAs that are guaranteed to be derived from the original RNAi-competent parents (Alcazar et al., 2008), and rde-4 animals can not produce primary siRNAs (Grishok et al., 2000; Parrish and Fire, 2001). rde-4 animals are, however, not defective in secondary siRNA production (Blanchard et al., 2011), and can therefore continue to amplify secondary siRNAs de novo; such autonomously-produced siRNAs will not be distinguishable from inherited ones. The detection of rare primary siRNAs is important, as even a single “trigger” siRNA can induce a full-blown RNAi-response that is not proportional to the primary trigger (Groenenboom et al., 2005).In agreement with the functional assays we detected different viRNAs complementary to several regions of the viral genome in the positive control (FR1gfp), no viRNAs in the negative control (rde-4(-/-)), and a number of viRNAs in the worms that could not generate their own viRNAs and thus inherited these viRNAs from their grandparents (F3 generation FR1gfp; rde-4(-/-))(Table 2; Figure 4). Moreover, we detect viRNAs in the worms in which the FR1gfp transgene had been crossed out, confirming that the viRNA transmit in a template-independent manner. The inherited viRNA matched the two most abundant types of viRNAs detected in the positive control (Figure 4) and these viRNAs were all of the reverse orientation (negative strand, which typically exists in much lower quantities than the positive strand (Felix et al., 2011)); both observations make it highly unlikely that the detected viRNAs merely represent unspecific break-down products of the viral RNA. In regard to the low number of inherited viRNA reads it needs to be considered that our protocol enriches specifically for rare primary viRNA species. Moreover, these viRNA species are derived from a response mounted in RNAi-competent grandparents, and are therefore possibly diluted over the course of several generations. Taken together, our results support the genetic experiments that argued for the existence of trans-acting factors that are transmitted in a non-Mendelian manner to ensuing generations.

overall_design: 4 samples examined. Small RNA libraries generated from: C. elegans animals.

first: Oded

last: Rechavi

first: Oliver

last: Hobert


title: The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. (COPRO-Seq)

city: Saint Louis

first: Nathan

last: McNulty

address: 4444 Forest Park Ave. (5th Floor)

department: Center for Genome Sciences and Systems Biology

institute: Washington University School of Medicine

summary: Understanding how the human gut microbiota and host are impacted by probiotic bacterial strains requires carefully controlled studies in humans, and in mouse models of the gut ecosystem where potentially confounding variables that are difficult to control in humans can be constrained. Therefore, we characterized the fecal microbiomes and metatranscriptomes of adult female monozygotic twin pairs through repeated sampling 4 weeks prior to, 7 weeks during, and 4 weeks following consumption of a commercially-available fermented milk product (FMP) containing a consortium of Bifidobacterium animalis subsp. lactis, two strains of Lactobacillus delbrueckii subsp. bulgaricus, Lactococcus lactis subsp. cremoris, and Streptococcus thermophilus. In addition, gnotobiotic mice harboring a 15-species model human gut microbiota whose genomes contain 58,399 known or predicted protein-coding genes were studied prior to and after gavage with all five sequenced FMP strains.

overall_design: 140 samples total.  Evaluation of changes in a model community's structure over time after exposure to a consortium of 5 fermented milk product (FMP) strains.


title: Genome-wide consequences of compromised NMD and their relavence for variable clinical phenotype of patients with UPF3B mutations [RNA-seq]

first: Jozef

last: Gecz

overall_design:
To assess the impact of UPF3B-NMD deficiency on human transcriptome, we sequenced polyA RNA extracted from lymphoblastoid cell lines of patients (n=4) and controls (n=2). We complemented the analysis using Affymetrix Human Exon 1.0 St array using total RNA of the same cell line from patients (n=5, 3 of whom were also sequenced) and controls (n=5). Moreover, we overlapped identified differently expressed genes with copy number variation data of the patients, obtained using Illumina Human Omniexpress chip, to exclude possible false positive.

Supplementary file: A splice junction reference file generated for alignment of junction reads.
Alignment files linked to individual Sample records.

first: Lam

last: Nguyen

first: Lachlan

last: Jolly

first: Cheryl

last: Shoubridge

first: Wai-kin

last: Chan

first: Lulu

last: Huang

first: Frederic

last: Laumonnier

first: Martine

last: Raynaud

first: Jayson

last: Rodriguez

first: Anand

last: Srivastava

first: A

last: Addington


title: The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. (RNA-Seq)

sample_organism: Lactobacillus delbrueckii subsp. bulgaricus

sample_organism: Lactococcus lactis subsp. lactis CNCM I-1631

sample_organism: Bifidobacterium animalis subsp. lactis CNCM I-2494

overall_design: 73 samples total.  Evaluation of changes in a model community's metatranscriptome over time after exposure to a consortium of 5 fermented milk product (FMP) strains (40 samples); evaluation of the gene expression of the FMP strains in other in vitro conditions, including MRS medium (B. animalis subsp. lactis only, 4 samples) and a commercial FMP fermentation (all 5 strains, 6 samples); evaluation of the gene expression of native human microbiomes before and after the consumption of a commercial FMP (23 samples).


title: 5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging

status: Public on Oct 30 2011

city: Atlanta

first: Keith

last: Szulwach

state: GA

address: 615 Michael Street, Whitehead Suite 301

department: Human Genetics

institute: Emory University

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

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: 5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging [5hmC Capture and Seq]

summary: DNA methylation dynamics influence brain function and are altered in neurological disorders. 5-hydroxymethylcytosine (5-hmC), a DNA base derived from 5-methylcytosine (5mC) accounts for ~40% of modified cytosine in brain, and has been implicated in DNA methylation-related plasticity. Here we map 5-hmC genome-wide across three ages in mouse hippocampus and cerebellum, allowing assessment of its stability and dynamic regulation during postnatal neurodevelopment through adulthood. We find developmentally programmed acquisition of 5-hmC in neuronal cells. Epigenomic localization of 5-hmC-regulated regions reveals stable and dynamically modified loci during neurodevelopment and aging. By profiling 5-hmC in human cerebellum we establish conserved genomic features of 5-hmC. Finally, we implicate 5-hmC in neurodevelopmental disease by finding that its levels are inversely correlated with methyl-CpG-binding protein 2 (Mecp2) dosage, a protein encoded by a gene in which mutations cause Rett Syndrome. These data point toward critical roles for 5-hmC-mediated epigenetic modification in neurodevelopment and diseases.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Here we map 5-hmC genome-wide across three ages in mouse hippocampus and cerebellum, allowing assessment of its stability and dynamic regulation during postnatal neurodevelopment through adulthood. Profiling of 5-hmC in human cerebellum we establish conserved genomic features of 5-hmC. Finally, we implicate 5-hmC in neurodevelopmental disease by profiling 5-hmC in mouse cerebellum lacking MeCP2, a protein encoded by a gene in which mutations cause Rett Syndrome.

first: Peng

last: Jin


title: Jarid1b targets genes regulating development and is involved in neural differentiation [ChIP-seq]

status: Public on Oct 27 2011

city: Copenhagen

first: Sandra

middle: Ursula

last: Schmitz

address: Ole Maaløes Vej 5

country: Denmark

institute: Biotech Research and Innovation Centre

summary: We analyzed the genome-wide binding profile of Jarid1b in mouse ESCs. We find that Jarid1b localizes mainly to transcription start sites, of which more than 50% are also bound by Polycomb proteins and are enriched for genes encoding developmental regulators. Furthermore, we generated genome-wide mapping of H3K4me3 in LKO Scramble and LKO Jarid1b mouse ESCs. Virtually all Jarid1b binding sites are positive for H3K4me3. Upon knockdown of Jarid1b, H3K4me3 is significantly increased at Jarid1b positive regions.

overall_design: Examination of Jarid1b and H3K4me3 in mouse ES cells


title: Epigenome characterization at single base-pair resolution

city: Seattle

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

institute: Fred Hutchinson Cancer Research Center

summary: We have combined standard micrococcal (MNase) digestion of nuclei with a modified protocol for construction paired-end DNA sequencing libraries to map both nucleosomes and subnucleosome-sized particles at single base-pair resolution throughout the budding yeast genome. We found that partially unwrapped nucleosomes and subnucleosome-sized particles can occupy the same position within a cell population, suggesting dynamic behavior. By varying the time of MNase digestion, we have been able to observe changes that reflect differential sensitivity of particles, including eviction of nucleosomes. Our protocol and mapping method provide a general strategy for characterizing full epigenomes.

overall_design: We used micrococcal nuclease mapping, chromatin immunoprecipitation and paired-end sequencing to determine the structure of yeast centromeres at single base-pair resolution.

first: Jason

last: Belsky

first: Kristina

last: Krassovsky

first: David

last: MacAlpine

first: Steven


title: GlcNAcylation of histone H2B facilitates its monoubiquitination [Illumina Genome Analyzer data]

city: Tokyo

first: Ryoji

last: Fujiki

address: 1-1-1 yayoi, Bunkyo-ku

department: Institute of Molecular and Cellular Biosciences

country: Japan

institute: The university of Tokyo

summary: We report that histone GlcNAcylation of H2B S112 is a vital histone modification which facilitates histone monoubiquitination (ub). In a genome-wide analysis, H2B S112 GlcNAcylation sites were observed widely distributed over entire chromosomes including transcribed gene loci, together with co-localization of H2B S112 GlcNAcylation and K120 ub.

overall_design: Examination of H2B S112 GlcNAc and H2B K120 ub in HeLa S3 cells

first: Shigeaki

last: Kato


title: GlcNAcylation of histone H2B facilitates its monoubiquitination


title: RNA-Seq of Sorghum bicolor 9d seedlings in response to osmotic stress and abscisic acid

city: College Station

first: Patricia

last: Klein

department: Department of Horticulture

institute: Texas A&M University

summary: This study utilized next generation sequencing technology (RNA-Seq) to examine the transcriptome of sorghum plants challenged with osmotic stress and exogenous abscisic acid (ABA) to elucidate those genes and gene networks that contribute to sorghum's tolerance to water-limiting environments with a long-term aim of developing strategies to improve plant productivity under drought.

overall_design: We examined the mRNA of 9 day old Sorghum bicolor (BTx623) from 2 tissue types (roots and shoots) for 2 treatments (20µM ABA and 20% PEG) with corresponding controls (0.2M NaOH and H2O) for 27 hrs  prior to harvesting, each done in triplicate biological replicates -- resulting in 24 unique runs

first: Diana

middle: V

last: Dugas

first: Marcela

last: Monaco

first: Andrew

last: Olsen

first: Robert

middle: R

first: Sunita

last: Kumari

first: Doreen

last: Ware


title: Gene Expression Profiling of Human Embryonic Neural Stem Cells and Dopaminergic Neurons from Adult Human Substantia Nigra

city: Mansoura

first: Hany

middle: El Sayed

last: Marei

state: Dakahlaya

address: Gomhoraya

department: Histology

country: Egypt

institute: Fac. Vet Med

summary: Our goal was to develop a list of genes that could be used effectively to highlight the genomic profiling of human embryonic neural stem cells (hENSCs), and to identify genes involved in the process of their differentiation to dopaminergic (DA) neurons. Our results showed that Agilent's Whole Human Genome Oligonucleotide Microarray permits the monitoring of at least 41000 genes as cells differentiate. In this study, we identified 13525 genes to be differentially expressed between undifferentiated hENSC and DA cells isolated from human substansia nigra. Approximately 3737 genes were up-regulated in the embryonic NSC, and 4116 genes were up-regulated in DA cells. Careful analysis of the emerged data using the web-accessible program named Database for Annotation, Visualization and Integrated Discovery (DAVID) has permitted us to distinguish several genes and pathways that are involved in dopaminergic differentiation, and to identify the crucial signaling pathways that direct the process of differentiation. Our study elucidated that genes related to midbrain development, such as Nr4a2 (nuclear receptor subfamily 4, group A, member 2, Nurr1) and En1 (engrailed 1), were increased to 3.76- and 6.41-folds, respectively. In addition, the transcriptions of the genes for DA neuron phenotype, such as Ddc (doapmine decarboxylase, AADC), Slc6a3 (solute carrier family 6, member 3, DAT), and Th (tyrosine hydroxylase), were significantly increased to 8.08, 4.01, and 5.91, respectively. As data accumulate with different populations and different methods of differentiation, one will perhaps be able to identify the key regulators and biomarkers that may allow selective selection of limited number of genes or transcription factors to be used for direct reprogramming of NSC into DA cells, with an ultimate goal of obtaining different types of allogenic neurons including personalized DA neurons to be used in replacement therapy for neurodegenerative diseases such as Parkinson's disease (PD).

overall_design: Two-condition experiment: hENSC S vs. DA cells. Biological replicates: 2 hENSC, and 2 DA neuron samples from human substantia nigra cells.

first: Wenben

last: Deng

first: Nahla

last: Afifi


title: DNA methylation in the colon of Dnmt3b-induced and control mice

status: Public on Oct 26 2011

city: Cambridge

first: Eveline

last: Steine

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

summary: The methylation status of colon epithelial cells was profiled in wild type mice and mice expressing a Dnmt3b transgene.  Genome-scale methylation profiles were generated using reduced representation bisulfite sequencing (RRBS), with CpG methylation scored by promoter and also summarized by gene.  Dnmt3b expression is associated with a strong increase in de novo methylation of a discrete subset of "methylation sensitive" genes which show a strong concordance with genes methylated in human colon cancer.  These results, together with further analysis, indicate that colon epithelial cell methylation in the Dnmt3b mouse model predicts DNA methylation of human colon cancer with high confidence.

overall_design: Three each of Dnmt3b-induced and control mice, each split into two fractions.

first: E

first: G

last: Bell

first: R

last: Jaenisch

first: H

middle: G

last: Linhart


title: DNA methylation of dnmt3a deficient Kras lung tumors and dnmt3a wt Kras lung tumors

first: Qing

last: Gao

summary: To examine whether Dnmt3a deficiency resulted in genomic methylation changes we performed an unbiased methylome analysis. Methylated DNA isolated from three Dnmt3a deficient and two WT tumors was immunoprecipitated and subjected to high throughput sequencing (MeDIP-Seq). We observed that genes that were less expressed in Dnmt3a deficient tumors tended to have lower methylation levels in gene bodies.

overall_design: Examination of methylcytosine in two tumor types

first: M

middle: I

last: Barrasa

first: George

first: Rudolf


title: Identification and characterization of novel and conserved microRNAs in self-grafted and grafted watermelon by high-throughput sequencing

city: Hangzhou

last: Liu

address: No.198, Shiqiao Road, Jianggan District

country: China

institute: Zhejiang Academy of Agricultural Sciences

summary: In this study, Solexa sequencing technology has been used to discover small RNA populations of self-grafted watermelon and grafted watermelon (bottle gourd and squash were used as rootstocks). A total of 11,458,476, 11,614,094 and 9,339,089 raw reads representing 2,957,751, 2,880,328 and 2,964,990 unique sequences were obtained from the scions of self-grafted watermelon and watermelon grafted on-to bottle gourd and squash at two true-leaf stage, respectively. 39 known miRNAs belonging to 30 miRNA families and 80 novel miRNAs were identified in our small RNA dataset. Compared with self-grafted watermelon, 20 (5 known and 15 novel miRNAs) and 51 (21 known miRNAs and 30 novel miRNAs) miRNAs were expressed significantly different with higher abundance or lower abundance in watermelon grafted on to bottle gourd and squash, respectively. The differentially expressed miRNA target various transcriptional factors and other genes which involved in a wide range of biological processes. This study was firstly conducted to identify and compare miRNAs on genome-wide scale in watermelon grafting system. The miRNAs expressed differentially when watermelon was grafted onto different rootstocks suggesting that miRNAs might play an important role in diverse biological and metabolic processes in watermelon and grafting may possibly by changing miRNAs expression to regulate plant growth and response to stresses. The small RNA transcriptomes obtained in this study provided insights into molecular basis of miRNA regulation of genes expressed in self-grafted and grafted watermelon.

overall_design: Examination of 3 different small RNA expression profilings in self-grafted and grafted watermelon

first: Mingfang

last: Zhang


title: Retroviral mutagenesis in haploid ES cells

status: Public on Oct 25 2011

city: Vienna

first: Ulrich

last: Elling

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA

summary: Retroviral integration sites were mapped using inverse PCR to assess preferred integration sites of this virus in the genome after infection with the retrovirus and its impact on gene expression.

overall_design: Inverse PCR was applied on genomic DNA to identify retroviral integration sites. Inverse PCR allows to identify multiple genomic insertions of a gene trap virus in parallel.

first: Alexander

last: Stark

first: Andreas

last: Sommer

first: Josef

last: Penninger


title: Transposon-mediated gene regulatory network rewiring contributed to the evolution of pregnancy in mammals

city: Chicago

first: Vincent

middle: J.

last: Lynch

address: 920 E. 58th Street

institute: The University of Chicago

sample_organism:
Dasypus novemcinctus
Homo sapiens
Monodelphis domestica

overall_design: We report the gene expression profile of human endometriual stromal cells and armadillo endometrial samples generated with Illumina GA2

middle: J

first: Gunter

last: Wagner


title: Gene expression and DNA methylation of lung tumors in Dnmt3a deficient vs. WT mice


title: Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Terry Furey mailto:tsfurey@duke.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

These tracks display a synthesis of evidence from different assays as part of the four Open Chromatin track sets. This track displays open chromatin regions and/or transcription factor binding sites identified in multiple cell types by one or more complementary methodologies, DNaseI hypersensitivity (HS) (Duke DNaseI HS), Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (UNC FAIRE), and chromatin immunoprecipitation (ChIP) for select regulatory factors (UTA TFBS). Each methodology was performed on the same cell type using identical growth conditions. (Note: Data for some or all ChIP experiments may not be available for all cell types). Regions that overlap between methodologies identify regulatory elements that are cross-validated indicating high confidence regions.  In addition, multiple lines of evidence suggest that regions detected by a single assay (e.g., DNase-only or FAIRE-only) are also biologically relevant (Song et al., submitted).
DNaseI HS data: DNaseI is an enzyme that has long been used to map general chromatin accessibility, and DNaseI "hypersensitivity" is a feature of active cis-regulatory sequences.The use of this method has led to the discovery of functional regulatory elements that include promoters, enhancers, silencers, insulators, locus control regions, and novel elements. DNaseI hypersensitivity signifies chromatin accessibility following binding of trans-acting factors in place of a canonical nucleosome.
FAIRE data: FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements) is a method to isolate and identify nucleosome-depleted regions of the genome. FAIRE was initially discovered in yeast and subsequently shown to identify active regulatory elements in human cells (Giresi et al., 2007). Similar to DNaseI HS, FAIRE appears to identify functional regulatory elements that include promoters, enhancers, silencers, insulators, locus control regions and novel elements.
ChIP data: ChIP (Chromatin Immunoprecipitation) is a method to identify the specific location of proteins that are directly or indirectly bound to genomic DNA. By identifying the binding location of sequence-specific transcription factors, general transcription machinery components, and chromatin factors, ChIP can help in the functional annotation of the open chromatin regions identified by DNaseI HS mapping and FAIRE.
Input data: As a background control experiment, we sequenced the input genomic DNA sample that was used for ChIP. Crosslinked chromatin is sheared and the crosslinks are reversed without carrying out the immunoprecipitation step. This sample is otherwise processed in a manner identical to the ChIP sample as described below. The input track is useful in revealing potential artifacts arising from the sequence alignment process such as copy number differences between the reference genome and the sequenced samples, as well as regions of poor sequence alignability.

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:
For each site, the maximum F-Seq Density Signal value has been calculated for each assay that was performed in that cell type. F-Seq employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). Significant regions, or peaks, were determined by fitting the data to a gamma distribution to calculate p-values. Contiguous regions where p-values were below a 0.05 (DNaseI HS, ChIP) or 0.1 (FAIRE) threshold were considered significant. See assay specific description pages ( Duke DNaseI HS, UNC FAIRE and UTA TFBS) for more details.
A Fisher's Combined P-value for DNaseI HS and FAIRE was calculated using Fisher's combined probability test. First, a test statistic is calculated using the formula x^2 = -2*sum(ln(pi)) where pi are the p-values calculated for DNaseI HS and FAIRE. X2 follows a chi-squared distribution, thus a combined p-value can be assigned to this test statistic.

first: Terry

last: Furey

first: Zhancheng

first: Lingyun

last: Song

first: Greg

last: Crawford

first: Paul

last: Giresi

first: Jason

last: Lieb

first: Zheng

first: Ryan

last: McDaniell

first: Bum-Kyu

last: Lee

first: Vishy

last: Iyer

last: Flicek

first: Damian

last: Keefe

first: Ewan

last: Birney

first: Stefan

last: Graf


title: Widespread Generation of Alternative UTRs Contributes to Sex-specific RNA Binding by UNR

city: Milan

first: Giulio

last: Pavesi

address: Via Celoria 26

country: Italy

institute: Università di Milano

summary: Upstream of N-ras (UNR) is a conserved RNA-binding protein that regulates mRNA translation and stability by binding to sites generally located in untranslated regions (UTRs). In Drosophila, sex-specific binding of UNR to msl2 mRNA and the non-coding RNA roX plays key roles in the control of X-chromosome dosage compensation in both sexes. In order to investigate broader sex-specific functions of UNR, we have identified its RNA targets in adult male and female flies by high-throughput RNA binding and transcriptome analysis. Here we show that UNR binds to a large set of protein-coding transcripts and to a smaller set of non-coding RNAs in a sex-specific fashion.

overall_design: Two replicates of UNR IP were performed in D.melanogaster adult males and females, and enrichment in either sex was compared with IgG IP as control. To correlate sex-specific UNR binding with sex-specific transcription and splicing we performed RNA-Seq experiments in males and females.

first: Fatima

last: Gebauer

first: Marija

last: Mihailovic

first: Irina

last: Ablaza

first: Guglielmo

last: Roma

first: Federico

last: Zambelli

first: Laurence

last: Wurth

first: Cristina

last: Militti

first: Francesco

middle: M

last: Mancuso


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Nrl-/- Retinal Transcriptomes

city: BETHESDA

first: HARSHA

middle: KARUR

last: RAJASIMHA

state: MD

address: 6 CENTER DR RM 303D

department: ITMB

institute: NEI

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis.

Methods: Retinal mRNA profiles of 21-day-old wild-type (WT) and neural retina leucine zipper knockout (Nrl−/−) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays.

Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the retinas of WT and Nrl−/− mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and Nrl−/− retina, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling.

Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Retinal mRNA profiles of 21-day old wild type (WT) and Nrl-/- mice were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Matthew

last: Brooks

first: Harsha

middle: K

last: Rajasimha

first: Jerome

last: Roger

first: Anand

last: Swaroop


title: Transcriptomic profiling of a glioblastoma multiforme patient with matched control brain tissue

first: Leslie

last: Chen

address: 401 Terry Avenue North

institute: Institute for Systems Biology

summary: To investigate differential gene expression, we analyzed the entire transcriptomes of tumor and matched normal brain tissues obtained from a patient who had glioblastoma multiforme.  We extracted and sequenced the mRNA using Illumina GA2 platform. The raw data was analyzed using our recently developed program called RNASEQR, as well as ERANGE, MapSplice, SpliceMap, and TopHat.

overall_design: Tumor and matched control brain tissues were obtained from a Han-Chinese patient.

first: Kuo-Chen

last: Wei


title: Mobile 24 nt small RNAs direct transcriptional gene silencing in the root meristems of Arabidopsis thaliana

status: Public on Oct 24 2011

first: Krys

last: Kelly

address: Downing Street

department: Plant Sciences

institute: University of Cambridge

summary: We grafted Transcriptional Gene Silencing (TGS)-inducing wild type Arabidopsis and a mutant that is compromised in 24 nucleotide (nt) small RNA (sRNA) production onto a wild type reporter line. We observed that 21-24 nt sRNAs were transmitted across a graft union yet only the 24 nt sRNAs directed RNA-dependent DNA methylation (RdDM) and TGS of a transgene promoter in meristematic cells.

overall_design:
Analysis of sRNAs associated with mobile TGS by deep sequencing, biological replicates.
10 unique samples, 5 biological replicates.

first: Charles

middle: W

last: Melnyk

first: Attila

last: Molnar

first: Andrew

last: Bassett

first: David

middle: C

last: Baulcombe


title: miRNAs target conserved motifs of diverse genes encoding NB-LRRs to trigger trans-acting siRNAs in legumes.

city: St. Louis

first: Blake

middle: C.

last: Meyers

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: Trans-acting siRNAs (tasiRNAs) negatively regulate target transcripts and are characterized by siRNAs spaced in 21-nucleotide 'phased' intervals. TasiRNAs have not been extensively described in many plant species. We identified dozens of new miRNAs in Medicago and soybean and confirmed 119 Medicago targets. A search for phased tasiRNA-like small RNAs ('phasiRNAs') found at least 114 Medicago loci, the majority of which were NB-LRR encoding genes. Notably, conserved domains in NB-LRR-encoding RNAs  are targeted by several 22-nt miRNA families to trigger phasiRNA production. DCL2 and SGS3 transcripts were also cleaved by these 22-nt miRNAs, generating phased small RNAs, suggesting synchronization between silencing and pathogen defense pathways. A second example of 'two-hit' phasiRNA processing was identified, utilizing miR156-miR172 sites. Our data illustrate a complex tasiRNA-mediated regulatory circuit that potentially modulates plant-microbe interactions. A few miRNA triggers regulate an extremely large gene family by targeting highly conserved protein motif-encoding sequences, representing a new paradigm for miRNA function.

sample_organism:
Arachis hypogaea
Glycine max
Medicago truncatula
Phaseolus vulgaris

overall_design: Examination of different tissue types in legumes (Medicago, soybean, common bean, peanut) by high throughput sequencing for small RNA profiling

first: Jixian

last: Zhai


title: Oncogenic ETS proteins replace activated Ras/MAPK signaling in prostate cells.

status: Public on Oct 20 2011

city: Bloomington

first: Peter

last: Hollenhorst

state: IN

address: 1001 E Third St, Jordan Hall 104

institute: Indiana University

summary: Approximately 50% of prostate cancers have chromosomal translocations resulting in the over-expression one of four ETS family transcription factors. However, it is not known why these four four family members are selected for oncogenic roles, while other ETS proteins are not.  We found that the four oncogenic ETS family members have a specific role in prostate cell migration.  Using chromatin immunoprecipitation coupled with next-generation sequencing, this specific biological function was matched to a specific set of genomic targets highlighted by the presence of an AP-1 binding site.  ETS/AP-1 binding sites are prototypical Ras-responsive elements, but oncogenic ETS proteins could activate a Ras/MAPK transcriptional program in the absence of MAPK activation.  These findings indicate that the specific function of ETS proteins over-expressed in prostate cancer is the activation of a Ras/MAPK gene expression program in the absence of signaling pathway mutations.

overall_design: ChIP sequencing two transcription factors in PC3 cells, four transcription factors plus a FLAG control in RWPE-1 cells and input DNA sequencing from each cell line.

first: Barbara

last: Graves


title: Genome-wide analyses of Su(Hw) binding in Drosophila ovary

status: Public on Oct 19 2011

city: Iowa City

first: Alexey

last: Soshnev

state: Iowa

address: 3159C MERF 375 Newton Rd

institute: University of Iowa

summary: The twelve zinc finger Suppressor of Hairy-wing [Su(Hw)] protein binds thousands of sites in Drosophila genome and is essential for the function of the gypsy insulator. Loss of the globally expressed Su(Hw) protein causes female sterility due to tissue-specific defect limited to female germline. Using chromatin immunoprecipitation followed by next generation sequencing (ChIP-Seq), we determine the extent of tissue-specific binding of Su(Hw) in Drosophila ovary. We demonstrate that Su(Hw) binding sites (SBSs) are largely constitutively occupied in the germline and soma. Our analyses indicate that SBSs fall into several non-uniform classes, as determined by the partner protein distribution and DNA sequence conservation. Further, we show that only a subset of SBSs is required for the female fertility. These sites are maintained in the su(Hw)f zinc finger 10 mutant background, which is fertile but does not support gypsy insulator function. Together, our data are consistent with the model where Su(Hw) serves multiple regulatory roles in the genome, and contribute to understanding of how loss of a single zinc finger affects chromosome localization of a DNA binding protein.

overall_design: Examination of Su(Hw) localization in the ovaries of less than 6 hour old  wild type and su(Hw)f mutant Drosophila females

first: Pamela

last: Geyer


title: Systems analysis of Chlamydomonas Cu nutrition reveals connections between Cu and multiple O2-dependent metabolic steps

city: Los Angeles

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

summary: We used digital gene expression (NlaIII sequence tags) and RNA-Seq to compare the transcriptomes of Cu-replete vs. Cu–deficient Chlamydomonas wild-type cells to reveal dozens of mRNAs whose abundance is modified. Half of the corresponding genes are targets of CRR1, a master regulator of nutritional copper sensing, and are associated with candidate CRR1 binding sites. The targets include many plastid-localized proteins, like FDX5 encoding a ferredoxin isoform, and CGL78, encoding a protein conserved in the green lineage, indicative of modified plastid metabolism. Immunoblot analysis and proteome profiles recapitulate the transcriptome profiles. New evidence for Cu sparing is suggested by up-regulation of AOF1 encoding a copper-independent but flavin-dependent amine oxidase and down-regulation of two metal- binding proteins. Genes encoding redox proteins, many of which function in lipid metabolism, are over-represented, which is compatible with the role of Cu in biology. Lipid profiles indicate a CRR1-dependent increase in Cu-deficient cells in the proportion of unsaturated (16:2, 16:3, 16:4, 18:2) fatty acids at the expense of the more saturated (16:0, 16:1, 18:0) precursors, especially on plastid galactolipids, which validates the increased expression of acyl-ACP and plastid-localized w-6 desaturases. CRR1-independent changes in the transcriptome suggest a role for Cu in oxygen sensing in Chlamydomonas.

overall_design:
Sampling of Chlamydomonas CC-1021 (2137) and  crr1-2, crr1:CRR1 mutant cells (the mutant is knock-down for the transcription factor crr1, which plays a key role in the transcriptional response to copper levels) cultivated in TAP or minimal medium under Cu-sufficient (control) and Cu-defficient conditions.
poly-A purification, NlaIII digestion/random fragmentation

first: Madeli

last: Castruita

last: Casero

first: Steven

last: Karpowicz

first: Janette

last: Kropat

first: Astrid

last: Vieler

first: Scott

last: Hsieh

first: Weihong

last: Yan

first: Shawn

last: Cokus

first: Joseph

last: Koo

first: Christoph

last: Benning

first: Matteo

last: Pellegrini

middle: S


title: Jarid1b targets genes regulating development and is involved in neural differentiation

first: Sandra

last: Schmitz

address: Ole Maaløes Vej 5

institute: Biotech Research and Innovation Centre

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

overall_design: Refer to individual Series


title: A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii

summary: Interest in exploiting algae as a biofuel source and the role of nutrient deficiency in inducing triacylglyceride (TAG) accumulation in cells necessitates a strategy to efficiently formulate species-specific culture media that can be easily manipulated. Using the reference organism Chlamydomonas reinhardtii, we tested the hypothesis that modeling trace element supplements on the ionomes of cells would result in optimized cell growth. We characterized the ionomes of multiple wild-type Chlamydomonas strains in various culture conditions and developed a revised trace element solution to parallel our measurements. Comparison of cells growing in the revised supplement versus a traditional trace element solution revealed faster growth rates and higher maximum cell densities with the revised recipe. RNA-seq analysis of cultures growing in the traditional versus revised medium suggest that the variation in transcriptomes was smaller than that found between laboratories using the same supplement.  Visual observation did not reveal defects in cell motility or mating efficiency. Ni2+-inducible expression from the CYC6 promoter remained a useful tool, albeit with an increased amount of Ni2+ supplementation due to the introduction of an EDTA buffer system in the revised medium. Equilibrium modeling of the revised supplement predicts less metal precipitation in the revised medium. Other advantages include more facile preparation of trace element stock solutions that can readily be adapted for deficiency studies, a reduction in total chemical use, a more consistent batch-to-batch formulation, and long-term stability (up to 5 years). Under the new growth regime, we analyzed cells growing under different macro- and micronutrient-deficiencies. In N and S deficiency, cells accumulate TAG as well in the new medium as previously demonstrated. Fe and Zn deficiency also induced TAG accumulation as suggested by Nile Red and Bodipy staining. This ionomic approach can be used to efficiently optimize culturing conditions for other algal species to improve growth and assay cell physiology.

overall_design: Sampling of Chlamydomonas CC-1021 (2137) cultivated in TAP medium supplemented with a revised trace element recipe based on ionomic data.

first: Anne

last: Hong-Hermesdorf

first: David

first: Petr

last: Ent

middle: D

first: Davin

last: Malasarn


title: Expression profile of third instar larval salivary gland tissue

status: Public on Oct 18 2011

first: Terry

middle: L.

last: Orr-Weaver

institute: Whitehead Institute for Biomedical Research

summary: We use mRNA-seq to transcriptionally profile larval salivary gland tissue from Drosophila third instar larvae. These data provide insights into tissue physiology and can be used to identify tissue specific transcripts.

overall_design: Salivary glands were dissected from 200 wandering third instar larvae and the associated fat body was removed.Salivary glands were transferred to Graces unsupplemented medium on ice prior to RNA extraction with TRIzol reagent. mRNA-seq samples were prepared from 10 ug of total RNA and subject to Illumina based sequencing.

first: Noa

last: Sher

first: Sharon

last: Li

first: George

last: Bell

first: Jared

last: Nordman

first: Thomas

last: Eng

first: Mathew

last: Eaton

last: MacAlpine

middle: L


title: Identification of stromally expressed molecules in the prostate by Tag profiling of cancer-associated fibroblasts, normal fibroblasts and fetal prostate

status: Public on Oct 22 2011

city: Edinburgh

first: Axel

last: Thomson

address: 47 Little France Crescent

institute: MRC Human Reproductive Sciences Unit

summary: The stromal microenvironment plays key roles in prostate development and cancer. Cancer associated fibroblasts (CAFs) and other stromal cells stimulate tumourigenesis via several mechanisms including the expression of pro-tumourigenic factors. Mesenchyme (embryonic stroma) controls prostate organogenesis, and in some circumstances can re-differentiate prostate tumours. Epithelia are regulated by powerful paracrine signalling from the stroma in both development and disease, and identification of these stromal signals is important.  We have applied next-generation Tag profiling to fetal human prostate, normal human prostate fibroblasts (NPFs) and CAFs to identify molecules expressed in prostatic stroma

overall_design: Each sample was used for Tag library construction, by Solexa Inc

middle: A


title: Deep sequencing of pyrethroid-resistant bed bugs reveals multiple mechanisms of resistance within a single population

city: Blacksburg

first: Zach

middle: N.

last: Adelman

state: VA

address: 305 Fralin Life Science Institute

department: Entomology

institute: Virginia Tech

summary: A frightening resurgence of bed bug infestations has occurred over the last 10 years in the US. Current chemical methods have been inadequate for controlling bed bugs due to widespread insecticide resistance. Little is known about the mechanisms of resistance present in US bed bug populations, making it extremely difficult to develop intelligent strategies to control this pest. We have identified bed bugs collected in Richmond, VA which exhibit both kdr-type (L925I) and metabolic resistance to pyrethroid insecticides. LD50 bioassays determined resistance ratios of ~6000-fold to the insecticide deltamethrin, with contact bioassays confirming cross-resistance to several other labeled formulations. To identify metabolic genes potentially involved in the detoxification of pyrethroids, we performed deep-sequencing of the adult bed bug transcriptome, obtaining more than 2.5 million reads on the 454 titanium platform. Following assembly, analysis of newly identified gene transcripts in both Harlan (susceptible) and Richmond (resistant) bed bugs revealed several candidate cytochrome P450 and carboxyesterase genes which were significantly over-expressed in the resistant strain, consistent with the idea of increased metabolic resistance. These data will accelerate efforts to understand the biochemical basis for insecticide resistance in bed bugs, and provide molecular markers to assist in the surveillance of metabolic resistance.

overall_design: Deep sequencing was performed from total RNA isolated from adult male bed bugs using the Titanium 454 platform

middle: N


title: Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells [new ChIP-Seq samples]

city: Austin

first: Vishy

last: Iyer

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary:
Cellular diversity in a multicellular organism like the human is achieved in part by distinct programs of gene expression at the level of transcription, which in turn are mediated by transcription factors (TFs). However, there are few systematic studies of the genomic binding of different types of TFs across a wide range of human cell types, especially in relation to gene expression. Using chromatin Immunoprecipitation followed by thigh-throughput sequencing (ChIP-seq) we identified an average of 45,000, 30,000 and 8,000 binding sites for CTCF, Pol2 and MYC respectively across eleven cell types.CTCF preferred to bind to intergenic regions while Pol2 and MYC tended to bind to core promoter regions. CTCF sites were highly conserved across diverse cell types, whereas MYC showed the greatest cell-type specificity. MYC co-localized with Pol2 at many of their binding sites and putative target genes. Cell-type specific binding sites, in particular for MYC and Pol II, were associated with cell-type specific functions. Patterns of binding in relation to gene features were generally invariant across different cell types. Pol II occupancy was higher over exons than adjacent introns, likely reflecting a link between transcriptional elongation and splicing. TF binding was positively correlated with the expression levels of their putative target genes, but combinatorial binding, in particular of MYC and Pol II was even more strongly associated with higher gene expression. Our ChIP-seq data sheds considerable light on how these transcription factors of different types function individually and in combination with one another to occupy target genomic loci and shape gene expression programs in a cell-type specific manner.

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: Genome binding/occupancy profiling by high throughput sequencing

overall_design:
ChIP-seq were performed on eleven human cell lines: GM12878 (lymphoblastoid), K562 (leukemia), HepG2 (hepatocellular carcinoma), HelaS3 (cervical carcinoma), HUVEC (human umbilical vein endothelial cells), NHEK (keratinocytes), H1-ES (embryonic stem cells), MCF7 (breast adenocarcinoma), FB8470 (Normal child fibroblasts), FB0167P (Progeria fibroblast), and H54 (glioblastoma). For each cell line, two or three replicates were independently grown and split into three, one for each of the three experimental methods.  Control ChIP experiments were performed on five of the cell lines with NHEK and H1-ES being excluded due to lack of material.

Additional ChIP-Seq data mentioned in the 'overall design' but not included in this Series are contained in the GSE30226 SubSeries.

first: Terrence

last: Furey

first: Vishwanath

middle: R

first: Gregory

middle: E

last: Crawford


title: Derivation of Rhesus Monkey Parthenogenetic Embryonic Stem Cells and its MicroRNA Signature

city: kunming

first: zhenghua

last: sun

address: jiaochangdong road 32#

institute: kunming institute of zoology.CAS

summary: We derived two novel rpESC lines and characterized their microRNA signature by Solexa deep sequencing. By characterizing their microRNA signature, we identified 91 novel microRNAs, except those are also detected in other primate ESCs. Moreover, these two novel rpESCs display a unique microRNA signature, comparing to their biparental counterpart ESCs.

overall_design: Examination of 2 different small RNA expression profilings in 2 rhesus parthenogenetic embryonic stem cell lines

first: Zhenghua

last: Sun


title: Analysis of Transcriptome Complexity via RNA-Seq in Normal and Failing Murine Hearts

first: Jae-Hyung

last: Lee

address: 611 Charles E. Young Drive

department: Department of Integrative Biology and Physiology

institute: University of California, Los Angeles

summary: Accurate and comprehensive de novo transcriptome profiling in heart is a central issue to better understand cardiac physiology and diseases. Although significant progress has been made in genome-wide profiling for quantitative changes in cardiac gene expression, current knowledge offers limited insights to the total complexity in cardiac transcriptome at individual exon level. To develop more robust bioinformatic approaches to analyze high-throughput RNA sequencing (RNA-Seq) data, with the focus on the investigation of transcriptome complexity at individual exon and transcript levels. In addition to overall gene expression analysis, the methods developed in this study were used to analyze RNA-Seq data with respect to individual transcript isoforms, novel spliced exons, novel alternative terminal exons, novel transcript clusters (i.e., novel genes) and long non-coding RNA genes. We applied these approaches to RNA-Seq data obtained from mouse hearts following pressure-overload induced by trans-aortic constriction. Based on experimental validations, analyses of the features of the identified exons/transcripts, and expression analyses including previously published RNA-Seq data, we demonstrate that the methods are highly effective in detecting and quantifying individual exons and transcripts. Novel insights inferred from the examined aspects of the cardiac transcriptome open ways to further experimental investigations. Our work provided a comprehensive set of methods to analyze mouse cardiac transcriptome complexity at individual exon and transcript levels. Applications of the methods may infer important new insights to gene regulation in normal and disease hearts in terms of exon utilization and potential involvement of novel components of cardiac transcriptome.

overall_design: Left ventricular tissues were collected from C57BL/6 mice after 1 week (hypertrophy stage, HY) and 8 weeks post trans-aortic constriction (TAC) procedure (heart failure stage, HF), respectively, and their corresponding Sham controls (Sham-HY, Sham-HF). To conduct RNA-Seq analysis, total RNAs from six TAC and Sham-operated mice at the HY stage and four TAC and corresponding Sham mice at the HF stage were obtained.

first: Chen

last: Gao

first: Guangdun

last: Peng

first: Christopher

last: Greer

first: Shuxun

last: Ren

first: Yibin

last: Wang

first: Xinshu

last: Xiao


title: ChIP-Seq of ORC2 bound to third instar salivary gland DNA in WT and mutant Drosophila, analyzed by Illumina sequencing

first: Terry

last: Orr-Weaver

address: 9 Cambridge Center

summary: We analyzed ORC2 ChIP-Seq from hand dissected salivary glands of wandering third instar larvae from OrR or SuUR Drosophila. Goals were to ascertain the difference in binding profile between salivary glands expressing and not expressing the Supressor of UnderReplication protein.

overall_design: One replicate is included for each of OrR (WT) or SuUR salivary glands.

first: Noa

last: Sher


title: Developmental Control of Gene Copy Number by Repression of Replication Initiation and Fork Progression

type: Genome variation profiling by genome tiling array


title: Transcript profiling reveals expression differences in wild-type and glabrous soybean lines

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: Two high throughput transcript sequencing methods, Digital Gene Expression (DGE) Tag Profiling and RNA-Seq, were used to compare the transcriptional profiles in wild-type (cv. Clark standard, CS) and a mutant (cv. Clark glabrous, i.e., trichomeless or hairless, CG) soybean isoline that carries the dominant P1 allele. DGE data and RNA-Seq data were mapped to the cDNAs (Glyma models) predicted from the reference soybean genome, Williams 82. Extending the model length by 250 bp at both ends resulted in significantly more matches of authentic DGE tags indicating that many of the predicted gene models are prematurely truncated at the 5’ and 3’ UTRs. The genome-wide comparative study of the transcript profiles of the wild-type versus mutant line revealed a number of differentially expressed genes. One highly-expressed gene, Glyma04g35130, in wild-type soybean was of interest as it has high homology to the cotton gene GhRDL1 gene that has been identified as being involved in cotton fiber initiation and is a member of the BURP protein family. Sequence comparison of Glyma04g35130 among Williams 82 with our sequences derived from CS and CG isolines revealed various SNPs and indels including addition of one nucleotide C in the CG and insertion of ~60 bp in the third exon of CS that causes a frameshift mutation and premature truncation of peptides in both lines as compared to Williams 82.

overall_design: 2 samples examined: Clark standard (wild type) and Clark glabrous (soybean hairless mutant)

middle: O

first: Navneet

last: Kaur

first: Matt

last: Hunt


title: Characterization of miRNA expression in response to short-term waterlogging in Maize roots

status: Public on Oct 15 2011

city: Cold Spring Harbor

first: Zhijie

last: Liu

state: New York

address: One Bungtown RD

institute: Cold Spring Harbor Labs

summary: Waterlogging of plants leads to low oxygen levels (hypoxia) in the roots and causes a metabolic switch from aerobic respiration to anaerobic fermentation that results in rapid changes in gene transcription and protein synthesis. Our research seeks to characterize the gene regulatory networks associated with short-term waterlogging. MicroRNAs (miRNAs) are small non-coding RNAs that regulate many genes involved in growth, development and various biotic and abiotic responses. To characterize the involvement of miRNAs in response to hypoxia conditions, a quantitative reverse transcriptase PCR (qRT-PCR) assay was used to profile the expression changes of the 22 candidate mature miRNAs, which were selected from small RNA library of waterlogging resistant line Hz32 and 84 of their predicted targets in three inbred Zea mays lines that showed different tolerance to waterlogging.  Based on our studies, miR164, miR167, miR172, miR408 and miR528, which are involved in aerenchyma and root cap formation, lateral root development, root/shoot elongation and plant cell detoxification, found to be key regulator under short-term waterlogging conditions in three inbred lines. Further, computational approaches were used to predict the stress-related cis-regulatory elements on the promoters of these miRNAs using the B73 reference and a miRNA-mediated gene regulatory network was constructed. The differential expression patterns of miRNAs and their targets in these three inbred lines suggest that the miRNAs are active participants in the signal transduction at the early stage of hypoxia conditions via a complex network and biochemical pathways. Our study also suggests that there might be a miRNA-mediated energy-saving strategy in surviving from waterlogging.

overall_design: Examination of miRNA expression in maize root under 4h waterlogging treatment

first: Jer-Ming

last: Chia

first: Lifang

last: Zhang

first: Yonglian

last: Zheng

first: Doreen

last: Ware


title: Glucosylated hydroxymethyluracil (DNA base J) prevents transcriptional read-through in Leishmania

city: SEATTLE

first: Gowthaman

last: Ramasamy

state: WASHINGTON

address: 307 WESTLAKE AVE N

department: GHBC

institute: SEATTLE BIOMEDICAL RESEARCH INSTITUTE

summary: Some T's in nuclear DNA of trypanosomes and Leishmania are hydroxylated and glucosylated to yield base J (β-D-glucosyl-hydroxymethyluracil). In Leishmania about 99% of J is located in telomeric repeats. We show here that most of the remaining J is located at chromosome-internal RNA Polymerase II termination sites. Both this internal J and telomeric J can be reduced by a knockout of J-binding protein 2 (JBP2), an enzyme involved in the first step of J biosynthesis. J levels are further reduced by growing Leishmania JBP2 knockout cells in BrdU-containing medium, resulting in cell death. The loss of internal J is accompanied by massive read-through at RNA Polymerase II termination sites. The degree of read-through varies between transcription units, but may extend over 100 kb. We conclude that J is required for proper transcription termination and infer that the absence of internal J kills Leishmania by massive read-through of transcriptional stops.

sample_organism:
Leishmania major
Leishmania tarentolae

platform_organism:
Leishmania major
Leishmania tarentolae

overall_design: We determined the exact location of base J in the genome of Leishmania by high-throughput sequencing of J containing DNA fragments. Samples were enriched for J-containing fragments by two independent methods: ChIP using an anti-J DNA antibody or by binding to a the J-binding protein JBP1. We studied the effect of loss of J on transcription using WT, JBP2 knockout (30-37% of WT level J), and JBP2 knockout cells grown in BrdU containing medium (13-16% of WT level of J). We used 6 RNA-seq libraries (three samples & two replica each) containing processed RNA products (transspliced and poly-adenylated) and 3 small RNA libraries representing the entire transcriptome.

first: Henri

middle: G

last: van Luenen

first: Carol

last: Farris

first: Sabrina

last: Jan

first: Paul-Andre

last: Genest

first: Pankaj

last: Tripathi

first: Arno

last: Velds

first: Ron

middle: M

last: Kerkhoven

first: Marja

last: Nieuwland

first: Andrew

last: Haydock

first: Saara

last: Vainio

first: Tatjana

last: Heidebrecht

first: Anastassis

last: Perrakis

first: Ludo

last: Pagie

first: Bas

last: van Steensel

first: Peter

middle: J

last: Myler

first: Piet

last: Borst


title: Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells

first: Vishy

last: Iyer

state: TX

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

This SuperSeries is composed of the SubSeries listed below.

relation:
SuperSeries of: GSE19622
SuperSeries of: GSE25416
SuperSeries of: GSE30226
SuperSeries of: GSE32692