title: Identification of Transcription Factor PHA-4::GFP Binding Regions in YA

first: DCC

last: modENCODE

summary:
modENCODE_submission_3161
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP37 (official name : OP37 genotype : unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. made_by : R. Waterston and S. Kim ); Developmental Stage: Young Adult; Genotype: unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage Young Adult; Target gene pha-4; Strain OP37 (official name : OP37 genotype : unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. made_by : R. Waterston and S. Kim ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

first: Mike

last: Snyder


title: 24 Hour RNA PolII ChIP-Seq experiment

status: Public on Mar 23 2011

city: Toronto

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
modENCODE_submission_3251
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes.  These experiments will be conducted in multiple cell types and developmental tissues.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Developmental Stage: Mixed Embryos 0-24h;  EXPERIMENTAL FACTORS: Developmental Stage Mixed Embryos 0-24h; Antibody  (target is PolII); read length (read_length 36)

first: David

last: MacAlpine

first: Heather

first: Matthew

last: Eaton

first: Joseph

last: Prinz


title: RNA-Seq transcriptome profiling of in vitro cultures of migrating porcine primordial germ cells and porcine fetal fibroblasts of mini pig embryos between days 17-24 of gestation

status: Public on Mar 24 2011

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen, RIMLS

type: Expression profiling by high throughput sequencing

summary: Porcine embryonic germ cells (EGC) are cultured pluripotent cells derived from primordial germ cells (PGC). This study explored the possibilities to establish porcine EGC lines in the domestic breed pig more efficiently and from earlier embryonic stages than reported to date. In vitro culture of PGC from both pooled and individual embryos at days 17-24 of gestation resulted in the successful derivation of putative EGC lines from days 20-24 with high efficiency, while no lines could be established from days 17-18. The EGC-like colonies had characteristic morphology and electron microscopy revealed tight junctions and presence of primary cilia on the cell surfaces.  The cells formed simple embryoid bodies in suspension culture and further differentiated into epithelial-like, mesenchymal-like, and neuronal-like cells. Our results show that putative porcine EGC can be derived from migrating PGC with high efficiency using individual embryos from different genetic backgrounds.

overall_design: RNA-Seq profiling of 2 different in vitro cultures of pig embryonic cells. The cells, both the pig Embryonic Germ cells (pEGCs) and the pig Fetal Fibroblasts (pFF) show properties of pluripotency and self renewal.

first: Stoyan

middle: G

last: Petkov

first: Tino

last: Klein

first: Yu

last: Gao

first: Rodrigo

middle: S

last: Garcia

first: Henk

last: Stunnenberg

first: Maddox-Hyttel

last: Poul


title: Phosphorylation of p53 Serine 46 contributes to target gene selectivity of p53

first: Marion

last: Lohrum

institute: NCMLS

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

overall_design: Refer to individual Series


title: Phosphorylation of p53 Serine 46 contributes to target gene selectivity of p53 (ChIP-seq)

summary: The tumor suppressor p53 plays a crucial role in cellular growth control inducing a plethora of cellular response pathways. The molecular mechanisms that discriminate between the distinct p53-responses towards different stress treatments have remained largely elusive. Here, we have analyzed the p53-regulated pathways induced by two chemotherapeutical treatments, Actinomycin D inducing growth arrest and Etoposide resulting in apoptosis. We found that the genome-wide p53-binding patterns are almost identical upon both treatments notwithstanding transcriptional differences that we observed in genome-wide transcriptome analysis. To assess the role of post-translational modifications in target gene choice and activation we investigated the extent of phosphorylation of Serine 46 of p53 bound to DNA (p53-pS46), a modification that has been linked to apoptosis-pathways, and the extent of phosphorylation of Serine 15 (p53-pS15), a general p53-activation mark. Interestingly, the overall extent of S46 phosphorylation of p53 bound to DNA is considerably higher in cells directed towards apoptosis while the degree of phosphorylation at S15 of DNA bound p53 remains highly similar upon both treatments. Moreover, our data suggest that, following different chemotherapeutical treatments, the extent of chromatin-associated p53 phosphorylated at S46 but not at pS15 is higher on certain apoptosis related target genes, including the BAX and PUMA genes. These data provide evidence that cell fate decisions are not made primarily on the level of general p53 DNA-binding, but possibly through post-translational modifications of chromatin bound p53.

overall_design: ChIP-seq profiles of p53, p53phosphorylated at Serine 15 (p53-pS15) and p53 phosphorylated at Serine 46 (p53-pS46) in U2OS cells treated with either Actinomycin D or Etoposide.

first: Leonie

last: Smeenk

first: Simon

middle: J

last: van Heeringen

first: Max

last: Koeppel

first: Eva

middle: M

last: Janssen-Megens


title: MCM S2-DRSC ChIP-Seq experiment

first: DCC

last: modENCODE

summary:
modENCODE_submission_2979
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes.  These experiments will be conducted in multiple cell types and developmental tissues.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody  (target is ); read length (read_length)


title: Mapping and analysis of chromatin state dynamics in nine human cell types (ChIP-Seq)

city: Los Angeles

first: Jason

last: Ernst

state: CA

address: 615 Charles E Young Dr South

department: Biological Chemistry

country: USA

institute: UCLA

summary: Chromatin profiling has emerged as a powerful means for annotating genomic elements and detecting regulatory activity. Here we generate and analyze a compendium of epigenomic maps for nine chromatin marks across nine cell types, in order to systematically characterize cis-regulatory elements, their cell type-specificities, and their functional interactions. We first identify recurrent combinations of histone modifications and use them to annotate diverse regulatory elements including promoters, enhancers, transcripts and insulators in each cell type. We next characterize the dynamics of these elements, revealing meaningful patterns of activity for promoter states and exquisite cell type-selectivity for enhancer states. We define multi-cell activity profiles that reflect the patterns of enhancer state activity across cell types, as well as analogous profiles for gene expression, regulatory motif enrichments, and expression of the corresponding regulators. We use correlations between these profiles to link enhancers to putative target genes, to infer cell type-specific activators and repressors, and to predict and validate functional regulator binding motifs in specific chromatin states. These functional annotations and regulatory predictions enable us to revisit intergenic single-nucleotide polymorphisms (SNPs) associated with human disease in genome-wide association studies (GWAS). We find that for several diseases, top-scoring SNPs are precisely positioned within enhancer elements specifically active in relevant cell types. In several cases a disease variant affects a motif instance for one of the predicted causal regulators, thus providing a potential mechanistic explanation for the disease association. Our study presents a general framework for applying multi-cell chromatin state analysis to decipher cis-regulatory connections and their role in health and disease.

overall_design: CTCF, H3K27ac, H3K27me3, H3K4me1, H3K4me2, H3K4me3, H3K9ac, H4K20me1, H3K36me3 and Whole Cell Extract (WCE) were profiled with ChIP-seq  in 9 cell types (H1, GM12878, K562, HepG2, Huvec, HSMM, NHLF, NHEK, HMEC) in almost all cases in duplicate. Also H3K9me3 was profiled with ChIP-seq in K562.

first: Pouya

last: Kheradpour

first: Tarjei

last: Mikkelsen

first: Noam

last: Shoresh

first: Lucas

middle: D

last: Ward

first: Charles

middle: B

last: Epstein

first: Xiaolan

last: Zhang

first: Li

last: Wang

first: Robbyn

last: Issner

first: Michael

last: Coyne

first: Manching

last: Ku

first: Timothy

last: Durham

first: Manolis

last: Kellis

first: Bradley

middle: E

last: Bernstein


title: SG ORC ChIP-Seq experiment

summary:
modENCODE_submission_3253
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes.  These experiments will be conducted in multiple cell types and developmental tissues.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: SuUR - Orr-Weaver(official name : SuUR genotype : SuUR mutant outcross : 3 tags : Transposon tag : GFP description : SuUR mutant as maintained by the Orr-Weaver lab. made_by : Orr-Weaver ); Tissue: salivary gland; Developmental Stage: L3 stage wandering larvae; Genotype: SuUR mutant;  EXPERIMENTAL FACTORS: read length (base pair 36) ; tissue: salivary glands; Developmental Stage L3 stage wandering larvae; Antibody  (target is dORC2); strain: SuUR

first: David

last: MacAlpine

first: Sher

last: Noa

last: Sharon

first: Bell

last: George

first: Matthew

last: Eaton

first: Joseph

last: Prinz


title: 24 Hour ORC ChIP-Seq experiment

first: DCC

last: modENCODE

summary:
modENCODE_submission_3247
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes.  These experiments will be conducted in multiple cell types and developmental tissues.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Developmental Stage: Mixed Embryos 0-24h;  EXPERIMENTAL FACTORS: Developmental Stage Mixed Embryos 0-24h; Antibody  (target is dORC2); read length (read_length 36)

first: Heather


title: Electron acceptor-dependent identification of key anaerobic toluene degraders at a tar-oil contaminated aquifer by Pyro-SIP

status: Public on Mar 18 2011

city: Neuherberg

first: Giovanni

last: Pilloni

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz-Centre Munich

type: Non-coding RNA profiling by high throughput sequencing

summary: Bioavailability of electron acceptors is probably the most limiting factor in the restoration of anoxic, contaminated environments. The oxidation of contaminants such as aromatic hydrocarbons, particularly in aquifers, often depends on the reduction of ferric iron or sulphate. We have previously detected a highly active fringe zone beneath a toluene plume at a tar-oil contaminated aquifer in Germany, where a specialized community of contaminant degraders co-dominated by Desulfobulbaceae and Geobacteraceae had established. Although on-site geochemistry links degradation to sulphidogenic processes, dominating catabolic (benzylsuccinate synthase alpha-subunit, bssA) genes detected in situ appeared more related to those of Geobacter spp. Therefore, a stable isotope probing (SIP) incubation of sediment samples with 13C7-toluene and comparative electron acceptor amendment was performed. We introduce pyrosequencing of templates from SIP microcosms as a powerful new strategy in SIP gradient interpretation (Pyro-SIP). Our results reveal the central role of Desulfobulbaceae for sulphidogenic toluene degradation in situ, and affiliate the detected bssA genes to this lineage. This, and the absence of 13C-labelled DNA of Geobacter spp. in SIP gradients preclude their relevance as toluene degraders in situ. In contrast, Betaproteobacteria related to Georgfuchsia spp. became labelled under iron-reducing conditions. Furthermore, secondary toluene degraders belonging to the Peptococcaceae detected in both treatments suggest the possibility of functional redundancy amongst anaerobic toluene degraders on site.

overall_design: 2 samples examined from the different electron-acceptors (sulphate or ferric iron) incubates at the time point of maximal toluene degradation.

first: Frederick

last: von Netzer

first: Marion

last: Engel

first: Tillmann

last: Lueders


title: Functional non-canonical microRNAs in the mammalian hippocampus and cortex

city: San Francisco

first: Robert

last: Blelloch

address: 513 Parnassus Avenue, Campus Box #0525

institute: University of California, San Francisco

summary: Non-canonical microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs) are distinct subclasses of small RNAs that bypass the DGCR8/Drosha Microprocessor but still require Dicer for their biogenesis.  What, if any, role they have in mammals remains unknown.  To identify potential roles for these Microprocessor-independent, Dicer-dependent small RNAs, we compared the phenotypes resulting from conditional deletion of dgcr8 versus dicer in post-mitotic neurons.  Loss of dicer resulted in an earlier lethality, more severe structural abnormalities, and increased apoptosis relative to dgcr8 loss.  Deep sequencing of small RNAs from the hippocampus and cortex of the conditional knockouts and control littermates identified multiple novel non-canonical microRNAs including new mirtrons H/ACA box snoRNA-derived small RNAs, and a previously unidentified mammalian subclass derived from C/D box snoRNAs.  These non-canonical miRNAs were expressed at high levels in the brain relative to other tissues. In contrast, we found no evidence for endo-siRNAs in the brain.  Taken together, our findings provide evidence for a diverse population of highly expressed non-canonical miRNAs that together play important functional roles in post-mitotic neurons.

overall_design: Examination of small RNA populations in the hippocampus and cortex of 2 conditional knockout and control littermates

first: Joshua

last: Babiarz


title: Systematic analysis of miRNA transcriptome of skeletal muscle identifies novel miRNAs and differentially expressed miRNAs in divergent skeletal muscle growth rates of broiler and layer chickens

city: Beijing

first: Tingting

last: Li

address: 38 Xueyuan Rd

department: Medical informatics

country: China

institute: Peking University


title: Systematic determination and analysis of chromatin state dynamics in nine human cell types

first: Jason

last: Ernst

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: GSE26312
SuperSeries of: GSE26320


title: Extensive imprinted gene expression in Arabidopsis endosperm

status: Public on Mar 10 2011

city: Berkeley

first: Toshiro

last: Nishimura

address: 211 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

summary:
Some flowering plant and vertebrate genes are expressed primarily or exclusively from either the maternal or paternal allele, a phenomenon called genomic imprinting. Flowering plant imprinted gene expression has been described primarily in endosperm, a terminal nutritive tissue consumed by the embryo during seed development or after germination. Imprinted expression in Arabidopsis thaliana endosperm is orchestrated by differences in cytosine DNA methylation between the paternal and maternal genomes, as well as by Polycomb group (PcG) proteins. Currently only eleven imprinted Arabidopsis genes are known. Here we use extensive sequencing of cDNA libraries to identify many new paternally and maternally imprinted genes in A. thaliana endosperm, including transcription factors, proteins involved in hormone signaling, and epigenetic regulators. The imprinted status of many maternally-expressed genes is not altered by mutations in the DNA-demethylating glycosylase DEMETER, the DNA methyltransferase MET1 or the core PcG protein FIE, indicating that these genes are regulated by novel mechanisms or deposited from maternal tissues. We did not find any imprinted genes in the embryo. Our results demonstrate that imprinted gene expression, particularly from the maternal genome, is an extensive, mechanistically complex phenomenon that likely affects multiple aspects of seed development.
Epigenetics

overall_design: Examination of genomic imprinting in Arabidopsis endosperm

first: Tzung-Fu

last: Hsieh

first: Juhyun

last: Shin

first: Rie

last: Uzawa

first: Pedro

last: Silva

first: Stephanie

last: Cohen

last: Bauer

first: Meryl

last: Hashimoto

first: John

last: Harad

first: Daniel

last: Zilberman

middle: L

last: Fischer


title: Characterization of miRNA transcriptome of skeletal muscle from broiler and layer chicken lines by deep sequencing

summary: In the current study, we expanded our previous work to identify miRNAs implicated in the myogenesis regulation through the comparison of miRNAs transcriptome in skeletal muscle tissues between broilers and layers. To address that, we firstly performed Solexa deep sequencing to profile miRNAs expressed in chicken skeletal muscle tissues. Sequence tags analyses not only  enable us to report a group of highly abundant known miRNAs expressed in skeletal muscles but most importantly to identify novel putative chicken miRNAs from skeletal muscle tissue. Further miRNA transcriptome comparison and real-time RT-PCR validation experiments revealed seveal differentially expressed miRNAs between broilers and layers.

overall_design: Examination of miRNA transcriptome in skeletal muscle of two kinds of chickens

first: Yong

last: Zhang

first: Dahai

last: Zhu


title: mRNA-Seq of whole flies from Drosophila

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary: We sequenced mRNA from whole flies of females and male of Drosophila melanogaster, D. simulans, D. yakuba, D. ananassae, D. pseudobscura, D. mojavensis, and D. virilis as part of the modENCODE project to validate novel gene models found in D. melanogaster, identify genes differentially expressed between the sexes and sex-specific alternative splicing events, and examine the evolution of gene expression.

sample_organism:
Drosophila ananassae
Drosophila melanogaster
Drosophila mojavensis
Drosophila pseudoobscura
Drosophila simulans
Drosophila virilis
Drosophila yakuba

overall_design: Comparison of expresssion profiles in female and male whole flies. These are the same samples used to generate the array data found in GSE6640.

middle: H

last: Malone

first: Carlo

last: Artieri

first: David

last: Sturgill

first: Yu


title: Deep Sequence Analysis of the Relationship between Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells

status: Public on Mar 16 2011

city: Rochester

first: Zhifu

last: Sun

state: MN

address: 200 1st ST SW

department: HSR-BSI

institute: Mayo Clinic

type: Methylation profiling by high throughput sequencing

summary: We used deep sequencinge technology to profile the transcriptome, gene copy number, and CpG island methylation status simultaneously in eight commonly used breast cell lines to develop a model for how these genomic features are integrated in estrogen receptor positive (ER+) and negative breast cancer. Total mRNA sequence, gene copy number, and genomic CpG island methylation were carried out using the Illumina Genome Analyzer. Sequences were mapped to the human genome to obtain digitized gene expression data, DNA copy number in reference to the non-tumor cell line (MCF10A), and methylation status of 21,570 CpG islands to identify differentially expressed genes that were correlated with methylation or copy number changes. These were evaluated in a dataset from 129 primary breast tumors. Gene expression in cell lines was dominated by ER-associated genes. ER+ and ER- cell lines formed two distinct, stable clusters, and 1,873 genes were differentially expressed in the two groups. Part of chromosome 8 was deleted in all ER- cells and part of chromosome 17 amplified in all ER+ cells. These loci encoded 30 genes that were overexpressed in ER+ cells; 9 of these genes were overexpressed in ER+ tumors. We identified 149 differentially expressed genes that exhibited differential methylation of one or more CpG islands within 5kb of the 5' end of the gene and for which mRNA abundance was inversely correlated with CpG island methylation status. In primary tumors we identified 84 genes that appear to be robust components of the methylation signature that we identified in ER+ cell lines. Our analyses reveal a global pattern of differential CpG island methylation that contributes to the transcriptome landscape of ER+ and ER- breast cancer cells and tumors. The role of gene amplification/deletion appears to more modest, although several potentially significant genes appear to be regulated by copy number aberrations.

overall_design: 8 commonly used breast cancer cell lines were sequenced for mRNA expression, CpG methylation and DNA copy number

first: Yan

middle: W

last: Asmann

first: Krishna

middle: R

last: Kalari

last: Bot

first: Jeanette

last: Eckel-Passow

first: Tiffany

last: Baker

first: Jennifer

last: Carr

first: Irina

last: Khrebtukova

first: Shujun

last: Luo

first: Lu

first: Gary

middle: P

last: Schroth

first: Edith

middle: A

last: Perez

first: E

last: Thompson


title: Diurnal changes of HDAC3, Rev-erbα, NCoR and Pol II recruitment to the mouse liver genome and of H3K9Ac

status: Public on Mar 11 2011

city: Buffalo

first: Tao

last: Liu

state: NY

address: Elm and Carlton St

department: Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Institute

summary: We reported a diurnal changes in the recruitment of HDAC3, Rev-erbα, NCoR and Pol II to the mouse liver genome as well as H3K9 acetylation in vivo at ZT10 and ZT22.

overall_design: ChIP-Seq profiling of HDAC3, Rev-erbα, NCoR and Pol II binding and H3K9Ac in mouse liver harvested at 2 different times (ZT10 and ZT22) of the day

first: Dan

last: Feng

first: Mitchell

last: Lazar


title: Global Analysis of the Transcriptional Response of Whitefly to Tomato Yellow Leaf Curl China Virus (TYLCCNV)

status: Public on Mar 22 2011

city: Hangzhou

first: Xiaowei

last: Wang

address: 866 Yuhangtang Road

department: Insect Sciences

institute: Zhejiang University

summary: We investigated the transcriptional response of invasive B. tabaci B biotype to tomato yellow leaf curl China virus (TYLCCNV) using Illumina sequencing technology. We found that 1,606 genes involved in 157 biochemical pathways were differentially expressed in the viruliferous whiteflies.

overall_design: Culture of B biotype whitefly was maintained on cotton plants. Three thousands of newly emerged adults of whitefly on cotton were released onto the leaves of healthy and viruliferous tobacco plants. They were allowed to feed for 24 h. After that, non-viruliferous and viruliferous whiteflies were transferred respectively to cotton plants in different cages and allowed to feed for 120 h. Then approximately 1,000 non-viruliferous and viruliferous female adults of whitefly were collected, respectively. The RNA was extracted and sequenced using Illunima Analyzer II.

first: Jun-Bo

last: Luan

first: Shu-Sheng

first: Xiao-Wei


title: Genome-wide mapping of meiotic double-strand breaks by sequencing Spo11 oligos.

status: Public on Mar 07 2011

city: New York

first: Scott

last: Keeney

address: 1275 York Ave

department: Molecular Biology Program

institute: Memorial Sloan Kettering Cancer Center

summary: The nonrandom distribution of meiotic recombination shapes patterns of inheritance and  genome evolution, but chromosomal features governing this distribution are poorly understood.  Formation of the DNA double-strand breaks (DSBs) that initiate recombination results in  accumulation of Spo11 protein covalently bound to small DNA fragments. We show here that  sequencing these fragments provides a genome-wide DSB map of unprecedented resolution  and sensitivity. We use this map to explore the influence of large-scale chromosome structures,  chromatin, transcription factors, and local sequence composition on DSB distributions. Our  analysis supports the view that the recombination terrain is molded by combinatorial and  hierarchical interaction of factors that work on widely different size scales. Mechanistic aspects  of DSB formation and early processing steps are also uncovered. This map illuminates the  occurrence of DSBs in repetitive DNA elements, repair of which can lead to chromosomal  rearrangements. We discuss implications for evolutionary dynamics of recombination hotspots.

overall_design: We deep sequenced 4 samples of Spo11 oligos on Roche 454 platform. Three samples are technical replicates of Spo11 oligo products prepared from one meiotic culture and the fourth sample was prepared from an independent culture.

first: Jing

last: Pan

first: Mariko

last: Sasaki

first: Ryan

last: Kniewel

first: Hajime

last: Murakami

first: Hannah

last: Blitzblau

first: Sam

last: Tischfield

first: Xuan

last: Zhu

first: Matthew

last: Neale

first: Maria

last: Jasin

first: Nicholas

last: Socci

first: Andreas

last: Hochwagen


title: modENCODE_Lieb and White Lab: unltra-deep sequencing data of genomic DNA, chromatin input, and ChIP of Su(Hw)  and H3K36me3 from S2 cells on Illumina Genome Analyzer.

status: Public on Mar 04 2011

city: Houston

first: Yiwen

last: Chen

state: TX

address: 1400 Pressler Street

department: Bioinformatics and Computational Biology

institute: University of Texas MD Anderson Cancer Center

summary:
This is a dataset generated by the modENCODE Project. It contains both the pair-end and single-end sequencing data of genomic DNA, chromatin input and the ChIP of the factors Su(Hw) and H3K36me3 from Drosophila S2 cells and it was generated on Illumina Genome Analyzer. The goal was to sequence ~120M tags of each sample and used this ultra-deep dataset to systematically evaluate both experimental and computational factors that influence the results of ChIP-seq experiments.

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: S2 cells from the modENCODE batch were amplified before transferring to  the plates. 15 plates were put in culture until the cells reached the appropriate concentration. Cells were harvested from 2 plates to extract the genomic DNA. The remaining 13 plates were then treated with formaldehyde at the same time and the chromatin were extracted. 3 plates were used to produce an Input sample corresponding to the chromatin DNA of the treated cells. Each plate corresponding to an eppendorff tube of chromatin, ChIP experiments were performed on 5 tubes for H3K36me3 and on 5 tubes for Su(Hw). ChIP and DNA extraction were performed independently on each tube. After the purification of the DNA, the tubes corresponding to the same sample (Su(Hw), H3K36me3, Input and gDNA) were pooled together. After mixing, each sample was aliquoted again into 5 tubes. 1 aliquot of each was used for ChIP-chip on Affymetrix tiling arrays for quality control, 1 aliquot was used for single-end sequencing at the University of Chicago HGAC, 1 aliquot was used for single-end sequencing at UNC, 1 aliquot was used for paired-end sequencing at UNC and the remaining aliquot was kept as a back-up of the original samples. For each sample, >100M single-end tags were produced (~5 runs), along with the tags from 1 lane of paired-end sequencing experiment. Besides several experimental factors, the performance of multiple peak callers were evaluated at different sequencing depths.

first: Nicolas

last: Negre

first: Joanna

middle: O

last: Mieczkowska

first: Kevin

last: White

first: Xiaole

last: Liu

first: Jason

last: Lieb


title: Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43 (RNA-seq)

status: Public on Mar 03 2011

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: Cross-linking and immunoprecipitation coupled with high-throughput sequencing was used to identify binding sites within 6,304 genes as the brain RNA targets for TDP-43, an RNA binding protein which when mutated causes Amyotrophic Lateral Sclerosis (ALS). Use of massively parallel sequencing and splicing-sensitive junction arrays revealed that levels of 601 mRNAs are changed (including Fus/Tls, progranulin, and other transcripts encoding neurodegenerative disease-associated proteins) and 965 altered splicing events are detected (including in sortilin, the receptor for progranulin), following depletion of TDP-43 from adult brain with antisense oligonucleotides. RNAs whose levels are most depleted by reduction in TDP-43 are derived from genes with very long introns and which encode proteins involved in synaptic activity. Lastly, TDP-43 was found to auto-regulate its synthesis, in part by directly binding and enhancing splicing of an intron within the 3’ untranslated region of its own transcript, thereby triggering nonsense mediated RNA degradation.

overall_design: RNAseq in control and Tdp-43 knockdown mouse striatum

first: Don

last: Cleveland


title: Cardiac transcription factors in HL-1 cells: gene expression and genome binding profiling

status: Public on Mar 02 2011

city: Boston

first: Sek Won

last: Kong

state: MA

address: 300 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary:
[1] Gene expression profiling in Gata4, Mef2a knockdown in HL-1 cells.
HL-1 cells infected with adenovirus expressing either control siRNA or Gata4, and Gata4 & Mef2a siRNA.

[2] Genome-wide maps of cardiac transcription factors binding region in HL-1 cells.
We performed bio-ChIP-seq using streptavidin beads immunoprecipitation of biotinylated 5 cardiac transcription factors (fbio) and P300 antibody ChIP-seq.
We used a dox-inducible dual adenovirus system to express biotinylated Core Cardiac TFs in HL1. One adenovirus expressed the dox-activated reverse tet activator protein (rtTA) and the E. coli biotinylating enzyme BirA from the cardiac specific rat troponin T promoter. The second virus expressed a Core Cardiac TF fused to a C-terminal flag-bio epitope tag, where bio is the 15 amino acid substrate for BirA. This in vivo biotinylation approach permits pulldown of different factors to be performed under identical, stringent conditions, and circumvents limitations posed by available antibodies. We titrated adenovirus and dox doses to express GATA4flbio and MEF2Aflbio at near endogenous levels. The same conditions were then used to express SRFflbio, TBX5flbio, and NKX2-5flbio.
Reference:
12. de Boer E, Rodriguez P, Bonte E, Krijgsveld J, Katsantoni E et al. (2003) Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice. Proc Natl Acad Sci U S A 100: 7480-7485.

overall_design:
[1] Gene expression profiling: Identify differentially expressed genes after siRNA Gata4 or Gata4_Mef2a double knockdown in HL-1 cells

[2] Genome occupancy profiling: Identify cardiac active enhancers by identified 5 cardiac transcription factors and P300 peaks.

first: SekWon

first: Aibin

last: He

first: William

middle: T

last: Pu


title: Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium  [ChIP-Seq]

status: Public on Mar 01 2011

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Here we describe the application of high-throughput sequencing technology for profiling histone and DNA methylation, and gene expression patterns of normal human mammary progenitor-enriched and luminal lineage-committed cells. We observed significant differences in histone H3 lysine 27 tri-methylation (H3K27me3) enrichment and DNA methylation of genes expressed in a cell type-specific manner, suggesting their regulation by epigenetic mechanisms and a dynamic interplay between the two processes that together define developmental potential. The technologies we developed and the epigenetically regulated genes we identified will accelerate the characterization of primary cell epigenomes and the dissection of human mammary epithelial lineage-commitment and luminal differentiation.

overall_design: Examination of histone H3K27me3 modifications in 2 cell types from 3 individuals and H3K4me3 modifications in 2 cell types from one individual sample.

first: Maruyama

last: Reo

first: Sibgat

last: Choudhury

first: Zhenhua

last: Wu

first: Vanessa

last: Merino

first: Pang-Kuo

last: Lo

first: X

first: Saraswati

last: Sukumar


title: Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium  [SAGE-Seq]

overall_design: Global transcriptome profilings of 15 samples in normal breast tissue using Sage-Seq.


title: The transcriptome of Aedes aegypti (Liverpool strain) females kept on a sugar diet versus those blood-fed

city: Irvine

first: Anthony

last: James

address: 2315 McGaugh Hall

department: Molecular Biology and Biochemistry

institute: University of California, Irvine

summary: We report the RNA-seq based analyses of the transcriptional changes in the Aedes aegypti transcriptome 5 hours after blood feeding.

overall_design: Comparison of the transcriptome of Aedes aegypti females at two physiological conditions and one time point.

first: Osvaldo

last: Marinotti

first: Mariangela

last: Bonizzoni

last: Dunn


title: X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila males (Control & MSL2 RNAi)

first: Peter

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

summary: MSL (Male-specific lethal) complex increases transcription on the single X chromosome of Drosophila males in order to equalize expression of X-linked genes between males (XY) and females (XX). The increase in transcript levels correlates with MSL- dependent acetylation of histone H4 at K16 within the bodies of active genes, but identification of the transcriptional step affected has not been possible. In this study, we use global run-on sequencing (GRO-seq) to examine the specific effect of MSL complex on RNA Polymerase II (RNAP II) on a genome-wide level. Results indicate that MSL complex enhances transcription by facilitating the progression of RNAP II across the bodies of active X-linked genes. Improving transcriptional output downstream of typical gene-specific control may explain how dosage compensation can be imposed on the diverse set of genes along an entire chromosome.

overall_design: Global Run-On Sequencing (GRO-Seq) reads, i.e., RNA-Seq of nascent RNA transcripts, from D. Melanogaster SL2 cells.  Two biological replicates of cells treated with control GFP RNAi and cells treated with MSL2 RNAi were analyzed.

first: Erica

last: Larschan

first: Eric

last: Bishop

middle: V

last: Kharchenko

first: Leighton

last: Core

first: John

last: Lis

first: Mitzi

middle: I

last: Kuroda


title: Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43 (CLIP)

first: Gene

last: Yeo

overall_design: CLIP of Tdp-43 in 8 week mouse brain.

first: Don

last: Cleveland


title: Genome-wide identification of putative cis-regulatory elements through epigenetic profiling in zebrafish

status: Public on Feb 25 2011

city: Worcester

first: Lihua

middle: Julie

last: Zhu

address: 364 Plantation St

department: Program in Gene Function and Expression

institute: Umass Medial School

summary: In this study, we have applied ChIP-Seq to identify putative regulatory elements throughout the zebrafish genome.  For this purpose we identified sequences within the zebrafish genome that associate with H3K4me1 and H3K4me3, which are epigenetic modifications known to be associated with active cis-regulatory elements in other species.

overall_design: Determination of H3K4me1- and H3K4me3-binding sites in the zebrafish genome.

first: Aaron

last: Aday

first: Nathan

last: Lawson

first: Abirami

last: Lakshmanan


title: Identification of Transcription Factor ZTF-4::GFP Binding Regions in L3

status: Public on May 24 2011

city: Toronto

first: DCC

last: modENCODE

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

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_3218
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP322(official name : ZTF-4 genotype : unc119(ed3);wgIs322(ztf-4::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The spatio-temporal expression pattern of ZTF-4::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-4 transcription factor. made_by : Bob Waterston's lab from UW ); Developmental Stage: L3; Genotype: unc119(ed3);wgIs322(ztf-4::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene ztf-4; Strain OP322(official name : ZTF-4 genotype : unc119(ed3);wgIs322(ztf-4::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The spatio-temporal expression pattern of ZTF-4::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-4 transcription factor. made_by : Bob Waterston's lab from UW ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Slightam

first: Stuart

last: Kim

last: Murray

first: Robert

last: Waterston

first: Mark

last: Gerstein

first: Wei

last: Niu

first: Judi

last: Janette

first: Debasish

last: Raha

first: Ashish

last: Agarwal

first: Valerie

last: Reinke

first: Mihail

last: Sarov

last: Hyman


title: Interplay between c-Jun and TAp73α/β contributes to the apoptosis-survival balance

city: Nijmegen

first: Marion

last: Lohrum

institute: NCMLS

summary: The p53-family member p73 functions in various cellular signaling pathways and can have tumor suppressor properties. Several isoforms of p73 exist that differ considerably in their function. Whereas the functions of the N-terminal isoforms (TA and ΔNp73) and their opposing pro- and anti-apoptotic roles became evident, the functional differences of the distinct C-terminal spliceforms of TAp73 have remained unclear. Here, we characterized the genomic binding sites for TAp73α and TAp73β and identified a specific p73 consensus binding-motif. Furthermore, an AP1 motif is strongly enriched close to binding sites for TAp73α. These AP1 motif-containing target genes are selectively upregulated by TAp73α, while their mRNA expression is repressed upon TAp73β induction. Recruitment of c-Jun to the respective AP1 sites was impaired upon TAp73β expression in part due to downregulation of c-Jun. We show that several of these AP1-site containing TAp73α-induced genes reduce on apoptosis-induction suggesting an underlying molecular mechanism for the observed functional differences between TAp73α and TAp73β.

overall_design: ChIP-seq and RNA-seq profiles of TAp73alpha, TAp73beta and p53 stably transfected in human osteosarcoma Saos cells

first: Max

last: Koeppel

first: Simon

last: van Heeringen

first: Daniela

last: Kramer

first: Leonie

last: Smeenk

first: Marleen

last: Forkink

first: Eva

last: Janssen-Megens

first: Hendrik

middle: G

last: Stunnenberg


title: Methylome analysis of 18 wild-type and mutant mouse ES, NP and MEF cells

status: Public on Feb 24 2011

city: London

first: Gareth

last: Wilson

address: 23 Huntley Street

country: United Kingdom

institute: UCL Cancer Institute

summary: The analysis of the 18 methylomes comprise 3 biological replicates of TDG+/- ES cells, 3 biological replicates of TDG-/- ES cells, 3 biological replicates of TDG+/- NP cells, 3 biological replicates of TDG-/- NP cells, 3 biological replicates of TDG+/+ MEF cells and 3 biological replicates of TDG-/- MEF cells.

overall_design: Analysis of the 18 methylomes comprise 3 biological replicates of TDG+/- ES cells, 3 biological replicates of TDG-/- ES cells, 3 biological replicates of TDG+/- NP cells, 3 biological replicates of TDG-/- NP cells, 3 biological replicates of TDG+/+ MEF cells and 3 biological replicates of TDG-/- MEF cells

first: Pawan

last: Dharmi

first: Yusuke

last: Saito

first: Daniel

last: Cortazar

first: Christophe

last: Kunz

first: Primo

last: Schär

first: Stephan

last: Beck


title: Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43

first: Gene

last: Yeo

type: Genome binding/occupancy profiling by array

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

overall_design: Refer to individual Series


title: Identification of Transcription Factor PES-1::GFP Binding Regions in L4

status: Public on Mar 31 2011

first: DCC

last: modENCODE

summary:
modENCODE_submission_3157
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP87 (official name : OP87 genotype : unc-119(ed3) III; wgIs87 [unc-119(+) pes-1::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The PES-1::EGFP fusion protein is expressed in the correct pes-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PES-1 transcription factor. made_by : R. Waterston ); Developmental Stage: L4; Genotype: unc-119(ed3) III; wgIs87 [unc-119(+) pes-1::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene pes-1; Strain OP87 (official name : OP87 genotype : unc-119(ed3) III; wgIs87 [unc-119(+) pes-1::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The PES-1::EGFP fusion protein is expressed in the correct pes-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PES-1 transcription factor. made_by : R. Waterston ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Slightam

first: Stuart

last: Kim

first: John

last: Murray

first: Robert

last: Waterston

first: Mark

last: Gerstein

first: Wei

last: Niu

first: Judi

last: Janette

first: Debasish

last: Raha

first: Ashish

last: Agarwal

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: Extensive Chromatin Remodeling and Establishment of Transcription Factor 'Hotspots' during Early Adipogenesis

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Adipogenesis is tightly controlled by a complex network of transcription factors  acting at different stages of differentiation. Peroxisome proliferator-activated receptor gamma (PPAR gamma) and CCAAT/enhancer binding protein (C/EBP) family members are key  regulators of this process. We have employed DNase I hypersensitive site analysis to  investigate the genome-wide changes in chromatin structure that accompany the binding  of adipogenic transcription factors. These analyses revealed a dramatic and dynamic  modulation of the chromatin landscape during the first hours of adipocyte differentiation  that coincides with cooperative binding of multiple early transcription factors (including  glucocorticoid receptor, retinoid X receptor, Stat5a, C/EBPbeta and -delta) to transcription  factor 'hotspots'. Our results demonstrate that C/EBPbeta marks a large number of these  transcription factor 'hotspots' prior to induction of differentiation and chromatin  remodeling and is required for their establishment. Furthermore, a subset of early  remodeled C/EBP binding sites persists throughout differentiation and is later occupied  by PPAR gamma , indicating that early C/EBP family members, in addition to their well  established role in activation of PPAR gamma  transcription, may act as pioneering factors for  PPAR gamma  binding.

overall_design: DNase I hypersensitive chromatin regions and transcription factor binding sites were identified at various time points of 3T3-L1 differentiation using DHS-seq and ChIP-seq, respectively.

first: Rasmus

last: Siersbaek

first: Ronni

last: Nielsen

first: Sam

last: John

first: Myong-Hee

last: Sung

first: Songjoon

last: Baek

first: Anne

last: Loft

first: Gordon

last: Hager


title: Conserved generation of short products at piRNA loci

city: Grenoble

first: Philipp

last: Berninger

address: 6, rue Jules Horowitz

country: France

institute: EMBL Grenoble

summary: We analyzed small RNAs from three mammalian species, and found that in all these species piRNA-directed targeting is accompanied by the generation of short sequences that have a very precisely defined length and a specific spatial relationship with the guide piRNAs.

overall_design: small RNA-seq of testes lysate (beta-eliminated)

first: Mihaela

last: Zavolan


title: Identification of Transcription Factor PQM-1::GFP Binding Regions in L3

status: Public on Feb 18 2011

first: DCC

last: modENCODE

summary:
modENCODE_submission_2623
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP201(made_by : S Kim description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The PQM-1::EGFP fusion protein is expressed in the correct pqm-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PQM-1 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs201(pqm-1::TY1 EGFP FLAG C;unc119) official name : OP201 ); Developmental Stage: L3; Genotype: unc119(ed3);wgIs201(pqm-1::TY1 EGFP FLAG C;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene pqm-1; Strain OP201(made_by : S Kim description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The PQM-1::EGFP fusion protein is expressed in the correct pqm-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PQM-1 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs201(pqm-1::TY1 EGFP FLAG C;unc119) official name : OP201 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Slightam

first: Stuart

last: Kim

first: John

last: Murray

first: Robert

last: Waterston

first: Mark

last: Gerstein

first: Wei

last: Niu


title: Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium  [MSDK-Seq]

first: Kornelia

last: Polyak

overall_design: Global profiling of differentially methylated regions in 2 cell types from 6 individuals.

first: Maruyama

last: Reo

first: Sibgat

last: Choudhury

first: Adam

last: Kowalczyk

first: Izhak

last: Haviv

first: Bryan

last: Beresford-Smith

first: Thomas

last: Conway

first: Antony

last: Kaspi

first: Vanessa

last: Merino

first: Pang-Kuo

last: Lo

first: Saraswati

last: Sukumar


title: Identification of Transcription Factor EGL-27::GFP Binding Regions in L1

first: DCC

last: modENCODE

summary:
modENCODE_submission_2621
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP177(made_by : S Kim description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EGL-27::EGFP fusion protein is expressed in the correct egl-27 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-27 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs177(egl-27::TY1 EGFP FLAG;unc119) official name : OP177 ); Developmental Stage: fed L1; Genotype: unc119(ed3);wgIs177(egl-27::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene egl-27; Strain OP177(made_by : S Kim description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EGL-27::EGFP fusion protein is expressed in the correct egl-27 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-27 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs177(egl-27::TY1 EGFP FLAG;unc119) official name : OP177 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Slightam

first: Judi

last: Janette

first: Debasish

last: Raha

first: Ashish

last: Agarwal

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: Identification of Transcription Factor SKN-1::GFP Binding Regions in L1

summary:
modENCODE_submission_2622
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP178(made_by : S Kim tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs178(skn-1::TY1 EGFP FLAG;unc119) official name : WBGene00004804 ); Developmental Stage: fed L1; Genotype: unc119(ed3);wgIs178(skn-1::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene skn-1; Strain OP178(made_by : S Kim tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs178(skn-1::TY1 EGFP FLAG;unc119) official name : WBGene00004804 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq

first: Stuart

last: Kim

first: John

last: Murray

first: Robert

last: Waterston

first: Mark

last: Gerstein

first: Wei

last: Niu


title: Genome-Wide And Phase-Specific DNA-Binding Rhythms Of BMAL1 Control Circadian Output Functions In Mouse Liver

status: Public on Feb 23 2011

city: Geneva

first: Guillaume

last: Rey

address: Campus Biotech, Chemin des Mines 9

country: Switzerland

institute: University of Geneva

summary: Using chromatin immuno-precipitation (ChIP) combined with deep sequencing (ChIP-seq) we obtained a time resolved and genome-wide map of BMAL1 binding in mouse liver, which allowed to identify over two thousand binding sites with peak binding narrowly centered around Zeitgeber time (ZT) 6. Annotation of BMAL1 targets confirms carbohydrate and lipid metabolism as the major output of the circadian clock in mouse liver. Moreover, transcription regulators are largely overrepresented, several of which also exhibit circadian activity. Genes of the core circadian oscillator stand out as strongly bound, often at promoter and distal sites. Genomic sequence analysis of the sites identified E- boxes and tandem E1-E2 consensus elements. Electromobility shift assays (EMSA) showed that E1-E2 sites are bound by a dimer of BMAL1/CLOCK heterodimers with a spacing-dependent cooperative interaction that was further validated in transactivation assays. BMAL1 target genes showed cyclic mRNA expression profiles with a phase distribution centered at ZT10. Importantly, sites with E1-E2 elements showed tighter phases both in binding and mRNA accumulation. Finally, comparing the temporal accumulation of precursor mRNA and mature mRNA helped distinguish direct BMAL1 targets from targets with more complex regulation, and showed how transcriptional and post-transcriptional regulation contribute differentially to circadian expression phase. Together, our analysis of a dynamic protein-DNA interactome uncovered how genes of the core circadian oscillator are wired together and drive phase-specific circadian output programs in a complex tissue.

overall_design:
ChIP-Seq of BMAL1 in mouse liver during one circadian cycle at 4 hour time resolution presented in this Series (GSE26602).

mRNA profiling data used in this study are already published (Kornmann et al, PLoS Biol 2007) and have been deposited on ArrayExpress repository (accession number: E-MEXP-842).

first: François

last: Cesbron

first: Jacques

last: Rougemont

first: Hans

first: Michael

last: Brunner

first: Felix

last: Naef


title: Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium

first: Kornelia

last: Polyak


title: Mapping of INS promoter interactions reveals its role in long-range  regulation of SYT8 transcription

status: Public on Feb 22 2011

city: Cincinnati

first: Iouri

last: Chepelev

state: OH

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center

summary: Insulin (INS) synthesis and secretion from pancreatic β cells are tightly regulated;  their deregulation causes diabetes. Here we map INS-associated loci in human  pancreatic islets by 4C and 3C techniques and show that the INS gene physically  interacts with the SYT8 gene, located over 300 kb away. This interaction is  elevated by glucose and accompanied by increases in SYT8 expression.  Inactivation of the INS promoter by promoter-targeting siRNA reduces SYT8  gene expression. SYT8-INS interaction and SYT8 transcription are attenuated by  CTCF depletion. Furthermore, SYT8 knockdown decreases insulin secretion in  islets. These results reveal a non-redundant role for SYT8 in insulin secretion  and indicate that the INS promoter acts from a distance to stimulate SYT8  transcription. This suggests a function for the INS promoter in coordinating  insulin transcription and secretion through long-range regulation of SYT8  expression in human islets.

overall_design: Circular Chromosome Conformation Capture (4C)-Seq experiments to profile interactions of INS promoter in human pancreatic  islets isolated from two donors: donor 1 and donor 2.

first: Zhixiong

last: Xu

first: Gang

last: Wei

first: Keji

last: Zhao

first: Gary

last: Felsenfeld


title: DNA Methylation by Reduced Representation Bisulfite Seq from ENCODE/HudsonAlpha

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 (Florencia Pauli mailto:fpauli@hudsonalpha.org). 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 project. The track reports the percentage of DNA molecules that exhibit cytosine methylation at specific CpG dinucleotides. In general, DNA methylation within a gene's promoter is associated with gene silencing, and DNA methylation within the exons and introns of a gene is associated with gene expression. Proper regulation of DNA methylation is essential during development and aberrant DNA methylation is a hallmark of cancer. DNA methylation status is assayed at more than 500,000 CpG dinucleotides in the genome using Reduced Representation Bisulfite Sequencing (RRBS). Genomic DNA is digested with the methyl-insensitive restriction enzyme MspI, small genomic DNA fragments are purified by gel electrophoresis, and then used to construct an Illumina sequencing library. The library fragments are treated with sodium bisulfite and amplified by PCR to convert every unmethylated cytosine to a thymidine while leaving methylated cytosines intact. The sequenced fragments are aligned to a customized reference genome sequence and for each assayed CpG we report the number of sequencing reads covering that CpG and the percentage of those reads that are methylated.
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:
DNA methylation at CpG sites was assayed with a modified version of Reduced Representation Bisulfite Sequencing (RRBS; Meissner et al., 2008). RRBS was performed on cell lines grown by many ENCODE production groups. The production group that grew the cells and isolated genomic DNA is indicated in the "obtainedBy" field of the metadata. When a cell type was provided by more than one lab, the data for the cells from only one lab are displayed in the table above. However, the data for every cell type from every lab is available from the Downloads page. RRBS was carried out by the Myers production group at the HudsonAlpha Institute for Biotechnology.
Isolation of genomic DNA
Genomic DNA is isolated from biological replicates of each cell line using the QIAGEN DNeasy Blood & Tissue Kit according to the instructions provided by the manufacturer. DNA concentrations for each genomic DNA preparation are determined using fluorescent DNA binding dye and a fluorometer (Invitrogen Quant-iT dsDNA High Sensitivity Kit and Qubit Fluorometer). Typically, 1 µg of DNA is used to make an RRBS library; however, we have also had success in making libraries with 200 ng genomic DNA from rare or precious samples.
RRBS library construction and sequencing
RRBS library construction starts with MspI digestion of genomic DNA , which cuts at every CCGG regardless of methylation status. Klenow exo- DNA Polymerase is then used to fill in the recessed end of the genomic DNA and add an adenosine as a 3prime overhang. Next, a methylated version of the Illumina paired-end adapters is ligated onto the DNA. Adapter ligated genomic DNA fragments between 105 and 185 basepairs are selected using agarose gel electrophoresis and Qiagen Qiaquick Gel Extraction Kit. The selected adapter-ligated fragments are treated with sodium bisulfite using the Zymo Research EZ DNA Methylation Gold Kit, which converts unmethylated cytosines to uracils and leaves methylated cytosines unchanged. Bisulfite treated DNA is amplified in a final PCR reaction which has been optimized to uniformly amplify diverse fragment sizes and sequence contexts in the same reaction. During this final PCR reaction uracils are copied as thymines resulting in a thymine in the PCR products wherever an unmethylated cytosine existed in the genomic DNA. The sample is now ready for sequencing on the Illumina sequencing platform. These libraries were sequenced with an Illumina Genome Analyzer IIx according to the manufacturer's recommendations.
Data analysis
To analyze the sequence data, a reference genome is created that contains only the 36 base pairs adjacent to every MspI site and every C in those sequences is changed to T. A converted sequence read file is then created by changing each C in the original sequence reads to a T. The converted sequence reads are aligned to the converted reference genome, and only reads that map uniquely to the reference genome are kept. Once reads are aligned the percent methylation is calculated for each CpG using the original sequence reads. The percent methylation and number of reads is reported for each CpG.

first: Katherine

last: Varley

first: Jason

last: Gertz

first: Richard

last: Myers


title: Genome-wide Myb chromatin occupancy in murine myeloid progenitor cells

city: Brisbane

first: Evgeny

last: Glazov

address: Ipswich Road

department: Diamantina Institute

country: Australia

institute: University of Queensland

summary: We report genome-wide pattern of Myb chromatin occupancy in vivo. We used ERMYB, a myeloid progenitor cell line derived by transformation of primary cells by ER-Myb fusion protein, as our model system. In these cells, activation of the ER-Myb fusion protein by estrogen is required to maintain a proliferative progenitor-like phenotype. We performed ChIP-seq with biological duplicate samples from ERMYB cells with Myb either “on” or “off” (i.e. + or - β-E2 for 6 hr). By comparing enrichment signals between Myb-on, Myb-off and isotype control samples, we identified 7,646 high-confidence Myb binding regions, which can be assigned to 4,892 annotated genes according to their distances to the nearest transcriptional start sites.

overall_design: Examination of Myb chromatin occupany in myeloid cells transformed by a switchable form of Myb

first: Liang

first: Diwakar

last: Pattabiraman

first: Faisal

last: Al-Owaidi

first: Ping

last: Zhang

first: Matthew

last: Brown

first: Paul

last: Leo

first: Thomas

middle: J

last: Gonda


title: Identification of Transcription Factor LIN-13::GFP Binding Regions in Embryos

first: DCC

last: modENCODE

summary:
modENCODE_submission_2613
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP51(made_by : R Waterston description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The LIN-13::EGFP fusion protein is expressed in the correct LIN-13 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-13 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119 (ed3) III; wgIs73 [lin-13::TY1::EGFP::FLAG; unc-119 (+)] official name : OP51 ); Developmental Stage: embryo; Genotype: unc-119 (ed3) III; wgIs73 [lin-13::TY1::EGFP::FLAG; unc-119 (+)]; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage embryo; Target gene lin-13; Strain OP51(made_by : R Waterston description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The LIN-13::EGFP fusion protein is expressed in the correct LIN-13 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-13 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119 (ed3) III; wgIs73 [lin-13::TY1::EGFP::FLAG; unc-119 (+)] official name : OP51 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Slightam

first: Stuart

last: Kim

first: John

last: Murray

first: Robert

last: Waterston

first: Mark

last: Gerstein

first: Wei

last: Niu

first: Judi

last: Janette

first: Debasish

last: Raha

first: Ashish

last: Agarwal

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: Identification of Transcription Factor ELT-3::GFP Binding Regions in L1

summary:
modENCODE_submission_2614
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP75(made_by : R Waterston description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The ELT-3::EGFP fusion protein is expressed in the correct elt-3 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ELT-3 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119 (ed3) III; wgIs75 [elt-3::TY1::EGFP::FLAG; unc-119 (+)] official name : OP75 ); Developmental Stage: fed L1; Genotype: unc-119 (ed3) III; wgIs75 [elt-3::TY1::EGFP::FLAG; unc-119 (+)]; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene elt-3; Strain OP75(made_by : R Waterston description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The ELT-3::EGFP fusion protein is expressed in the correct elt-3 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ELT-3 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119 (ed3) III; wgIs75 [elt-3::TY1::EGFP::FLAG; unc-119 (+)] official name : OP75 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq


title: Identification of Transcription Factor LIN-15B::GFP Binding Regions in L3

summary:
modENCODE_submission_2610
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP184(made_by : S Kim description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The LIN-15B::EGFP fusion protein is expressed in the correct lin-15B spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-15B transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs184(lin-15B::TY1 EGFP FLAG;unc119) official name : OP184 ); Developmental Stage: L3; Genotype: unc119(ed3);wgIs184(lin-15B::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene lin-15B; Strain OP184(made_by : S Kim description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The LIN-15B::EGFP fusion protein is expressed in the correct lin-15B spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-15B transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs184(lin-15B::TY1 EGFP FLAG;unc119) official name : OP184 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq


title: Multiplexed identification of the genomic targets of DNA-binding proteins

city: Collegeville

first: David

last: Mayhew

state: PA

address: 1250 South Collegeville Road

department: Target Sciences, Computation Biology, R&D

institute: GlaxoSmithKline

summary: Transcription factors direct gene expression, and so there is much interest in mapping their genome-wide binding locations.  Current methods do not allow for the multiplexed analysis of TF binding, and this limits their throughput. We describe a novel method for determining the genomic target genes of multiple transcription factors simultaneously. DNA-binding proteins are endowed with the ability to direct transposon insertions into the genome near to where they bind. The transposon becomes a “Calling Card” marking the visit of the DNA-binding protein to that location. A unique sequence “barcode” in the transposon matches it to the DNA-binding protein that directed its insertion. The sequences of the DNA flanking the transposon (which reveal where in the genome the transposon landed) and the barcode within the transposon (which identifies the TF that put it there) are determined by massively-parallel DNA sequencing. To demonstrate the method’s feasibility, we determined the genomic targets of eight transcription factors in a single experiment. The Calling Card method promises to significantly reduce the cost and labor needed to determine the genomic targets of many transcription factors in different environmental conditions and genetic backgrounds.

overall_design: These data contain Ty5 insertion sites mapped by an Illumina GAII analyzer in the S. cerevisiae genome for the background strain without any Sir4 present (1 run), in strains expressing Sir4-tagged copies of three well-characterized TFs: Gal4, Leu3, and Gcn4 (1 run each), and a multiplex of eight Sir4-tagged TFs pooled in a single experiment (2 biological replicates), and insertions from the Thi2-Sir4 fusion expressed from its native locus in two conditions (1 run each).  The format of each insertions file is [chromosome number] [position of genomic base] [direction of insertion] [number of reads at that position].  Raw sequencing data comes in two varieties.  Paired-end data contains a 5 bp barcode at the beginning of read #2.  Single-end data contains a 2 bp barcode on the beggining of read #1.

first: Mitra

last: Robi

first: Johnston

last: Mark


title: RNA polyadenylation landscape in human and mouse cells

status: Public on Feb 26 2011

first: Peter

last: Shepard

address: Med Sci B233

department: M&G

summary: Alternative polyadenylation (APA) of mRNAs has emerged as an important mechanism for post-transcriptional gene regulation in higher eukaryotes. Although microarrays have recently been used to characterize APA globally, they have a number of serious limitations that prevents comprehensive and highly quantitative analysis. To better characterize APA and its regulation, we have developed a deep sequencing-based method called Poly(A) Site Sequencing (PAS-Seq) for quantitatively profiling RNA polyadenylation at the transcriptome level. PAS-Seq not only accurately and comprehensively identifies poly(A) junctions in mRNAs and noncoding RNAs, but also provides quantitative information on the relative abundance of polyadenylated RNAs.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We first analyzed HeLa cell transcriptome using PAS-Seq to demonstrate that PAS-Seq not only accurately and comprehensively identifies poly(A) junctions, but also provide quantitative information on the relativel abundance of APA isoforms. Next we analyzed the mouse embryonic stem cells, neural stem/progenitor cells, and neurons by PAS-Seq to characterize the dynamic changes of mRNA polyadenylation during stem cell differentiation.

first: Yongsheng

last: Shi


title: Identification of Transcription Factor BLMP-1::GFP Binding Regions in L1

first: DCC

last: modENCODE

summary:
modENCODE_submission_2612
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP109(made_by : R Waterston description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The BLMP-1::EGFP fusion protein is expressed in the correct blmp-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the BLMP-1 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119 (ed3) III; wgIs109 [blmp-1::TY1::EGFP::FLAG; unc-119 (+)] official name : OP109 ); Developmental Stage: fed L1; Genotype: unc-119 (ed3) III; wgIs109 [blmp-1::TY1::EGFP::FLAG; unc-119 (+)]; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene blmp-1; Strain OP109(made_by : R Waterston description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The BLMP-1::EGFP fusion protein is expressed in the correct blmp-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the BLMP-1 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119 (ed3) III; wgIs109 [blmp-1::TY1::EGFP::FLAG; unc-119 (+)] official name : OP109 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Slightam


title: Identification of Transcription Factor MDL-1::GFP Binding Regions in L1

summary:
modENCODE_submission_2601
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP106(made_by : R Waterston description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The MDL-1::EGFP fusion protein is expressed in the correct mdl-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MDL-1 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119 (ed3) III; wgIs106 [mdl-1::TY1::EGFP::FLAG; unc-119(+))] official name : OP106 ); Developmental Stage: fed L1; Genotype: unc-119 (ed3) III; wgIs106 [mdl-1::TY1::EGFP::FLAG; unc-119(+))]; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene mdl-1; Strain OP106(made_by : R Waterston description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The MDL-1::EGFP fusion protein is expressed in the correct mdl-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MDL-1 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119 (ed3) III; wgIs106 [mdl-1::TY1::EGFP::FLAG; unc-119(+))] official name : OP106 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq

first: Stuart

last: Kim

first: John

last: Murray

first: Robert

last: Waterston

first: Mark

last: Gerstein


title: Identification of Transcription Factor PHA-4::GFP Binding Regions in Late Embryo

summary:
modENCODE_submission_2598
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP37(made_by : R. Waterston and S. Kim description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] official name : OP37 ); Developmental Stage: late embryo; Genotype: unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage late embryo; Target gene pha-4; Strain OP37(made_by : R. Waterston and S. Kim description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] official name : OP37 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq

first: Wei

last: Niu

first: Judi

last: Janette

first: Debasish

last: Raha

first: Ashish

last: Agarwal


title: Identification of Transcription Factor GEI-1::GFP Binding Regions in L4

summary:
modENCODE_submission_2451
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP179(made_by : R. Waterston description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] official name : OP179 ); Developmental Stage: L4; Genotype: unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene gei-11; Strain OP179(made_by : R. Waterston description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] official name : OP179 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: Identification of Transcription Factor MEP-1::GFP Binding Regions in Embryos

summary:
modENCODE_submission_2600
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP70(made_by : R Waterston tags : GFP::3xFlag mutagen : Bombard genotype : unc119(ed3);wgIs70(mep-1::TY1 EGFP FLAG C;unc119) official name : WBGene00003218 ); Developmental Stage: embryo; Genotype: unc119(ed3);wgIs70(mep-1::TY1 EGFP FLAG C;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage embryo; Target gene mep-1; Strain OP70(made_by : R Waterston tags : GFP::3xFlag mutagen : Bombard genotype : unc119(ed3);wgIs70(mep-1::TY1 EGFP FLAG C;unc119) official name : WBGene00003218 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq


title: Identification of Transcription Factor N2::POL II Binding Regions in Young Adult

summary:
modENCODE_submission_2441
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2(genotype : wild type genotype : DR subclone of DB original (Tc1 pattern I) official name : N2 ); Developmental Stage: Young Adult; Genotype: wild type; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage Young Adult; Target gene ama-1; Strain N2(genotype : wild type genotype : DR subclone of DB original (Tc1 pattern I) official name : N2 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq


title: Identification of Transcription Factor N2::POL II Binding Regions in L3

summary:
modENCODE_submission_2439
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2(genotype : wild type genotype : DR subclone of DB original (Tc1 pattern I) official name : N2 ); Developmental Stage: L3; Genotype: wild type; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene ama-1; Strain N2(genotype : wild type genotype : DR subclone of DB original (Tc1 pattern I) official name : N2 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq


title: Identification of Transcription Factor N2::POL II Binding Regions in L1

summary:
modENCODE_submission_2437
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2(genotype : wild type genotype : DR subclone of DB original (Tc1 pattern I) official name : N2 ); Developmental Stage: fed L1; Genotype: wild type; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene ama-1; Strain N2(genotype : wild type genotype : DR subclone of DB original (Tc1 pattern I) official name : N2 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq


title: Identification of Transcription Factor N2::POL II Binding Regions in L2

summary:
modENCODE_submission_2438
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2(genotype : wild type genotype : DR subclone of DB original (Tc1 pattern I) official name : N2 ); Developmental Stage: L2; Genotype: wild type; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene ama-1; Strain N2(genotype : wild type genotype : DR subclone of DB original (Tc1 pattern I) official name : N2 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq