title: Oncogenic PI3K mutations lead to NF-kB-dependent cytokine expression following growth

status: Public on May 01 2012

summary:
While growth factor-independent signaling and proliferation are well-established hallmarks of cancer, little is known regarding growth factor-independent changes in gene expression which occur downstream from oncogenes. The PI3K pathway is one of the most commonly misregulated signaling pathways in human cancers. Here, MCF10A cells expressing the two most common PI3K mutations, PIK3CA E545K and H1047R, were used to identify the repertoire of genes altered by oncogenic PI3K mutations following growth factor deprivation.
This gene set most closely correlated with gene signatures from claudin-low and basal-like breast tumors, and categorical enrichment analyses suggested that NF-kB target genes were dramatically upregulated by these mutations. An IKKb inhibitor was used to identify the subset of PI3K-driven genes that is NF-kB dependent. Interestingly, virtually all of these NF-kB dependent genes were secreted proteins, suggesting a paracrine role for this gene set. Among these genes was IL-6, a cytokine frequently expressed in tumors which plays a critical role in
generating a tumor-promoting microenvironment. Consistent with this, conditioned media from cells expressing the E545K or H1047R mutations led to increased STAT3 activation in recipient THP-1 monocytes or normal epithelial cells in a NF-kB and IL-6-dependent manner. Together,
these data describe a PI3K-driven, NF-kB-dependent gene expression profile which may play a critical role in promoting a microenvironment amenable to tumor progression.

overall_design: 39 normal cell lines vs treated cell lines for micorarray analysis

first: Jessica

last: Hutti

first: Adam

last: Pfefferle


title: Genome-wide dMTF-1-binding sites in Drosophila S2 cells in the absence or presence of copper or cadmium

status: Public on Sep 01 2012

city: Waltham

first: Hillel

last: Sims

state: MA

address: 415 South Street

department: Biology

country: USA

institute: Brandeis University

type: Genome binding/occupancy profiling by genome tiling array

summary: Cells respond to changes in environment by shifting their gene expression profile to deal with the new conditions. The cellular response to changes in metal homeostasis is an important example of this. Transition metals such as iron, zinc, and copper are essential micronutrients but other metals such as cadmium are simply toxic. The cell must maintain metal concentrations in a window that supports efficient metabolic function but must also protect against the damaging effects of high concentrations of these metals. One way a cell regulates metal homeostasis is to control genes involved in metal mobilization and storage. Much of this regulation occurs at the level of transcription and the protein most responsible for this is the conserved metal responsive transcription factor, MTF-1. Interestingly, the nature of the changes in the gene expression profile depends on the type of exposure. The cell somehow senses the kind of metal challenge and responds appropriately. We have been using the Drosophila system to try to understand the mechanism of this metal discrimination. Using genome-wide mapping of MTF-1 binding under different metal stresses, we find that, surprisingly, MTF-1 chooses different DNA binding sites depending on the specific nature of the metal insult. We also find that the type of binding site chosen is an important component of the capability to induce the metal-specific transcription activation.

overall_design: Chromatin immunoprecipitation coupled with Drosophila genomic tiling arrays (ChIP-chip) was used to identify genomic regions directly bound by dMTF-1 in untreated and metal (Cu and Cd) challenged S2 cells. The dMTF-1 antibody was raised against amino acids 1-113 and 406-540 of MTF-1.

middle: I

first: Michael

middle: T

last: Marr II

first: Gung

middle: W

last: Chirn


title: Targeting serous epithelial ovarian cancer with designer zinc finger transcription factors

status: Public on Sep 29 2012

city: CHAPEL HILL

first: PILAR

last: BLANCAFORT

state: NORTH CAROLINA

address: 4009 MASON FARM RD

department: PHARMACOLOGY

institute: UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL

summary: Ovarian cancer is the leading cause of death among gynecological malignancies. It is usually detected at late stages when the disease is spread through the abdominal cavity in form of ascitic fluids. Thus, there is an urgent need to develop novel therapeutic interventions to target advanced stages of ovarian cancer, particularly metastatic disease. Mammary serine protease inhibitor (Maspin) represents an important metastasis suppressor initially identified in breast cancer. In this work we have generated a sequence-specific zinc finger artificial transcription factor (ATF) to up-regulate the Maspin promoter in aggressive ovarian cancer cell lines, to interrogate the therapeutic potential of Maspin in ovarian cancer. We found that while Maspin was expressed in some primary ovarian tumors, the promoter was epigenetically silenced in cell lines derived from ascites. Transduction of the ATF in MOVCAR 5009 cells derived from ascitic cultures of a TgMISIIR-Tag mouse model of ovarian cancer resulted in tumor cell growth, impaired cell invasion, and severe disruption of actin cytoskeleton. Systemic delivery of lipid-protamine-RNA (LPR) nanoparticles encapsulating a chemically modified ATF mRNA resulted in inhibition of ovarian cancer cell growth in nude mice, accompanied with Maspin re-expression in the treated tumors. Finally, gene expression microarrays of ATF-transduced cells revealed an exceptional potency and specificity for the Maspin promoter. These analyses revealed targets co-regulated with Maspin in human short-term cultures derived from ascitic fluids from ovarian cancer patients, such as TSPAN12, which could mediate the anti-metastatic phenotype of the ATF. Our work outlined the first targeted, non-viral delivery of designer ATFs into tumors with potential application in clinical trials for metastatic ovarian cancers.

overall_design: reference X sample with 6 samples

first: Haydee

last: Lara

first: Adriana

middle: S

last: Beltran

first: Pilar

last: Blancafort


title: Nf1 deletion and recurrent copy number alterations in mammary tumorigenesis

status: Public on Aug 21 2012

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Breast cancer is the most prevalent cancer in women, and most cases are believed to have a sporadic, rather than heritable basis.  Therefore,  a major challenge in cancer research is to determine the underlying genomic alterations leading to carcinogenesis and malignancy, and then use this information for personalized therapies.  Genomic studies of human cancers that aim to identify causative mutations are complicated by the prevalence of passenger mutations, genetic heterogeneity, and the diversity of breast cancer etiologies and tumor subtypes.  Mouse cancer models are powerful for untangling the genomic basis of cancers because genetic and phenotypic variation can be eliminated or controlled.  To identify genes contributing to mammary tumorigenesis, we exploited the C3H-Mcm4Chaos3/Chaos3 (“Chaos3”) mouse model that, by virtue of bearing a defective DNA replicative helicase subunit that causes elevated genomic instability (GIN), sustains somatic alterations ultimately causing mammary adenocarcinomas.  Genomic analysis of Chaos3 mammary tumors revealed recurrent copy number alterations (CNAs) of specific genomic regions, most notably deletion of the Neurofibromin 1 (Nf1) tumor suppressor gene in all cases.  NF1, a negative regulator of RAS, is traditionally recognized for its role in driving the development of neurofibromas in the context of the human disease Neurofibromitosis but not breast cancer.  We observed elevated RAS activation and increased sensitivity of both Chaos3 and human Nf1-mutated breast cancer lines to MAPK and/or PI3K/AKT pathway inhibitors.  We also found striking overlap between Chaos3 CNAs and human breast cancer CNA data curated in public genomic databases, including Nf1 deletion.  Together, our results indicate that spontaneous NF1 loss can drive breast cancer and suggests a potential therapeutic strategy in that subset of patients.

overall_design: reference x sample

first: Marsha

middle: D

last: Wallace

middle: M

first: John

middle: C

last: Schimenti


title: Maintenance of Hormone Responsiveness in Luminal Breast Cancers by Suppression of Notch

status: Public on Dec 21 2011

summary: Luminal breast cancers express estrogen (ER) and/or progesterone (PR) receptors and respond to hormone therapies. Basal-like “triple negative” (TN) cancers lack steroid receptors but are cytokeratin (CK) 5-positive and require chemotherapy. Here we show that over half of primary ER+PR+ breast cancers contain an ER–PR–CK5+ “luminobasal” subpopulation exceeding 1% of cells. Starting from ER+PR+ luminal cell lines, we generated novel lines with varying luminal to luminobasal-cell ratios and studied their molecular and biological properties. In luminal disease, luminobasal cells expand in response to antiestrogen or estrogen withdrawal therapies. The phenotype and gene signature of the hormone resistant cells matches that of clinical TN basal-like and claudin-low disease. Luminobasal-cell expansion in response to hormone therapies is regulated by Notch1 signaling and can be blocked by gamma-secretase inhibitors (GSI). Our data establish a previously unrecognized plasticity of ER+PR+ luminal breast cancers that, without genetic manipulation, mobilizes outgrowth of hormone-resistant basal-like disease in response to treatment. This undesirable outcome can be prevented by combining endocrine therapies with Notch inhibition.

overall_design: 24 array samples

first: James

last: Haughian

first: Kathryn

middle: B

last: Horwitza


title: Genome-wide identification of SCARECROW (SCR) direct targets using a custom Agilent promoter array

status: Public on Nov 23 2011

city: Durham

first: Anjali

last: Iyer-Pascuzzi

institute: Duke University

summary:
ChIP-chip analysis was used to identify direct targets of the transcription factor SCR
SCARECROW (SCR) is a key regulatory of radial patterning and stem cell renewal in the primary root. We have shown in previous studies that SCR is a direct transcriptional regulator in Arabidopsis thaliana. With the aim of understanding the molecular pathway acting downstream of SCR in primary root development, we identified SCR direct targets at the genome-wide level in primary roots.To do this we designed a promoter microarray (chip) for Arabidopsis containing probes tiling the intergenic regions, first intron, and 3’UTR of all annotated genes. We performed Chromatin Immunoprecipitation (ChIP) using an antibody to Green Fluorescent Protein (GFP) on roots of transgenic plants expressing a functional fusion protein of SCR and GFP that is driven by the SCR promoter. Our control was performing ChIP in parallel using the same anti-GFP antibody on roots of Columbia-O wild-type plants.  DNA recovered from the SCR and wild-type ChIP experiments with Cy5 and Cy3 dye, respectively, and then hybridized to the same microarray. The array was scanned using an Agilent scanner and the signal intensity for each channel was retrieved and normalized by Agilent feature extraction software. Two biological replicates of this ChIP-chip experiment were performed.

overall_design: Two biological replicates of the ChIP-chip experiment were performed using samples isolated from primary roots. Each Agilent array was hybridized with both SCR ChIP and wild-type control samples differentially labeled with Cy5 and Cy3 dye, respectively.

first: Wolfgang

last: Busch

first: Jalean

middle: J

last: Petricka


title: Adaptation to transposon invasion in Drosophila melanogaster

status: Public on Dec 23 2011

city: Worcester

first: Jie

last: Wang

address: 364 Plantation St.

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

type: Genome variation profiling by genome tiling array

summary: Transposons evolve rapidly and can mobilize and trigger genetic instability. piRNAs silence these genome pathogens, but it is unclear how the piRNA pathway adapts to new transposons.  In Drosophila piRNAs, encoded by heterochromatic clusters are maternally deposited in the embryo.  Paternally inherited P-element transposons thus escape silencing and trigger a genetic instability and sterility.  We show that this syndrome, termed P-M hybrid dysgenesis, also disrupts the piRNA biogenesis machinery and activates resident transposons.   As dysgenic hybrids age, however, fertility is restored, P-elements are silenced, and P-element piRNAs are produced de novo. In addition, the piRNA biogenesis machinery is restored and resident elements are silenced.  Significantly, new resident transposons insertions accumulate in piRNA clusters, and these new insertions are transmitted to progeny with high fidelity, produce novel piRNAs, and are associated with reduced transposition.  P-M hybrid dysgenesis thus leads to heritable changes in chromosome structure that appear to enhance transposon silencing.

overall_design: 3 replicates of each sample (Har 2-4 days, w1 x Har 2-4 days, w1 x Har 21 days), total RNA samples hybridized to tiling array.

first: Jaspreet

last: Khurana


title: A genomewide association study for bronchopulmonary dysplasia using DNA pooling

status: Public on Nov 22 2011

city: Créteil

first: Alice

last: Hadchouel

address: 8 rue du général Sarrail

country: France

institute: INSERM

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Bronchopulmonary dysplasia (BPD) is the most common chronic respiratory disease in premature infants. Recent studies have highlighted the contribution of genetic factors to BPD susceptibility. Our aim was to identify the genetic variants associated to BPD, through a genomewide association study. Two discovery series were performed, using a DNA pooling-based strategy in Caucasian and black African neonates.

overall_design:
DNA pooling studies were performed in two discovery series. The first discovery series was made up of 22 Caucasian infants with BPD and 76 Caucasian controls. The second discovery series was composed of 21 black African infants with BPD and 86 black African controls. Equimolar amounts of each DNA sample were then added to either the case or control pool, for each series. To control for experimental errors, several independent sets of pools were constructed. Concerning the Caucasian series, 3 sets of identical pools were constructed with one made in double quantity in order to hybridize it twice, which led to 4 independent replicates. Concerning the black African series, 4 sets of identical pools were constructed and each was hybridized once, leading also to 4 independent replicates. Genotyping was performed using the Infinium II Illumina HumanHap300 Genotyping BeadChip array for the Caucasian population and the Illumina HumanHap650Y array for the black African population. Each replicate was hybridized once which led to 4 arrays for each case and control pools and for each population. A total of 16 arrays were performed.
technical replicate: Sample 1, Sample 2, Sample 3, Sample 4
technical replicate: Sample 5, Sample 6, Sample 7, Sample 8
technical replicate: Sample 9, Sample 10, Sample 11, Sample 12
technical replicate: Sample 13, Sample 14, Sample 15, Sample 16

first: Christophe

last: Delacourt


title: Obesity Promotes Epithelial-To-Mesenchymal Transition and Tumor Progression in a Mouse Model of Claudin-Low Breast Cancer.

status: Public on Jun 30 2012

summary:
ABSTRACT:
Obesity is responsible for decreased overall survival for breast cancer patients. Here, we describe the generation, characterization and application of a novel murine mammary tumor initiating cell model (M-Wnt) that recapitulates the claudin-low subtype of human breast cancer and permits the study of TIC’s in wild-type, immunocompetent mice. M-Wnt cells readily form mammospheres in suspension culture, express markers consistent with epithelial-to-mesenchymal transition (EMT), and generate claudin-low mammary tumors when as few as 50 cells are orthotopically injected. Using the M-Wnt cell lines in tandem with a more basal-like epithelial breast cancer cell line, E-Wnt, we found that diet induced obesity significantly downregulates epithelial markers, such as E-cadherin, and upregulates mesenchymal markers including fibronectin, N-cadherin, SNAIL, Oct-4, and TGF-b.  This reveals a previously unidentified link between energy balance and EMT.  The ability of calorie restriction (CR) to reverse EMT, upregulate epithelial markers and downregulate mesenchymal markers indicates the plasticity of the TICs, as well as the potential importance of lifestyle modifications as cancer prevention strategies.

overall_design: 28 array samples

first: Sarah

last: Dunlap

first: Jerry

last: Usary

first: Stephen

last: Hursting


title: Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner

status: Public on Dec 12 2011

city: Rotterdam

first: Yuri

last: Moshkin

address: Dr. Molewaterplein 50

country: Netherlands

institute: Erasmus University Medical Center

summary:
We assessed the interplay between DNA sequences and ATP-dependent chromatin remodelers in defining the nucleosomal organization of the eukaryotic genome. We compared the genome-wide distribution and impact on chromatin of NURD, (P)BAP, INO80 and ISWI representing four major families of Drosophila remodelers. Each remodeler has a unique set of genomic targets, and generates distinct chromatin signatures. Remodeler loci have characteristic DNA sequence features, predicted to influence nucleosome formation. Strikingly, remodelers counteract DNA sequence-driven nucleosome distribution in two ways: NURD, (P)BAP and INO80 increase histone density at their target sequences, which disfavor positioned nucleosome formation. In contrast, ISWI promotes open chromatin at sites that are propitious for precise nucleosome placement. Thus, both selective targeting and distinct mechanisms of remodeling underlie the functional differentiation of remodelers. We conclude that chromatin organization involves a class-specific antagonism between remodeler activity and DNA sequence-driven nucleosome placement.
The supplementary bed files (P)BAP_sites.bed, NURD_sites.bed, INO80_sites.bed, ISWI_sites.bed contain high quality binding sites for each remodeler obtained by intersecting the sets of significant ChIP-chip peaks for each antibody.

overall_design: Genome-wide remodelers and chromatin profiling in Drosophila by ChIP-chip and FAIRE-chip

first: C

middle: P

last: Verrijzer


title: Genome-wide profiling of RNA associated to the chromosome 4 specific protein POF in Drosophila melanogaster

status: Public on May 31 2012

city: Umea

first: Jan

last: Larsson

address: Umea University

department: Molecular Biology

country: Sweden

institute: Umea University

type: Expression profiling by genome tiling array

summary: In Drosophila, two chromosome-wide compensatory systems have been characterized; the dosage compensation system acting on the male X-chromosome and the chromosome specific regulation of genes located on the heterochromatic 4th chromosome. Dosage compensation in Drosophila is accomplished by hypertranscription of the single male X-chromosome mediated by the MSL-complex. The mechanism for this compensation is suggested to be an MSL-complex mediated enhanced transcriptional elongation while the mechanism for the compensation mediated by Painting of fourth (POF) on the 4th chromosome has remained elusive. Here we show that POF binds to nascent RNA and this binding is associated with an increase in amount of chromosome 4 transcripts. Furthermore, genes located on the 4th chromosome are enriched in binding of the nucleoplasmic nucleporin component NUP98 and this enrichment correlates to increased POF binding. We also show that genes located in heterochromatic regions have a shorter transition time from site of transcription and to the nuclear envelope. Our current work broadens the understanding about how genes in heterochromatic regions can overcome the repressive influence of their hostile environment.

overall_design: In total 10 samples; 5 Input files (5 different conditions) with the corresponding 5 RIP samples

first: Anna-Mia

last: Johansson

first: Per

last: Stenberg

first: Anders

last: Allgardsson


title: Combined PI3K/mTOR and MEK Inhibition Provides Broad Anti-Tumor Activity in Faithful Murine Cancer Models

first: Charles

last: Perou

summary: Anticancer drug development is an inefficient process, with potential therapeutics demonstrating a high attrition rate due to lack of efficacy in Phase II/III testing.  In an effort to develop improved pre-clinical predictors of efficacy, we and others have turned to testing in genetically engineered murine models (GEMMs) of cancer, which may offer some advantages to in vitro and xenograft systems. Specifically, we assessed the activity of 16 treatment regimens in a Ras-driven, Ink4a/Arf-deficient melanoma GEMM.  Like human RAS-mutant melanoma, this GEMM was refractory to standard chemotherapy and single-agent small molecule therapies.  Only one regimen exhibited significant anti-tumor activity in this model: combined treatment with AZD6244 (MEK inhibitor) and BEZ235 (dual PI3K/mTOR inhibitor), which produced marked tumor regression and improved survival. Given the surprising activity of the “AZD/BEZ” combination in a melanoma GEMM, we next tested this regimen in a Ras-driven orthotopic-transplant model of “claudin-low” breast cancer, which shares some gene expression features with melanoma.  The AZD/BEZ regimen also exhibited significant activity in this related Ras-driven model, leading us to testing in even more diverse GEMMs of basal-like and luminal breast cancer.  The AZD/BEZ combination was highly active in each of these distinct breast models, demonstrating equal or greater efficacy compared to any other regimen tested in studies of over 700 tumor-bearing mice.  This regimen even exhibited activity in tumors selected for resistance to another effective chemotherapy agent, lapatinib, in HER2+ models.  These results demonstrate the utility of credentialed murine models for large-scale efficacy testing of diverse anti-cancer regimens, and predict combinations of PI3K/mTOR and MEK inhibitors will demonstrate anti-tumor activity in a wide-range of human malignancies.

overall_design: 16 array samples

first: Patrick

last: Roberts

first: Norman

middle: E

last: Sharpless


title: Pof mutant

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

overall_design: Refer to individual Series


title: TBCRC 001:  Randomized Phase II Study of Cetuximab in Combination with Carboplatin in Stage IV Triple Negative Breast Cancer

status: Public on Jul 14 2012

summary:
Abstract
Background. Epidermal growth factor receptor (EGFR) is a targetable molecule in basal-like breast cancer, which comprises most “triple negative” breast cancer (TNBC), the only breast cancer subtype without established targeted therapy.
Methods. In this randomized phase II trial, metastatic TNBC patients received the anti-EGFR antibody cetuximab (250mg/kg/week iv) with carboplatin (AUC2/wk iv) added on progression, or concomitant cetuximab + carboplatin. Molecular subtyping was done on archival specimens and those with accessible tumors provided fresh tissue, before and after 7-14 days of therapy, for microarray analyses to explore EGFR pathway inhibition.
Results. Of 102 TNBC patients 74% were of the basal-like molecular subtype.  Response rate to cetuximab was 6% (2/31), and was 16% (4/25) to cetuximab + carboplatin after progression. Upfront cetuximab + carboplatin produced responses in 17% (12/71); 31% responded or had prolonged disease stabilization. Time to progression was 2.1 months (95% CI 1.8-5.5) and overall survival 10.4 months (95% CI 7.7-13.1) for those treated with the combination regimen. Among 16 patients with evaluable serial biopsies, genomic patterns of the EGFR pathway showed activated status in 13 and inhibition by therapy in 5.
Conclusions.  While most TNBC were basal-like, a significant proportion were different subtypes. The aggressive nature of metastatic TNBC leads to limited survival. Despite a promising preclinical rationale and evidence of EGFR pathway activation in most, targeted treatment with cetuximab as a single agent had marginal activity and cetuximab added to carboplatin demonstrated modest activity.  Serial biopsies as part of metastatic breast cancer studies are feasible, and this study confirmed that the EGFR pathway was inhibited by therapy in only a minority suggesting ligand-independent activation in most tumors. Tissue acquisition and drug selection based upon individualized pathway activation status should be an important part of future studies of TNBC.

overall_design:
This series contains 36 microarrays that are from 18 patients with fresh frozen tissue  available from the metastatic site.  Pretreatment samples (Bx0) are available for two patients.  Pretreatment and post single agent treatment (7-14 days after start of treatment with cetuximab; BxSingle) are available for three patients.  Pretreatment and post combination treatment (7-14 days after start of treatment with cetuximab plus carboplatin; BxCombo) are available for eight patients.  Two patients have a pretreatment sample, a sample after 7-14 days of treatment with single agent cetuximab, and a third sample 7-14 days on cetuximab plus carboplatin after switching to the combination arm upon progression on the single agent arm.
Samples were hybridized with Stratagene common reference spiked with RNA from two breast cancer cell lines (ME16C and MCF-7) on Custom 1x44K Agilent microarrays.  Arrays were scanned on an Axon 4000B scanner and analyzed with GenePix Pro software.

first: Lisa

middle: A

last: Carey

first: Hope

last: Rugo

first: Kelly

last: Marcom

first: Erica

last: Mayer

first: Francisco

last: Esteva

first: Cynthia

last: Ma

first: Minetta

last: Liu

first: AnnaMaria

last: Storniolo

first: Mothaffar

last: Rimawi

first: Andres

last: Forero

first: Antonio

last: Wolff

first: Timothy

last: Hobday

first: Anastasia

last: Ivanova

first: Michael

last: Chiu

first: Madlyn

last: Ferraro

first: Emily

last: Burrows

first: Philip

last: Bernard

first: Katherine

last: Hoadley

first: Eric

last: Winer


title: Su(var)3-9-Q2598.Kc

status: Public on Oct 13 2011

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_3899
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody Su(var)3-9-Q2598 (target is Su(var)3-9)

first: Gary

last: Karpen

first: Sarah

last: Elgin

first: Andrey

last: Gortchakov

first: Greg

last: Shanower

last: Tolstorukov

first: Peter

last: Kharchenko

first: Mitzi

last: Kuroda

first: Vincenzo

last: Pirrotta

last: Park

first: Aki

last: Minoda

first: Nicole

last: Riddle

first: Yuri

last: Schwartz

first: Art

last: Alekseyenko

first: Cameron

last: Kennedy


title: LKB1/STK11 Inactivation Leads to Expansion of Pro-Metastatic Tumor Sub-Population in Melanoma

status: Public on Jun 25 2012

first: Charles

last: Perou

summary: Germline mutations in LKB1 (STK11) are associated with the Peutz–Jeghers syndrome (PJS), which includes aberrant mucocutaneous pigmentation, and somatic LKB1 mutations occur in 10% of cutaneous melanoma. By somatically inactivating Lkb1 with K-Ras activation (+/- p53 loss) in murine melanocytes, we observed variably pigmented and highly metastatic melanoma with 100% penetrance. LKB1 deficiency resulted in increased phosphorylation of the SRC-family kinase (SFK) YES and the subsequent expansion of a CD24+ cell population which showed increased metastatic behavior in vitro and in vivo relative to isogenic CD24- cells. These results suggest that LKB1 inactivation in the context of RAS activation facilitates metastasis by inducing a SFK-dependent expansion of a pro-metastatic, CD24+ tumor sub-population

first: Wenjin

last: Liu

first: Adam

last: Pfefferle

first: Norman

last: Sharpless


title: Lunatic Fringe Deficiency Cooperates with the Met/Caveolin Gene Amplicon to Induce Basal-Like Breast Cancer

status: Public on May 30 2012

summary:
SUMMARY:
Basal breast cancer has been associated with mutations in a number of specific tumor suppressor genes, however, the mechanism by which these tumors express a basal lineage remains unknown.  Notch signaling suppresses mammary stem cell (MaSC) self-renewal, while promoting luminal cell fate specification. Here we show that Lfng, a sugar transferase that facilitates Notch activation, suppresses mammary stem/bipotent progenitor cell proliferation. Targeted deletion of Lfng in mammary epithelium induces basal tumors with reduced expression of Notch targets, amplification of the Met/Caveolin gene locus, and elevated Met and Igf-1R signaling. Human basal breast cancer, a disease associated with elevated MET receptor signaling and Caveolin protein, express low levels of LFNG. Thus, reduced LFNG expression cooperates with a Met/ Caveolin amplicon to promote basal breast disease.

SIGNIFICANCE:
Anti-Notch therapy is currently being tested for efficacy against basal-like breast cancer in humans.  Here we report that LFNG, which controls Notch receptor activation, is consistently expressed at a low level in basal tumors and that deletion of this gene in the mouse mammary gland reduces Notch signaling, increases proliferation and induces basal mammary tumors in cooperation with amplification of the Met/Caveolin gene locus.  These mutations interact to promote basal gene expression by decreasing Notch pathway activation, as well as to enhance Met and Igf-1R signaling. These pathways can be targeted at multiple levels in humans harboring basal breast cancer with amplification of MET and CAV1/2

overall_design: 35 array samples

first: Keli

last: Xu

first: Jerry

last: Usary

first: Sean

last: Egan


title: Development and validation of a 31,918-genes oyster cDNA Microarray: Tissue-specific expression profiles

status: Public on Oct 16 2011

city: Caen

first: Nolwenn

middle: Marie

last: Dheilly

address: Esplanade de la Paix

department: Biological sciences

institute: Universite de caen

summary: Research using the oyster Crassostrea gigas as a model has experienced a rapid growth in recent years thanks to the development of high throughput molecular technologies. As many as 56,268 EST sequences have so far been sequenced, representing a genome-wide resource that can be used for microarray investigations. We have developed an oyster microarray containing cDNAs representing 31,918 unique transcribed sequences. The genes spotted on the array have been selected from the publicly accessible GigasDatabase established from cDNA libraries derived from a wide variety of tissues and different developmental stages.    n this paper, we report the transcriptome of male and female gonads, mantle, gills, posterior adductor muscle, visceral ganglion, hemocytes, labial palps and digestive gland. Following validation of the microarray, statistical analyses were used to identify genes differentially expressed among tissues and define clusters of tissue-specific genes. These genes reflect well major tissue-specific functions at the molecular level. Analysis of hierarchical clustering data also predicted the involvement of un-annotated genes in selected functional pathways. In a second instance, microarray data were used to accurately select housekeeping genes common to all tissues. Their expression profiles was compared to common oyster standard genes used for quantitative RT-PCR calibration (actin, g3apdh and ef1α). The novel candidate housekeeping gene, adp-ribosylation factor 1 (arf1) and g3apdh gene seem to be more robust for normalizing gene expression data of tissues.  This study provides a new source for annotating the oyster genome. It also identified new candidate housekeeping genes, a prerequisite for accurate quantitative RT-PCR expression profiling.

overall_design: Gene expression was measured in 9 tissues: Female gonad, male gonad, mantle, gills, posterior adductor muscle, visceral ganglion, hemocytes, labial palps, digestive gland.Three to four biological replicates were analysed per tissue. These were from distinct animals for female gonad, male gonad, mantle, gills, posterior adductor muscle, labial palps and digestive glands, or obtained from a pool of 6 individuals for hemocytes and visceral ganglion.

first: Christophe

last: Lelong

first: Arnaud

last: Huvet

first: Pascal

last: Favrel


title: Drosophila CLOCK Target Gene Characterization: Implications for Circadian Tissue-Specific Gene Expression

status: Public on Nov 15 2011

first: Katharine

last: Abruzzi

address: 415 South St.

institute: Brandeis University; Howard Hughes Medical Institute

summary: CLOCK (CLK) is a master transcriptional regulator of the circadian clock in Drosophila. To identify CLK direct target genes and address circadian transcriptional regulation in Drosophila, we performed chromatin immunoprecipitation-tiling array assays (ChIP-chip) with a number of circadian proteins. CLK binding cycles on at least 800 sites with maximal binding in the early night. The CLK partner protein CYCLE (CYC) is on most of these sites. The CLK/CYC heterodimer is joined 4-6 hrs later by the transcriptional repressor PER, indicating that the majority of CLK targets are regulated similarly to core circadian genes (Menet et al. 2010). About 30% of target genes also show cycling Pol II binding. Many of these generate cycling RNAs despite not being documented in prior RNA cycling studies. This is due in part to different RNA isoforms and to fly head tissue heterogeneity. CLK has specific targets in different tissues, implying that important CLK partner proteins and/or mechanisms contribute to gene-specific and tissue-specific regulation.

overall_design: 5 different datasets are included including: CLK ChIP-chip (samples collected at 6 timepoints, 2 replicates each, input and IP samples), PER ChIP-chip (samples collected at 6 timepoints, 2 replicates each, input and IP samples), RNA Pol II ChIP-chip (samples collected at 6 timepoints, 2 replicates each, input and IP samples), CYC-ChIP-chip (samples from ZT14, samples in triplicate, input and IP samples), GMR-hid CLK ChIP-chip (2 replicates at ZT14 of both WT and GMR-hid, input and IP samples).  Total of 62 arrays

first: Michael

last: Rosbash


title: Su(var)3-9-Q2598.D.mel 3rd Instar Larvae Nuclei

first: DCC

last: modENCODE

summary:
modENCODE_submission_3898
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: 3rd Instar Larvae; Genotype: wild type;  NUMBER OF REPLICATES: 7;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody Su(var)3-9-Q2598 (target is Su(var)3-9); Developmental Stage 3rd Instar Larvae

first: Gary

last: Karpen

first: Sarah

last: Elgin

first: Andrey

last: Gortchakov

first: Greg

last: Shanower

last: Tolstorukov

first: Peter

last: Kharchenko

first: Mitzi

last: Kuroda

first: Vincenzo

last: Pirrotta

last: Park

first: Aki

last: Minoda

first: Nicole

last: Riddle


title: Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

summary: To study the population genetic structure and genome-wide signals of positive selection we carried out Illumina genotyping for 142 individuals of Sout Asian origin

overall_design:
142 samples are analysed on thwo different Illumina platforms. 48 of them with  Human610-Quad v 1.0 are described herein.
142 samples are analysed on thwo different Illumina platforms. 94 of them with  HumanHap650Yv3_A are described herein.

first: Richard

last: Villems


title: Transcriptome profiling of wild type and Pof mutant Drosophila melanogaster females

first: Jan

last: Larsson

overall_design: Pof mutant vs. wild type, 3 replicates

first: Anna-Mia

last: Johansson

first: Per

last: Stenberg

first: Anders

last: Allgardsson


title: POF (MO 459).S2

last: modENCODE

summary:
modENCODE_submission_3897
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 6;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody POF (MO 459) (target is POF)

last: Karpen

first: Michael

first: Yuri

last: Schwartz

first: Art

last: Alekseyenko

first: Cameron

last: Kennedy


title: Pho.S2

first: DCC

summary:
modENCODE_submission_3894
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody Pho (target is Pho)

first: Gary

first: Sarah

last: Elgin

first: Andrey

last: Gortchakov

last: Shanower

last: Tolstorukov

last: Kharchenko


title: H3K23ac.D.mel 3rd Instar Larvae Nuclei

summary:
modENCODE_submission_3887
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: 3rd Instar Larvae; Genotype: wild type;  NUMBER OF REPLICATES: 6;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody H3K23ac (target is H3K23ac); Developmental Stage 3rd Instar Larvae

first: Greg

first: Peter

first: Mitzi

last: Kuroda

first: Vincenzo

last: Pirrotta

last: Park

last: Minoda

last: Riddle


title: HP1 wa191.S2.HP1a_RNAi

summary:
modENCODE_submission_3893
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The goal of these experiments are to validate and confirm the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. To do this, we are using RNAi to deplete individual non-histone chromosomal proteins in Drosophila BG3 and S2 tissue culture cells, and then using antibodies to perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. Comparison of a protein factor's binding profiles before and after depletion will increase the confidence of our predictions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody HP1 wa191 (target is HP1a); dsRNA (RNAi_reagent) CG8409_RNAi&oldid=39599

first: Aki

first: Nicole


title: ZW5.S2

summary:
modENCODE_submission_3804
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody ZW5 (target is ZW5)


title: H3K9me2-Ab2 (new lot).D.mel 3rd Instar Larvae Nuclei

summary:
modENCODE_submission_3890
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: 3rd Instar Larvae; Genotype: wild type;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody H3K9me2-Ab2 (new lot) (target is H3K9me2); Developmental Stage 3rd Instar Larvae


title: Genome-wide IMPDH profiling in Drosophila larvae and S2 cells by ChIP-chip.

status: Public on May 01 2012

last: Moshkin

summary: Division of labor is a central feature of cellular organization. Consequently, gene regulation and intermediary metabolism are generally believed to be conducted by strictly separate classes of proteins. Here, we show that inosine monophosphate dehydrogenase (IMPDH), the central enzyme in guanine nucleotide biosynthesis, moonlights as a gene-specific transcription factor. Nuclear exclusion during S phase coordinates IMPDH’s transcriptional activities with the cell cycle. IMPDH represses target gene expression, including the histone genes. Unexpectedly, genomic IMPDH loci have the propensity to unwind. Genome-wide profiling and in vitro experiments revealed that IMPDH binds sequence-specifically to single stranded C/T-rich DNA elements. Thus, a classic biosynthetic enzyme can act as a DNA-binding transcription factor, suggestive of a more reciprocal and intimate relationship between metabolism and gene expression than commonly assumed.

overall_design:
Genome-wide IMPDH profiling in Drosophila S2 cells by ChIP-chip.

The supplementary bed file 'S2_IMPDH_regions.bed' contains high-quality binding sites for IMPDH obtained by intersecting the sets of significant ChIP-chip peaks from 3 biological replicates.

Genome-wide IMPDH profiling in Drosophila larvae by ChIP-chip

The supplementary bed file larvae_IMPDH_regions.bed contains high quality binding sites for IMPDH obtained by intersecting the sets of significant ChIP-chip peaks from 4 biological replicates.

first: Elena

middle: N

last: Kozhevnikova

first: C

last: Verrijzer


title: Smc3_Q2580.Kc

last: modENCODE

summary:
modENCODE_submission_3800
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody Smc3 Q2580 (target is Smc3)

last: Karpen


title: ZW5.Kc

summary:
modENCODE_submission_3803
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

last: Schwartz

last: Alekseyenko


title: RNA Pol II (abcam).D.mel 3rd Instar Larvae Nuclei

summary:
modENCODE_submission_3799
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: 3rd Instar Larvae; Genotype: wild type;  NUMBER OF REPLICATES: 6;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody RNA Pol II (abcam) (target is PolII); Developmental Stage 3rd Instar Larvae

last: Elgin

last: Kennedy


title: Psc.Kc

summary:
modENCODE_submission_3797
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody Psc (target is Psc)

last: Gortchakov

last: Shanower


title: PCL Q3412.Kc

summary:
modENCODE_submission_3792
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody PCL Q3412 (target is PCL)

last: Tolstorukov

last: Kharchenko


title: POF (MO 459).D.mel 3rd Instar Larvae Nuclei Sexed Female

summary:
modENCODE_submission_3795
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: 3rd Instar Larvae; Genotype: wild type;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody POF (MO 459) (target is POF); Developmental Stage 3rd Instar Larvae

last: Kuroda

last: Pirrotta


title: MLE_Q4143.S2

summary:
modENCODE_submission_3788
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody MLE Q4143 (target is MLE)

last: Park

last: Minoda


title: LSD1_Q3430.Kc

summary:
modENCODE_submission_3786
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody LSD1 Q3430 (target is LSD1)

last: Riddle


title: MBD-R2(Q4167).Kc

summary:
modENCODE_submission_3787
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody MBD-R2(Q4167) (target is MBD-R2)


title: mod2.2-VC.Kc

summary:
modENCODE_submission_3789
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody mod2.2-VC (target is MOD(MDG4)67.2)


title: Characterization of expression changes in qin by tiling array

status: Public on Nov 18 2011

first: Zhao

last: Zhang

address: LRB-870N, 364 Plantation Street

department: BMP

institute: UMass Medical School

summary: Qin, a novel protein comprising amino-terminal E3 ligase and five carboxy terminal Tudor domains, silences transposons and ensures genome stability in the Drosophila germline by promoting antisene piRNA amplification via Aubergine:Ago3 Ping-Pong and preventing futile Aubergine:Aubergine interactions.

overall_design: Extract total ovary RNAs, and using tiling array to test transposon as well as gene expression in wild-type and qin mutant flies. Three biological replicates are used.

first: Phillip

last: Zamore

first: Zhiping

last: Weng

first: William

last: Theurkauf


title: HP4 Q4072.D.mel 3rd Instar Larvae Nuclei

last: modENCODE

summary:
modENCODE_submission_3782
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: 3rd Instar Larvae; Genotype: wild type;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody HP4 Q4072 (target is HP4); Developmental Stage 3rd Instar Larvae

last: Karpen

first: Michael

first: Yuri

last: Schwartz

first: Art

first: Cameron


title: JMJD2A-KDM4A_Q2541.BG3

first: DCC

summary:
modENCODE_submission_3783
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody JMJD2A-KDM4A Q2541 (target is JMJD2A/KDM4A)

first: Gary

first: Sarah

last: Elgin

first: Andrey

last: Alekseyenko

last: Kennedy


title: H4K16ac(M).D.mel 3rd Instar Larvae Nuclei

summary:
modENCODE_submission_3776
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: 3rd Instar Larvae; Genotype: wild type;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody H4K16ac(M) (target is H4K16ac); Developmental Stage 3rd Instar Larvae

last: Gortchakov

first: Greg

last: Shanower

last: Tolstorukov

first: Peter

first: Mitzi

first: Vincenzo


title: H3K9me1.S2

summary:
modENCODE_submission_3770
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 5;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody H3K9me1 (target is H3K9me1)

last: Kharchenko

last: Kuroda

last: Pirrotta

first: Aki

first: Nicole


title: H3K9me1 (new lot).Kc

summary:
modENCODE_submission_3769
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody H3K9me1 (new lot) (target is H3K9me1)

last: Park

last: Minoda

last: Riddle


title: HP1a_hinge.S2

summary:
modENCODE_submission_3777
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody HP1a hinge (target is HP1a)


title: JMJD2A_Q2541.S2

summary:
modENCODE_submission_3784
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf


title: H3K9me2-Ab2 (new lot).D.mel 3rd Instar Larvae Nuclei Sexed Male

summary:
modENCODE_submission_3772
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: 3rd Instar Larvae; Genotype: wild type;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody H3K9me2-Ab2 (new lot) (target is H3K9me2); Developmental Stage 3rd Instar Larvae


title: H3K9me1 (new lot).BG3

summary:
modENCODE_submission_3768
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf


title: H3K9ac.BG3

summary:
modENCODE_submission_3765
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 6;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody H3K9ac (target is H3K9ac)


title: LSD1_Q3430.BG3

summary:
modENCODE_submission_3785
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf


title: H3K4me3 (ab8580 lot1).Kc

summary:
modENCODE_submission_3761
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody H3K4me3 (ab8580 lot1) (target is H3K4me3)


title: H3K79Me1.Kc

summary:
modENCODE_submission_3762
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody H3K79Me1 (target is H3K79me1)


title: GAF.Kc

summary:
modENCODE_submission_3753
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody GAF (target is GAF)


title: EZ-Q3419.Kc

summary:
modENCODE_submission_3752
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody EZ-Q3419 (target is E(Z))


title: H3K79Me2 AbCam.Kc

summary:
modENCODE_submission_3763
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody H3K79Me2 AbCam (target is H3K79me2)


title: H3K27me2.Kc

summary:
modENCODE_submission_3758
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody H3K27me2 (target is H3K27me2)


title: Pc.Kc

summary:
modENCODE_submission_3791
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody Pc (target is Pc)


title: NURF301_Q2602.Kc

summary:
modENCODE_submission_3790
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody NURF301 Q2602 (target is NURF301)


title: H3K4me1.Kc

summary:
modENCODE_submission_3760
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody H3K4me1 (target is H3K4me1)


title: H3K27Ac.Kc

summary:
modENCODE_submission_3757
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody H3K27Ac (target is H3K27ac)


title: dRING Q3200.Kc

summary:
modENCODE_submission_3750
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody dRING Q3200 (target is dRING)


title: H3K23ac.Clone_8

summary:
modENCODE_submission_3755
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 6;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody H3K23ac (target is H3K23ac)


title: dSFMBT Q2642.S2

summary:
modENCODE_submission_3751
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 8;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody dSFMBT Q2642 (target is dSFMBT)


title: CP190-HB.BG3.CP190_RNAi

summary:
modENCODE_submission_3747
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The goal of these experiments are to validate and confirm the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. To do this, we are using RNAi to deplete individual non-histone chromosomal proteins in Drosophila BG3 and S2 tissue culture cells, and then using antibodies to perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. Comparison of a protein factor's binding profiles before and after depletion will increase the confidence of our predictions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: ML-DmBG3-c2; Tissue: CNS-derived cell-line; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Unknown;  NUMBER OF REPLICATES: 5;  EXPERIMENTAL FACTORS: Cell Line ML-DmBG3-c2; Antibody CP190-HB (target is CP190); dsRNA (RNAi_reagent) CG6384_RNAi&oldid=39664


title: BEAF-HB.Kc

summary:
modENCODE_submission_3745
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody BEAF-HB (target is BEAF32A and BEAF32B)


title: ASH1 Q4177.Kc

summary:
modENCODE_submission_3744
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody ASH1 Q4177 (target is ASH1)


title: CTCF.Kc

summary:
modENCODE_submission_3749
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody CTCF (target is CTCF)


title: SU(HW)-HB.BG3.SU(HW)_RNAi

summary:
modENCODE_submission_3718
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The goal of these experiments are to validate and confirm the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. To do this, we are using RNAi to deplete individual non-histone chromosomal proteins in Drosophila BG3 and S2 tissue culture cells, and then using antibodies to perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. Comparison of a protein factor's binding profiles before and after depletion will increase the confidence of our predictions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: ML-DmBG3-c2; Tissue: CNS-derived cell-line; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Unknown;  NUMBER OF REPLICATES: 6;  EXPERIMENTAL FACTORS: Cell Line ML-DmBG3-c2; Antibody SU(HW)-HB (target is SU(HW)); dsRNA (RNAi_reagent) CG8573_RNAi&oldid=39388


title: SU(HW)-HB.S2.LacZ_RNAi

summary:
modENCODE_submission_3719
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The goal of these experiments are to validate and confirm the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. To do this, we are using RNAi to deplete individual non-histone chromosomal proteins in Drosophila BG3 and S2 tissue culture cells, and then using antibodies to perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. Comparison of a protein factor's binding profiles before and after depletion will increase the confidence of our predictions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody SU(HW)-HB (target is SU(HW)); dsRNA (RNAi_reagent) Fly_LacZ_RNAi&oldid=39667


title: CP190-HB.Kc

summary:
modENCODE_submission_3748
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody CP190-HB (target is CP190)