title: JL00003_DPY26_N2_MXEMB

summary:
modENCODE_submission_334

This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.

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: N2

DEVELOPMENTAL STAGE: embryo

GENOTYPE: wild type

NUMBER OF REPLICATES: 3, replicate 1 applied to 1 arrays, replicate 2 applied to 1 arrays, replicate 3 applied to 1 arrays
replicate 2 array 0 (sample id: JL00003_DPY26_N2_MXEMB_2 extraction1_array0) is dye swap

EXPERIMENTAL FACTORS: Antibody DPY26

first: Sevinc

last: Ercan

first: Jason

last: Lieb


title: Kc167 ORC2 Localization

status: Public on Jul 29 2009

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

type: Genome binding/occupancy profiling by genome tiling array

summary:
modENCODE_submission_674
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes.  These experiments will be conducted in multiple cell types and developmental tissues.

Keywords: CHIP-chip

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: Kc167; Tissue: embryo-derived cell-line; Genotype: se/e; Sex: Female NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Antibody dORC2

first: David

last: MacAlpine

first: Heather


title: Systematic evaluation of variability in simulated ChIP-chip experiments

status: Public on Dec 31 2008

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

country: USA

institute: Ludwig Institute for Cancer Research

summary:
The most widely used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms, amplification procedures, and signal detection algorithms in a simulated ChIP-chip experiment. Mixtures of human genomic DNA and "spike-ins" comprised of nearly 100 human sequences at various concentrations were hybridized to four tiling array platforms by eight independent groups. Blind to the number of spike-ins, their locations, and the range of concentrations, each group made predictions of the spike-in locations. We found that microarray platform choice is not the primary determinant of overall performance. In fact, variation in performance between labs, protocols and algorithms within the same array platform was greater than the variation in performance between array platforms. However, each array platform had unique performance characteristics that varied with tiling resolution and the number of replicates, which have implications for cost versus detection power. Long oligonucleotide arrays were slightly more sensitive at detecting very low enrichment. On all platforms, simple sequence repeats and genome redundancy tended to result in false positives. LM-PCR and WGA, the most popular sample amplification techniques, reproduced relative enrichment levels with high fidelity. Performance among signal detection algorithms was heavily dependent on array platform. The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated.
Keywords: ChIP-chip

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: See manuscript for details

first: Zhen

last: Ye

first: Keith

last: Ching


title: Large organized chromatin K9-modifications (LOCKs) distinguish differentiated from embryonic stem cells

status: Public on Jan 18 2009

city: Baltimore

first: Andrew

middle: P.

last: Feinberg

state: MD

address: 855 N. Wolfe Street

department: Center for Epigenetics and Department of Medicine

institute: Johns Hopkins University

summary: Higher eukaryotes must adapt a totipotent genome to specialized cell types with a stable but limited repertoire of functions. One potential mechanism for lineage restriction is changes in chromatin, and differentiation-related chromatin changes have been observed for individual genes. We have taken a genome-wide view of histone H3 lysine-9 dimethylation (H3K9Me2). We find that differentiated tissues exhibit surprisingly large K9-modified regions (up to 4.9 Mb), that are highly conserved between human and mouse, and differentiation-specific, covering only ~4% of the genome in undifferentiated mouse embryonic stem (ES) cells, compared to 31% in differentiated ES cells, ~46% in liver and ~10% in brain. They require histone methyltransferase G9a, and are inversely related to expression of genes within them, and we term them Large Organized Chromatin K9-modifications (LOCKs). LOCKs are are substantially lost in cancer cell lines, and they may provide a cell type-heritable mechanism for phenotypic plasticity in development and disease.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Chromatin was isolated without sonication or formalin cross linking, by digested with micrococcal nuclease, and then chromatin immunoprecipitation was performed with an antibody specific to H3K9Me2. ChIP and input DNA were amplified, labeled by Cy5 and Cy3 respectively, and hybridized to NimbleGen tilling arrays.

first: Bo

last: Wen

first: Hao

last: Wu

first: Yoichi

last: Shinkai

first: Rafael

middle: A

last: Irizarry

middle: P


title: JL00004_MIX1_N2_MXEMB

status: Public on Jun 02 2009

summary:
modENCODE_submission_336

This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.

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: N2

DEVELOPMENTAL STAGE: embryo

GENOTYPE: wild type

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 2 (Sample JL00004_MIX1_N2_MXemb_2 extraction2_array1) is dye swap. Replicate 3 applied to 1 array(s)

EXPERIMENTAL FACTORS: Antibody JL0004_MIX1


title: Mus musculus 22k comparison of samples

status: Public on Jan 01 2009

city: Pune

first: Dr. AnuKumar

last: Bala Krishnan

address: Dr. Ambedkar Road

department: Dept of Immunology

country: India

institute: NATIONAL INSTITUTE OF VIROLOGY(ICMR)

summary: Comparision of Mus musculus Control and Treated samples.

overall_design: Low RNA Input Fluorescent Linear Amplification Kit (Agilent, Santa Clara, CA) was used for labeling. Briefly, both first and second strand cDNA were synthesized by incubating 500ng of total RNA with 1.2ul of oligo dT-T7 Promoter Primer in nuclease-free water at 65 ◦C for 10 min followed by incubation with 4.0ul of 5× First strand buffer, 2ul of 0.1M DTT, 1 ul of 10mM dNTP mix, 1ul of 200 U/ul MMLV-RT, and 0.5ul of 40U/ul RNaseOUT, at 40 ◦C for 2 hour. Immediately following cDNA synthesis, the reaction mixture was incubated with 2.4 ul of 10 mM Cyanine-3-CTP or 2.4 ul of 10 mM Cyanine-5-CTP (Perkin-Elmer, Boston, MA), 20ul of 4X Transcription buffer, 8 ul of NTP mixture, 6 ul of 0.1M DTT, 0.5 ul of RNaseOUT, 0.6ul of Inorganic pyrophosphatase, 0.8 ul of T7 RNA polymerase, and 15.3ul of nuclease-free water at 40 ◦C for 2 hour. Qiagen’s RNeasy mini spin columns were used for purifying amplified aRNA samples. The quantity and specific activity of cRNA was determined by using NanoDrop ND-1000 UV-VIS Spectrophotometer version3.2.1. Samples with specific activity >8 were used for hybridization. 825ng of each Cyanine 3 or Cyanine 5 labeled cRNA in a volume of 41.8ul were combined with 11ul of 10x Blocking agent and 2.2ul of 25x Fragmentation buffer (Agilent), and incubated at 60deg C for 30 minutes in dark. The fragmented cRNA were mixed with 55ul of 2x Hybridization Buffer (Agilent). About 110ul of the resulting mixture was applied to the Microarray and hybridized at 65degC for 17 hours in an Agilent Microarray Hybridization Chamber (SureHyb: G2534A) with Hybridization Oven. After hybridization, slides were washed with Agilent Gene expression Wash Buffer I for 1 minute at room temperature followed by a 1 min wash with Agilent Gene expression Wash Buffer II for 37C. Slides were finally rinsed with Acetonitrile for cleaning up and drying. Microarrays were scanned on an Agilent scanner (G2565AA) at 100% laser power, 30% PMT.Data extraction was carried out with Agilent Feature Extraction software (version 9.1), and normalization was done using linear per array algorithm according to the manufacturer’s protocol. The data was analysed by GeneSpring GX . The differential expression was considered if the Log 2 mean of at least -1 for the down regulated genes and +1 for the upregulated genes. We considered only the genes that were reproducible from all replicates.

first: AnuKumar

last: BalaKrishnan


title: OD00001_HCP3_N2_MXEMB

status: Public on May 01 2009

summary:
modENCODE_submission_194

This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.

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:
DESIGN ONTOLOGY: MO::binding_site_identification_design

EXPERIMENT TYPE: ChIP-chip

BIOLOGICAL SOURCE: strain official name:Strain:N2&oldid=14632, developmental stage:embryo, official name:N2, genotype:wild type, genotype:DR subclone of DB original (Tc1 pattern I)

REPLICATES: 3, replicate 0 applied to 3 arrays, replicate 1 applied to 3 arrays, replicate 2 applied to 3 arrays, NO dye swap

EXPERIMENTAL FACTORS: Ab:OD00001 HCP3:JL:1

Deposited by modENCODE DCC

first: Reto

last: Gassmann

first: Arshad

last: Desai


title: Transcriptional termini of genes on chromosomes 21-22 (RACE mapping)

status: Public on Aug 13 2009

city: Woodbury

first: Chris

last: Zaleski

state: NY

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Labs

type: Expression profiling by genome tiling array

summary:
The purpose of these experiments was to determine the 5' and 3' transcriptional termini of genes on chromosomes 21-22. Towards this end, we first carried out 5’ and 3’ RACE reactions from 1193 exons from 492 genes in these chromosomes using RNA isolated from 11 normal tissues and 5 cell lines. An average of 3 to 4 RACE reactions (5’ and 3’) was carried out from each gene. The products of the RACE reactions were analyzed by hybridization to tiling arrays interrogating the non-repeat portions of these chromosomes at 17 nucleotide resolution. A total of 26,688 RACE reactions were performed and pooled to be placed on to 1020 tiling arrays

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: polyA+ RNAs from 11 tissues (Brain Frontal Lobe, Brain Hippocampus, Brain Hypothalamus, Cerebellum, Ovary, Placenta, Prostate, Testis, Fetal Kidney, Fetal Spleen, Fetal Thymus; all from BD Clontech) and 5 cell lines (GM06990, HeLaS3, HepG2, K562, tert-BJ) using the BD SMARTTM RACE cDNA amplification kit (BD Clontech Cat. No.634914). A single array with no relplicas was run for each sample with a pool of ~23-24 RACE reactions per sample.

first: Thomas

last: Gingeras


title: N-isobutyl-decanamide (decanamide) treatment: Control vs. 60 uM treatment

status: Public on Jan 27 2009

city: morelia

first: alfonso

last: méndez-bravo

state: michoacan

address: ciudad universitaria

department: instituto de investigaciones químico-biológicas

country: Mexico

institute: universidad michoacana de san nicolas de hidalgo

summary:
Transcriptional profiling of 6 days-old Arabidopsis thaliana Col-0 seedlings transfered to alkamide decanamide-containing medium in a 1, 3, 7 and 14 d time course period.

Keywords: Pharmacological

overall_design: A dye balanced modified loop design was implemented. Four biological replicates representing each sampling point were obtained by pooling in a 1:1 proportion shoot and root purified RNA from 120 randomly chosen seedlings. This experiment involved a total of sixteen sets of microarray hybridizations, including direct and dye swap comparisons between treatments as well as across time points for the same treatment. This design allowed us to determine differences in gene expression between N-isobutyl decanamide-treated and control seedlings, and whether the differences were time dependent.

first: Alfonso

last: Méndez-Bravo

first: Carlos

last: Calderón-Vázquez

first: Enrique

last: Ibarra-Lacclete


status: Public on Feb 01 2008

city: Cambridge

first: Elizabeth

last: Herbolsheimer

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

summary:
The most widely-used method for detecting and measuring genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Many tiling array platforms, amplification methods, and analysis algorithms exist for ChIP-chip, but a rigorous assessment of the relative performance of these factors has not been reported. In a multi-lab simulation of a ChIP-chip experiment, we conducted the first objective analysis of tiling array platforms and analysis algorithms. We designed a complex mixture of human genomic DNA with a "spike-in" comprised of nearly 100 human sequences at various concentrations. Eight independent groups hybridized these mixtures to four different tiling array platforms. The groups were blind to the composition of the spike-in mix, the range of concentrations covered, or how many sequences it contained. Still blind to the key, each group made predictions of the spike-in locations based on their measurements. The results reveal that all commercial tiling array platforms perform well, although each platform and analysis algorithm has distinct performance characteristics. Simple sequence repeats and genome redundancy tend to result in false positives on oligonucleotide platforms. We also compare genome-wide platforms with regard to performance and cost. The spike-in DNA samples and the resulting array data presented in our study provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated.
Keywords: Spike in Control

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:
With the availability of sequenced genomes and whole-genome tiling microarrays, many researchers have conducted experiments using ChIP-chip and related methods to study genome-wide protein-DNA interactions1-9. These are powerful yet challenging techniques, which are comprised of many steps that can introduce variability in the final results. One potentially important factor is the relative performance of different types of tiling arrays. Currently the most popular platforms for performing ChIP-chip experiments are PCR-product based tiling arrays spotted in academic laboratories and commercial oligonucleotide-based tiling arrays from Affymetrix, NimbleGen, and Agilent. A second factor known to introduce variation is the DNA amplification protocol, which is often required because the low DNA yield from a ChIP experiment prevents direct detection on microarrays. A third factor is the algorithm used for detecting regions of enrichment from the tiling array data. A number of algorithms have been developed, but until this report there was no benchmark dataset to systematically evaluate them. In this study, we used a spike-in experiment to systematically evaluate the effects of tiling microarrays, amplification protocols, and data analysis algorithms on ChIP-chip results. There are other potentially important factors that from a practical standpoint are more difficult to systematically control and evaluate, and are not assessed here. These include the experimenter, the amount of starting material used, size of DNA fragments after shearing, DNA labeling method, and hybridization conditions.

There have been several studies evaluating the performance of gene expression microarrays and analysis algorithms10-13. However, because tiling arrays must cover large genomic regions, they have different probe properties and high probe densities, and therefore present different biochemical and informatics challenges. Thus the results from the expression array spike-in experiments are not necessarily directly relevant to tiling array experiments. One recent study compared the performance of array-based (ChIP-chip) and sequence-based (ChIP-PET) technologies on a real ChIP experiment14. However, because this was an exploratory experiment, the list of absolute “true positive” targets was and is unknown. Since this experiment was performed without a key, the sensitivity and specificity of each technology had to be estimated retrospectively by qPCR validation of targets predicted from each platform.

In our experiment, eight independent research groups at locations worldwide hybridized two different mixtures of DNA to one of four tiling array platforms, and predicted genome location and concentration of the spike-in sequences using a total of 13 different algorithms. Throughout the process, the research groups were entirely blind to the contents of the spike-in mixtures. Using the spike-in key, we analyzed several performance parameters for each platform, algorithm, and amplification method. While all commercial platforms performed well, we found that each had unique performance characteristics. We examined the implications of these results in planning human genome-wide experiments, in which trade-offs between probe density and cost are important.

first: David

middle: S

last: Johnson

first: Wei

last: Li

middle: B

last: Gordon

first: Arindam

last: Bhattacharjee

last: Curry

first: Jayati

last: Ghosh

first: Leonardo

last: Brizuela

first: Jason

last: Carroll

first: Myles

last: Brown

first: Paul

last: Flicek

first: Ian

last: Nix

first: Tom

first: Xinmin

last: Zhang

first: Heather

last: Holster

last: Jing

first: Roland

last: Green

first: Jun

last: Song

first: Scott

last: McCuine

last: Anton

first: Loan

last: Nguyen

first: Nathan

middle: D

last: Trinklein

first: Zhen

last: Ye

last: Hawkins

first: Bing

last: Ren

first: Peter

middle: C

last: Scacheri

first: Joel

last: Rozowsky

first: Alexander

last: Karpikov

first: Ghia

last: Euskirchen

first: Sherman

last: Weissman

first: Mark

last: Gertein

first: Michael

last: Synder

first: Annie

last: Yang

first: Zarmik

last: Moqtaderi

last: Hirsch

first: Hennady

last: Shulha

first: Yutao

last: FU

first: Zhiping

last: Weng

first: Kevin

last: Struhl

first: Richard

middle: M

last: Myers

last: Lieb

first: Shirley

last: Liu


title: Murine corticotroph pituitary AtT-20 cells:  Crh treatment time course

status: Public on Jan 31 2009

city: München-Neuherberg

first: Dietrich

last: Trümbach

address: Ingolstädter Landstraße 1

department: Institute for Developmental Genetics

country: Germany

institute: German Research Center for Environmental Health

summary:
As the Crh-system and the HPA-axis are known to be crucially involved in the onset, development and maintainance of psychiatric disorders like anxiety and depression and regulate the behavioural and endocrine stress responses the further analysis of Crhr1-dependent signaling cascades is essential to understand the molecular mechanisms behind these psychiatric diseases. In this project, new candidate genes involved in Crhr1-dependent signaling cascades were dissected in the cell line model of AtT-20 cells by transcriptional profiling of mouse pituitary corticotroph cells comparing control untreated AtT-20 cells with AtT-20 cells treated with 100 nM Crh at 1, 3, 6, 12 and 24 hours.

Keywords: time course, treatment response

overall_design: Two condition experiment: untreated vs. 100 nM Crh treated AtT-20 cells with a time curve of 1, 3, 6, 12, 24 hours. Technical replicates: 6 for each time point, including dye-swap each with 3 replicates

first: Cornelia

last: Graf

first: Benno

last: Pütz

first: Claudia

last: Kühne

first: Markus

last: Panhuysen

last: Weber

first: Florian

last: Holsboer

first: Wolfgang

last: Wurst

first: Gerhard

last: Welzl

first: Jan

last: Deussing


title: Aging Time course

status: Public on Jul 29 2008

city: Stanford

first: Stuart

last: Kim

department: Department of Developmental Biology

institute: Stanford University Medical Center

summary:
RNA was isolated from age-synchronous cultures of hermaphrodite worms grown at 25?C at 2, 5, 8, or 11 days of adulthood. We observed no deaths in the worm population at days 2 and 5 of adulthood, 30% at day 8 and 93% death at day 11.  The aging time course was repeated four times.
Groups of assays that are related as part of a time series.
Age: Age of adult worms (days)

Keywords: time_series_design

overall_design: User Defined

first: Min

last: Jiang


title: ChIP-chip analysis of HTZ-1 and RNA Polymerase II in wildtype (N2) embryos

status: Public on Jul 28 2008

city: Chapel Hill

first: Christina

last: Whittle

state: NC

address: 406 Fordham Hall, CB#3280

department: Biology

institute: University of North Carolina-Chapel Hill

summary:
In all eukaryotes, histone variants are incorporated into a subset of nucleosomes to create functionally specialized regions of chromatin. One such variant, H2A.Z, replaces histone H2A and is required for viability in all metazoans tested to date. However, the function of H2A.Z in chromatin organization, transcription, and development remains controversialunclear. We mapped the genome-wide distribution of the C. elegans H2A.Z ortholog HTZ-1 during embryogenesis by Chromatin ImmunoPrecipitation on DNA microarrays (ChIP-chip). We find that H2A.Z is incorporated upstream of approximatelybout 25% of C. elegans genes, preferentially upstream of genes required for development and occupied by RNA polymerase II. Fewer sites of HTZ-1 localization occur on the X chromosome relative to autosomes, consistent with the lack of essential genes on X. The data provide evidence for unexpectedly widespread independent regulation of genes within operons. In 37% of operons, HTZ-1 is incorporated upstream of internally encoded genes. In conjunction with ChIP-chip, we used genetic mutation, RNAi, and microscopy to establish that HTZ-1 is present in every cell, and that maternally supplied HTZ-1 is essential for normal development. We interpret these results to indicate that C. elegans HTZ-1 functions in establishing or maintaining an essential chromatin state at promoters regulated dynamically during development.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
Keywords: chip-chip

overall_design: 4 independent HTZ-1 ChIP biological replicates were performed with 1 dye-swap replicate (ChIP 4). RNA Polymerase II ChIPs were performed from extracts used for HTZ-1 ChIPs 1 and 2 (RNAPII ChIP2 is a dye-swap). HTZ-1, RNA Polymerase II, and no antibody raw intensities Data were normalized by median centering log ratios (IP/input). Normalized Log2 ratios from each experiment were converted to standardized z-scores, array sets were concatenated, and then the median of experiments was taken.

first: Karissa

middle: N

last: McClinic

first: Sevinc

last: Ercan

first: Xinmin

last: Zhang

first: Roland

last: Green

first: William

middle: G

last: Kelly

first: Jason


title: MuRF1-dependent regulation of systemic carbohydrate metabolism as revealed from transgenic mouse studies

status: Public on May 15 2008

city: Mannheim

first: Stephanie

last: Hirner

department: Universitätsklinikum Mannheim

institute: institute of anaesthesiology and intensive care

summary:
Under various pathophysiological muscle-wasting conditions like diabetes and starvation, a family of ubiquitin ligases, including MuRF1 (Muscle specific RING-Finger protein 1), are induced to target muscle proteins for degradation via ubiquitination. In an attempt to identify the in vivo targets of MuRF1 we have generated transgenic mouse lines overexpressing MuRF1 in a skeletal muscle specific fashion. MuRF1-TG lines were viable and had normal fertility. Characterization of their skeletal muscles did not reveal evidence for muscle wasting at 10 weeks of age. In this experiment we compared the skeletal muscle transcriptome of transgenic mice with wildtypes.
Keywords: MuRF1 transgene overexpression

overall_design: Transcriptional profiling was performed on an Affymetrix Mouse Genome 430 2.0 Array chip. In brief, total RNA from quadriceps was prepared (Quiagen kit RNAeasy kit), reverse transcribed with Superscript II (Invitrogen BRL) and labeled and hybridized as described in the Affymetrix manual. Two pairs of TG/WT at 12 weeks of age were compared.

first: Christian

last: Krohne

first: Siegfried

last: Labeit

first: Dittmar


title: ENCODE spikein, nonamplified DNA samples, NimbleGen arrays

status: Public on Jan 09 2008

city: Calgary

first: Mark

last: Bieda

state: AB

address: 3330 Hospital Dr NW

department: Biochemistry and Molecular Biology

institute: University of Calgary

summary:
The goals of the study were to assess array platform performance and analysis algorithm performance.

The most widely used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms, amplification procedures, and signal detection algorithms in a simulated ChIP-chip experiment. Mixtures of human genomic DNA and "spike-ins" comprised of nearly 100 human sequences at various concentrations were hybridized to four tiling array platforms by eight independent groups. Blind to the number of spike-ins, their locations, and the range of concentrations, each group made predictions of the spike-in locations. We found that microarray platform choice is not the primary determinant of overall performance. In fact, variation in performance between labs, protocols and algorithms within the same array platform was greater than the variation in performance between array platforms. However, each array platform had unique performance characteristics that varied with tiling resolution and the number of replicates, which have implications for cost versus detection power. Long oligonucleotide arrays were slightly more sensitive at detecting very low enrichment. On all platforms, simple sequence repeats and genome redundancy tended to result in false positives. LM-PCR and WGA, the most popular sample amplification techniques, reproduced relative enrichment levels with high fidelity. Performance among signal detection algorithms was heavily dependent on array platform. The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated.
Keywords: ChIP-chip, competition

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

overall_design: DNA was spiked-in to a background DNA sample.  Same DNA samples used in the arrays in this Series; these are technical array replicates.


title: Profiling of the response of genes in the rat liver to hepatotoxicants

status: Public on Apr 28 2009

city: RTP

first: Pierre

middle: Robert

last: Bushel

department: Biostatistics and Computational Biology Branch

institute: NIEHS

summary: This data set comprises of the standardized experimental design for the microarray gene expression data derived from the rat liver (target tissue) after treatment with eight known hepatotoxicants (at multiple time points and doses with multiple biological replicates and a fluor-flip for each biological sample).

overall_design: We analyzed the gene expression data from the livers of F344/N male rats 10-12 weeks of age exposed for 6, 24 or 48 hrs to a low, medium or high dose of one of eight hepatotoxicants.

middle: R

first: Richard

last: Paules

first: Edward

middle: K

last: Lobenhofer

first: Raymond

middle: W

last: Tennant


title: Spike-in Experiment for ChIP-chip Simulation

status: Public on Dec 01 2007

first: David

middle: Scott

last: Johnson

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

summary:
The most widely-used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms and analysis algorithms in a simulated ChIP-chip experiment. Mixtures of human genomic DNA and "spike-ins" comprised of nearly 100 human sequences at various concentrations were hybridized to four tiling array platforms by eight independent groups. Blind to the number of spike-ins, their locations, and the range of concentrations, each group made predictions of the spike-in locations. All commercial tiling array platforms performed well, although each platform and analysis algorithm had distinct performance and cost characteristics. Simple sequence repeats and genome redundancy tend to result in false positives on oligonucleotide platforms. The spike-in DNA samples and the resulting array data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated.
Keywords: chip-ChIP simulation

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

overall_design: For each replicate array, we labeled 1µg of spike-in sample and 1µg of control sample.  The Bioprime Plus Array CGH labeling Module (Invitrogen Catolog number 18095-014) was used.  The spike-in was labeled with the red channel dye (Alexa Fluor-647) and the control was labeled with the green channel dye (Alexa Fluor-555) in two of the replicates.  A dye swap was performed for the third replicate.  These samples were then competitively hybridized to three replicate 244k arrays from Agilent, (AMADID 25150451).  We hybridized the samples to the arrays using the Agilent Array CGH protocol, with some modifications.  Briefly, labeled DNA was combined with Cot-1 DNA, blocking reagent, and hybridization buffer.  The hybridizations were carried out at 60°C.  The arrays were scanned using an Agilent dual laser scanner, and the images were processed using Agilent Feature Extraction Software.

first: Elizabeth

last: Anton

first: Loan

last: Nguyen

last: Myers


title: CGH Follicle OregonR-Orr-Weaver

first: DCC

last: modENCODE

type: Genome variation profiling by genome tiling array

summary:
modENCODE_submission_724
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Most terminally differentiated Drosophila tissues are either polyploid or polytene.  Unlike  normal chromosomes, where the entire chromosome must be replicated exactly once, polytene chromosomes are often differentially replicated with many regions underreplicated and some overreplicated. We will characterize five different polytene tissues using comparative genomic hybridization (CGH) to identify differentially replicated regions of each chromosome. These studies will also identify tissue specific amplicons, where the replication mediated amplification of specific loci is essential for up-regulation of mRNA levels encoding proteins critical for development. The differential replication of polytene chromosomes in Drosophila will provide a unique opportunity to understand how developmental cues and chromosomal domains influence replication initiation.

Keywords: CGH

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: CGH. BIOLOGICAL SOURCE 1: Strain: Oregon-R Orr-Weaver; Tissue: oocyte associated follicle cell; Genotype: TBA; Sex: Female; BIOLOGICAL SOURCE 2: Strain: Oregon-R Orr-Weaver; Developmental Stage: Embryo 0-4h; Genotype: TBA; Sex: Unknown;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Tissue oocyte associated follicle cell

last: MacAlpine

first: Terry

last: Orr-Weaver

first: Thomas

last: Eng


title: ENCODE Spike-In, Yale Group

status: Public on Dec 28 2007

city: New Haven

first: Guoneng

last: Zhong

state: CT

address: 300 George St

institute: Yale Med

summary:
Simulated ChIP DNA labeled by random priming with Klenow; Samples were "Undiluted" and not amplified prior to labeling.
Keywords: other

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: Systematic analysis of a simulated ChIP-chip experiment

first: Alexander

last: Karpikov

first: Ghia

last: Euskirchen

first: Joel

last: Rozowsky

last: Gerstein


title: WAR1-C mutants

status: Public on Dec 20 2007

city: Tulln

first: Christoph

last: Schueller

address: Konrad Lorenz Strasse 24

department: Department of Applied Genetics and Cell Biology

country: Austria

institute: University of Natural Resources and Life Sciences, Vienna (BOKU)

summary:
The Saccharomyces cerevisiae Zn(II)2Cys6 zinc cluster transcription factor War1, mediates part of the transcriptional response to weak organic acids such as sorbate or benzoate.  We identified gain-of function alleles of War1 that map to a region in the center of the molecule conserved in War1 related proteins from other fungi. Independent of weak acids, they increase levels of plasma membrane ABC transporter Pdr12, the main target gene of War1. In the experiment, the constitutive War1 allele K762R was expressed from the GAL1 promoter. RNA was extracted after one hour induction of the GAL1 promoter by Galactose to exclude indirect effects of the constitutive allele.
Keywords: mutant vs wild type

overall_design: two repeats and one dye swap, all biological repeats

first: Christa

last: Gregori

last: Schüller

first: Karl

last: Kuchler


title: ENCODE Transcript Mapping for Human HeLa Total RNA

status: Public on Apr 06 2007

summary:
Transcript Mapping on Affymetrix ENCODE arrays for 3 different biological replicates of HeLa Total RNA
Keywords: other

overall_design: Experiments were done with 3 biological replicate samples each hybridized to replicates arrays in parallel. Array data was processed by combining the replicate arrays and integrating data using sliding genomic windows.

first: Zheng

last: Lian

first: Philipp

last: Kapranov

first: Olof

last: Emanuelsson

first: Ugrappa

last: Nagalakshmi

first: Alex

middle: E

last: Urban

first: Jill

last: Cheung

first: Sherman

last: Weissman

first: Mark

first: Tom

last: Gingeras

first: Michael

last: Snyder


title: Me3K27 Histone H3 ChIP DNA from HeLa S3 cells

status: Public on Jun 12 2007

first: Guoneng

last: Zhong

summary:
Me3K27 Histone H3 ChIP DNA was isolated from HeLa S3 cells and surveyed for binding in the ENCODE regions on NimbleGen ENCODE arrays. Use of this data requires permission from its producers.
Keywords: ChIP-chip

overall_design: Me3K27 Histone H3-ChIP DNA and reference ChIP DNA (background obtained with normal rabbit IgG) were isolated from untreated HeLa S3 cells. Combined Me3K27 Histone H3 and reference ChIP DNA samples were hybridized to a NimbleGen ENCODE tiling array that contains overlapping 50nt oligonucleotide probes. The series is comprised of three biological replicates, hybridized separately to three arrays.


title: Systematic evaluation of variability in simulated ChIP-chip experiments Kevin_Encode

status: Public on Dec 13 2007

city: Houston

first: Wei

last: Li

state: TX

address: one baylor plaza, MS BCM305

institute: Baylor College of Medicine

summary:
The most widely used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms, amplification procedures, and signal detection algorithms in a simulated ChIP-chip experiment. Mixtures of human genomic DNA and "spike-ins" comprised of nearly 100 human sequences at various concentrations were hybridized to four tiling array platforms by eight independent groups. Blind to the number of spike-ins, their locations, and the range of concentrations, each group made predictions of the spike-in locations. We found that microarray platform choice is not the primary determinant of overall performance. In fact, variation in performance between labs, protocols and algorithms within the same array platform was greater than the variation in performance between array platforms. However, each array platform had unique performance characteristics that varied with tiling resolution and the number of replicates, which have implications for cost versus detection power. Long oligonucleotide arrays were slightly more sensitive at detecting very low enrichment. On all platforms, simple sequence repeats and genome redundancy tended to result in false positives. LM-PCR and WGA, the most popular sample amplification techniques, reproduced relative enrichment levels with high fidelity. Performance among signal detection algorithms was heavily dependent on array platform. The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated.
Keywords: ChIP-chip

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: 9 spike-in replicates and 9 genomic input control replicates

first: Li

last: Wei


title: DNaseI/Array multiple cell types

status: Public on Jun 22 2007

city: SEATTLE

first: John

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

summary:
The goal of this study was to map DNaseI sensitivity and DNaseI hypersensitive sites over the ENCODE regions in multiple human cell types (GM06990, CACO2, HepG2).
Keywords: DNase/Array

overall_design: DNA fragments released from DNaseI cut sites in nuclear chromatin were collected and hybridized to the Nimblegen ENCODE array. DNaseI-fragmented naked DNA was used as a control.

first: P

middle: J

last: Sabo

last: Kuehn

first: B

last: Johnson

last: Stamatoyannopoulous

first: Noble

last: William

first: Richard

last: Sandstrom


title: Developmental analysis of Aedes aegypti gene expression

status: Public on May 15 2007

first: George

last: Dimopoulos

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

summary:
This analysis defines the adult female and developmental specific transcriptomes of Aedes aegypti.
Keywords: Aedews aegypti, development, gene expression

overall_design: Here we compare gene expression between the adult female and a pool of an equal amount of RNA from each developmental stage (embryo, larvae, pupae).

first: Zhiyong

last: Xi


title: Aedes aegypti sex specific gene expression

summary:
This analysis compare gene expression between 4 day old sugar fed female and male Aedes aegypti mosquitoes.
Keywords: Aedes aegypti sex specific expression

overall_design: This analysis compare gene expression between 4 day old sugar fed female and male Aedes aegypti mosquitoes. Samples were made from whole 4 day old sugar fed female and male mosquitoes.


title: ENCODE Transcript Mapping for Human HeLa Poly(A)+ RNA

summary:
Transcript Mapping on Affymetrix ENCODE arrays for 3 different biological replicates of HeLa Poly(A)+ RNA
Keywords: other

first: Joel

last: Rozowsky

first: Zheng

last: Lian

first: Philipp

last: Kapranov

first: Olof

last: Emanuelsson

first: Ugrappa

last: Nagalakshmi

last: Urban

last: Gerstein


title: NRSF ChIP-ChIP from HeLaS3 Cells using the NimbleGen ENCODE Array; [unpublished]

status: Public on Mar 28 2007

last: Zhong

summary:
NRSF ChIP DNA was isolated from HeLaS3 cells and surveyed for binding in the ENCODE regions on NimbleGen ENCODE arrays. Use of this data requires permission from its producers.
Keywords: ChIP-chip

overall_design: NRSF-ChIP DNA and reference ChIP DNA (background obtained with normal rabbit IgG) were isolated from untreated HeLaS3 cells. Combined NRSF and reference ChIP DNA samples were hybridized to a NimbleGen ENCODE tiling array that contains overlapping 50nt oligonucleotide probes. The series is comprised of three biological replicates, hybridized separately to three arrays.

first: Ghia

last: Euskirchen

first: Mark

last: Snyder


title: SMARCA6 ChIP-ChIP from HeLaS3 Cells using the NimbleGen ENCODE Array; [unpublished]

first: Guoneng

summary:
SMARCA6 ChIP DNA was isolated from HeLaS3 cells and surveyed for binding in the ENCODE regions on NimbleGen ENCODE arrays. Use of this data requires permission from its producers.
Keywords: ChIP-chip

overall_design: SMARCA6-ChIP DNA and reference ChIP DNA (background obtained with normal rabbit IgG) were isolated from untreated HeLaS3 cells. Combined SMARCA6 and reference ChIP DNA samples were hybridized to a NimbleGen ENCODE tiling array that contains overlapping 50nt oligonucleotide probes. The series is comprised of three biological replicates, hybridized separately to three arrays.

first: Michael


title: Systematic evaluation of variability in simulated ChIP-chip experiments Myles_Encode

first: Wei

last: Li

overall_design: 3 spike-in replicates and 3 genomic input control replicates

first: Li

last: Wei


title: Brg1 ChIP-ChIP from HeLaS3 Cells using the NimbleGen ENCODE Array; [unpublished]

summary:
Brg1 ChIP DNA was isolated from HeLaS3 cells and surveyed for binding in the ENCODE regions on NimbleGen ENCODE arrays. Use of this data requires permission from its producers.
Keywords: ChIP-chip

overall_design: Brg1-ChIP DNA and reference ChIP DNA (background obtained with normal mouse IgG) were isolated from untreated HeLaS3 cells. Combined Brg1 and reference ChIP DNA samples were hybridized to a NimbleGen ENCODE tiling array that contains overlapping 50nt oligonucleotide probes. The series is comprised of three biological replicates, hybridized separately to three arrays.


title: Ludwig Institute/UCSD ENCODE project March 2007 Release

status: Public on Mar 01 2007

first: Bing

last: Ren

institute: Ludwig Institute for Cancer Research

summary:
The readout of genome information is controlled by transcriptional regulatory elements, but a comprehensive view of the combinatorial control by these DNA sequences, which bind regulatory protein and/or the modified histones in regulating gene transcription, is clearly preliminary. We have developed an experimental strategy for comprehensive determination of such functional elements in human DNA. This strategy involves the application of genome-wide location analysis, also known as ChIP-chip, to a panel of well-characterized regulatory proteins and histones with specific modifications, known to generally associate with transcriptional regulatory elements in vivo. Identification of their genomic binding sites will allow us to determine the sequence features in the human genome that carry out transcriptional regulatory function. We have designed and produced DNA microarrays to represent all the non-repetitive sequences in the 30 million basepair ENCODE regions of the human genome to map various types of transcriptional regulatory elements in three model cell types. We have identified promoters by mapping the genomic sequences associated with RNA polymerase II and the general transcription factor TFIID in cells, enhancer elements by mapping the genomic sequences associated with transcriptional co-activators and enhancer-specific chromatin modifications, and insulators by mapping the genomic sequences associated with the insulator binding protein CTCF. The raw microarray results are released periodically prior to publication.
Keywords: ChIP-chip ENCODE

overall_design: ChIP-chip analyses were performed for various transcription factors and chromatin modifications in various cell types. Details to be described in publications.

first: C

last: Glass

first: M

last: Rosenfeld

first: N

last: Webster

first: K

last: Ching

first: L

last: Harp

first: Z

last: Ye

first: R

last: Stuart

first: S

middle: V

last: Calcar

first: T

middle: H

last: Kim

last: Hawkins

first: G

last: Hon

middle: O

last: Barrera

last: Luna

last: Wang


title: ENCODE ChIP-chip for Rel A (p65) using polyclonal antibody (C-20) on TNF-alpha-stimulated HeLaS3 Cells [unpublished]

status: Public on Feb 14 2007

last: Zhong

summary:
Rel A (p65) ChIP-chip using polyclonal antibody (C-20) performed on TNF-alpha-stimulated HeLaS3 cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts). Goal was to identify p65-binding regions in the inflammatory and immune response of human cells.
Keywords: ChIP-chip

overall_design: DNA from immunoprecipitated chromatin using p65 antibody (C-20) or normal rabbit IgG was hybridized to a Nimblegen ENCODE tiling array containing overlapping 50nt oligonucleotide probes. Samples are three biological replicates.

first: Mi-Young

last: Hong

first: Joel

middle: S

last: Rozowsky

last: Gerstein

middle: P

last: Snyder


title: BAF170 ChIP-ChIP from K562 Cells using the NimbleGen ENCODE Array [unpublished]

first: Guoneng

summary:
BAF170 ChIP DNA was isolated from K562 cells and surveyed for binding in the ENCODE regions on NimbleGen ENCODE arrays. Use of this data requires permission from its producers.
Keywords: ChIP-chip

overall_design: BAF170-ChIP DNA and reference ChIP DNA (background obtained with normal rabbit IgG) were isolated from untreated K562 cells. Combined BAF170 and reference ChIP DNA samples were hybridized to a NimbleGen ENCODE tiling array that contains overlapping 50nt oligonucleotide probes. The series is comprised of three biological replicates, hybridized separately to three arrays.

first: Ghia

last: Euskirchen

first: Milind

last: Mahajan

first: Mark

middle: B


title: Ini1 ChIP-ChIP from K562 Cells using the NimbleGen ENCODE Array

summary:
Ini1 ChIP DNA was isolated from K562 cells and surveyed for binding in the ENCODE regions on NimbleGen ENCODE arrays. Use of this data requires permission from its producers.
Keywords: ChIP-chip

overall_design: Ini1-ChIP DNA and reference ChIP DNA (background obtained with normal rabbit IgG) were isolated from untreated K562 cells. Combined Ini1 and reference ChIP DNA samples were hybridized to a NimbleGen ENCODE tiling array that contains overlapping 50nt oligonucleotide probes. The series is comprised of three biological replicates, hybridized separately to three arrays.

first: Michael


title: BAF155 ChIP-ChIP from K562 Cells using the NimbleGen ENCODE Array [unpublished]

summary:
BAF155 ChIP DNA was isolated from K562 cells and surveyed for binding in the ENCODE regions on NimbleGen ENCODE arrays. Use of this data requires permission from its producers.
Keywords: ChIP-chip

overall_design: BAF155-ChIP DNA and reference ChIP DNA (background obtained with normal rabbit IgG) were isolated from untreated K562 cells. Combined BAF155 and reference ChIP DNA samples were hybridized to a NimbleGen ENCODE tiling array that contains overlapping 50nt oligonucleotide probes. The series is comprised of three biological replicates, hybridized separately to three arrays.


title: E2F4 and Myc ChIP-chip perfomed on Nimblegen hg17 ENCODE arrays

status: Public on Jan 20 2007

city: Austin

first: Vishy

last: Iyer

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary:
Identifying the chromosomal targets of transcription factors is important for reconstructing the transcriptional regulatory networks underlying global gene expression programs. ChIP-chip is a powerful technique to map chromosomal targets of transcription factors. We applied ChIP-chip to map downstream targets of the transcription factor E2F4 and c-Myc. E2F4 is a member of the E2F family of transcriptional regulators that functions as a repressor in quiescent and early G1 cells. c-Myc is a oncogenic transcription factor implicated in almost all aspects of tumorigenesis. We mapped E2F4 and c-Myc binding sites in 1% of the human genome using Nimblegen hg17 ENCODE arrays.
Keywords: ChIP-chip

overall_design: Cultured cells are cross-linked in vivo using 1% formaldehyde and chromatin is sheared to less than 1 kb fragments using a sonicator. Specific protein-dna complexes are pulled down using a specific antibody. After adequate washing, the protein-dna complexes are eluted, reverse cross-linked and the DNA purified by phenol-chloroform extraction. ChIP-enriched DNA is now labeled with Cy5 while DNA derived from a mock IP is used as a reference and labeled with Cy3. Samples are then hybridized on ENCODE arrays.

first: Jonghwan

first: Akshay

last: Bhinge

first: Vishwanath

first: Mike

last: Singer

last: Jiang

first: Roland

last: Green


title: Identification of genes directly regulated by the oncogene ZNF217 using ChIP-chip assays

status: Public on Jan 25 2007

city: Columbus

first: Victor

middle: X

last: Jin

state: OH

address: 333 West 10th Ave

department: Biomedical Informatics

institute: OSU Medical Center

summary:
It has been proposed that ZNF217, which is amplified at 20q13 in various tumors, plays a key role during neoplastic transformation. ZNF217 has been purified in complexes that contain repressor proteins such as CtBP2, suggesting that it acts as a transcriptional repressor. However, the function of ZNF217 has not been well characterized due to a lack of known target genes. Using a global ChIP-chip approach, we have identified thousands of ZNF217 binding sites in three tumor cell lines (MCF7, SW480, and Ntera2). Further analysis of ZNF217 in Ntera2 cells has shown that many promoters are bound by ZNF217 and CtBP2, and that a subset of these promoters are activated upon removal of ZNF217. Thus, our in vivo studies corroborate the in vitro biochemical analyses of ZNF217-containing complexes and support the hypothesis that ZNF217 functions as transcriptional repressor. Gene ontology analysis shows that ZNF217 targets in Ntera2 cells are involved in organ development, suggesting that one function of ZNF217 may be to repress differentiation. Accordingly, we show that differentiation of Ntera2 cells with retinoic acid leads to downregulation of ZNF217. Our identification of thousands of ZNF217 target genes will enable further studies of the consequences of aberrant expression of ZNF217 during neoplastic transformation.
Keywords: ChIP-chip

overall_design: ChIP-chip assays using antibody of ZNF217 on ENCODE arrays

first: Sheryl

last: Krig

middle: C

last: Bieda

first: Henny

last: O'Geen

first: Peggy

last: Farnham


title: Ini1 ChIP-ChIP from HeLaS3 Cells using the NimbleGen ENCODE Array; [unpublished]

last: Zhong

summary:
Ini1 ChIP DNA was isolated from HeLaS3 cells and surveyed for binding in the ENCODE regions on NimbleGen ENCODE arrays. Use of this data requires permission from its producers.
Keywords: ChIP-chip

overall_design: Ini1-ChIP DNA and reference ChIP DNA (background obtained with normal rabbit IgG) were isolated from untreated HeLaS3 cells. Combined Ini1 and reference ChIP DNA samples were hybridized to a NimbleGen ENCODE tiling array that contains overlapping 50nt oligonucleotide probes. The series is comprised of four biological replicates, hybridized separately to four arrays.


title: Gene expression of organ of Corti (OC), modiolus (MOD) and stria vascularis (SV) of newborn rats

status: Public on May 31 2007

city: Berlin

first: Johann

last: Gross

address: Spandauer Damm 130

department: Otorhinolaryngology

institute: Charité

summary:
The aim of this study was to characterize the basal expression of OC, MOD and SV of newborn rats (3-5 day old) and its changes by short–term cultivation (24 hrs) and mild hypoxia (5 hrs). Three varieties of tissue samples were analyzed (i) Freshly prepared tissue, used as control; (ii) cultures held under normoxic conditions and (iii) cultures exposed during cultivation to 5 h hypoxia. The gene expression was analyzed using the Affymetrix GeneChip RN-U34.
The functional specificity of the cochlea regions are well reflected by the gene expression pattern. For example, the basal expression of Organ of Corti is characterized by genes involved in potassium and calcium homeostasis. The MOD is characterized by genes involved in regulation of maturation of neuronal cells. The SV is characterized by genes involved in ion homeostasis and blood flow.
Cultivation dramatically changes the gene expression. In contrast, mild hypoxia showed only small changes. The changes are interpreted as stress response.
We used this analysis as screening approach to detect significant changes in gene expression and used the RT-PCR analyses of independent sister cultures for confirmation. Correlation analysis showed close relations of the expression levels when aliquots of the biological material were compared. However, comparisons of the expression levels received by microarray and by RT-PCR analysis of independent sister samples resulted in 70-90 % in similar predictions. This data indicate that possible discrepancies has its basis in biological sampling rather than factors of methodical errors on the level of RT-PCR.
Keywords: Differential gene expression, stress response

overall_design:
Pooled samples of the following cochlea preparations were studied:
(i) Native preparations of Organ of Corti, modiolus and stria vascularis from newborn rats used as controls; (ii) Organotypic cultures of these preparations under normoxic conditions (24 h); (iii) Cultures which were exposed to 5 h hypoxia during cultivation. Samples were collected for total RNA immediately after preparation of the inner ear structures (native samples) or 24 h after onset of cultivation (normoxia, hypoxia).

first: Birgit

last: Mazurek

first: Astrid

last: Machulik

first: Nyamaa

last: Amarjargal

first: Ralf-Jürgen

last: Kuban

first: Ute

last: Ungethüm

first: Frank-Uwe

last: Fuchs

first: Heidemarie

last: Haupt


title: Analysis of the vertebrate insulator protein CTCF binding sites in the human genome

status: Public on Jan 01 2007

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

summary:
Insulators are an important class of transcriptional regulatory sequences that affect gene expression by preventing the spread of heterochromatin and restricting how transcriptional enhancers select their target genes.  The vertebrate insulators function by interacting with the CCCTC-binding factor (CTCF), an evolutionarily conserved DNA binding protein.  Knowledge of the CTCF binding sites in the human genome is crucial for identifying potential insulators and understanding the role of these elements in regulating genome expression in the human cells.  Here, we report the identification and characterization of a large number of CTCF binding sites in the human genome.  Using chromatin immunoprecipitation combined with high-resolution genome-tiling arrays, we have determined the locations of CTCF throughout the non-repetitive human DNA sequences, identifying 13,804 binding sites in the genome of human fibroblasts.  Computational analysis of these sequences revealed a single dominant CTCF consensus motif that is shared by a vast majority of the CTCF binding sites and is highly conserved in other vertebrate genomes. The CTCF binding segments the human genome into 5,969 domains, which contain an average of 2.5 genes each.  Many large gene families, such as the olfactory receptor genes, are bounded by the CTCF sites, implicating a role of CTCF in the regulation or evolution of these genes. We demonstrate that CTCF binding can occur in a cell type dependent manner, and that binding of CTCF between two neighboring genes coincides with a loss of coordinated expression, consistent with their role as insulators.  Our results provide a general resource and framework for analyzing the role of CTCF and insulator elements in the regulation of nearly every gene in the human genome.
Keywords: ChIP-chip

overall_design: Chromatin immunoprecipitation was performed using monoclonal antibodies against CTCF and formaldehyde crosslinked chromatin from primary human fibroblast, IMR90 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a series of 38 arrays containing a total of 14.6 million 50-mer oligonucleotides.  These oligonucleotides are evenly positioned every 100 basepairs (bp) to cover the non-repeat sequence of the entire human genome.

first: Tae

last: Kim

first: Ziyedulla

last: Abdullayev

first: Keith

middle: A

last: Ching

first: Andrew

last: Smith

first: Dmitri

last: Loukinov

middle: D

first: Michael

middle: Q

last: Zhang

last: Lobanenkov


title: ENCODE ChIP-chip for Rel A (p65) using polyclonal antibody (N-) on TNF-alpha-stimulated HeLaS3 Cells [unpublished]

first: Guoneng

last: Zhong

summary:
Rel A (p65) ChIP-chip using polyclonal antibody (N-terminus) performed on TNF-alpha-stimulated HeLaS3 cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts). Goal was to identify p65-binding regions in the inflammatory and immune response of human cells.
Keywords: ChIP-chip

overall_design: DNA from immunoprecipitated chromatin using p65 antibody (N-terminus) or normal rabbit IgG was hybridized to a Nimblegen ENCODE tiling array containing overlapping 50nt oligonucleotide probes. Samples are three biological replicates.

first: Mi-Young

last: Hong

first: Joel

last: Rozowsky

first: Mark

last: Gerstein

last: Snyder


title: ENCODE ChIP-chip for RNA Polymerase II using monoclonal antibody (8WG16) on GM06990 Cells [unpublished]

status: Public on Nov 30 2006

summary:
RNA Polymerase II ChIP-chip using monoclonal antibody (8WG16) performed on GM06990 cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts). Goal was to identify Pol II-binding regions. Use of this data requires permission from its producers.
Keywords: ChIP-chip

overall_design: DNA from immunoprecipitated chromatin using Pol II antibody (8WG16) or normal rabbit IgG was hybridized to a Nimblegen ENCODE tiling array containing overlapping 50nt oligonucleotide probes. Samples are three biological replicates.


title: Ludwig Institute/UCSD ENCODE project

summary:
The readout of genome information is controlled by transcriptional regulatory elements, but a comprehensive view of the combinatorial control by these DNA sequences, which bind regulatory protein and/or the modified histones in regulating gene transcription, is clearly preliminary.  We have developed an experimental strategy for comprehensive determination of such functional elements in human DNA.  This strategy involves the application of genome-wide location analysis, also known as ChIP-chip, to a panel of well-characterized regulatory proteins and histones with specific modifications, known to generally associate with transcriptional regulatory elements in vivo. Identification of their genomic binding sites will allow us to determine the sequence features in the human genome that carry out transcriptional regulatory function.  We have designed and produced DNA microarrays to represent all the non-repetitive sequences in the 30 million basepair ENCODE regions of the human genome to map various types of transcriptional regulatory elements in three model cell types.  We have identified promoters by mapping the genomic sequences associated with RNA polymerase II and the general transcription factor TFIID in cells,  enhancer elements by mapping the genomic sequences associated with transcriptional co-activators and enhancer-specific chromatin modifications, and insulators by mapping the genomic sequences associated with the insulator binding protein CTCF.  The raw microarray results are released periodically prior to publication.
Keywords: ChIP-chip

first: Christopher

last: Glass

middle: G

last: Rosenfeld

first: Nicholas

last: Webster

first: Lindsey

last: Harp

first: Zhen

last: Ye

first: Rhona

last: Stuart

first: Sara

last: Calcar

first: Nathanial

last: Heintzman

first: R

last: Hawkins

first: Gary

last: Hon

first: Leah

last: Barrera

first: Rosa

last: Luna

first: Kun

last: Wang


title: Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

first: Bing

last: Ren

summary:
Eukaryotic gene regulatory information is contained within the DNA sequences of cis-regulatory elements and the epigenetic features of the chromatin surrounding these elements.  Recent investigations in yeast, fly, and mammalian systems have made significant contributions toward our understanding of the relationship between gene activation and chromatin architecture at transcriptional promoters, but much work remains to improve our knowledge of this relationship at human promoters and other transcriptional regulatory elements, such as enhancers. Here, we report that human promoters and enhancers are associated with distinct chromatin signatures that can be employed to predict these classes of regulatory elements in the human genome. Using a combination of chromatin immunoprecipitation (ChIP) and microarray (ChIP-chip) experiments, we generated high-resolution maps of the chromatin architecture along 30 Mbp of the human genome, located promoters and enhancers in these regions, and characterized the histone modification features of these regulatory elements. We found that active promoters are marked by tri-methylation of histone H3 lysine 4 (H3K4me3) at the transcriptional start site (TSS) and mono-methylation of this residue (H3K4me1) downstream and upstream of the TSS. In contrast, enhancers are marked by H3K4me1 but not H3K4me3. Both types of regulatory elements are also associated with nucleosome depletion and varying degrees of histone acetylation and H3K4me2. We developed computational prediction algorithms that employ the distinct chromatin signatures to identify new promoters and enhancers, predicting over 200 promoters and 400 enhancers within the 30 Mbp regions. This approach correctly predicted over 84% of the regulatory elements identified in an independent, unbiased study of transcription factor binding in the same regions. Our results suggest a histone code for distinct classes of transcriptional regulatory elements, offering insights into the functional relationships between chromatin modifications and regulatory activity in human cells and providing a new resource for the functional annotation of the human genome.
Keywords: ChIP-chip

overall_design: ChIP-chip analysis was performed to determine the chromatin architecture along 44 human loci selected by the ENCODE consortium as common targets for genomic analysis, totalling 30 Mbp. We investigated the patterns of core histone H3 and five histone modifications: acetylated histone H3 lysine 9/14 (H3ac), acetylated histone H4 lysine 5/8/12/16 (H4ac), and mono-, di-, and tri-methylated histone H3 lysine 4 (H3K4me1, H3K4me2, H3K4me3). We also examined binding of two components of the basal transcriptional machinery (RNAPII and TAF1) and the transcriptional coactivator p300 to identify active promoters and enhancers, respectively. Three biological replicate ChIP-chip experiments were carried out for each marker in HeLa cells before and after treatment with interferon-gamma (IFNγ), as p300 is known to be involved in the cellular response to this cytokine. ChIP samples were amplified, labelled, and hybridized to tiling oligonucleotide microarrays covering the non-repetitive sequences of 30 Mbp at 38-bp resolution.

first: Nathaniel

middle: K

first: Yutao

last: Fu

first: Christina

last: Ching

first: Chunxu

last: Qu

first: Keith

first: Wei

first: Zhiping

last: Weng

first: Roland

last: Green

first: Gregory

last: Crawford


title: ENCODE ChIP-chip for Tetra-acetylated Histone H4 on GM06990 Cells [unpublished]

first: Guoneng

last: Zhong

summary:
Tetra-acetylated Histone H4 ChIP-chip performed on GM06990 cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts). Goal was to identify acetylated Histone H4-binding regions. Use of this data requires permission from its producers.
Keywords: ChIP-chip

overall_design: DNA from immunoprecipitated chromatin using acetyl-Histone H4 antibody or normal rabbit IgG was hybridized to a Nimblegen ENCODE tiling array containing overlapping 50nt oligonucleotide probes. Samples are three biological replicates.

first: Stephen

last: Hartman

first: Joel

last: Rozowsky

first: Mark

last: Gerstein

first: Michael

last: Snyder


title: ENCODE ChIP-chip for RNA Polymerase II using polyclonal antibody on GM06990 Cells [unpublished]

summary:
RNA Polymerase II ChIP-chip using polyclonal antibody (N-20) performed on GM06990 cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts). Goal was to identify Pol II-binding regions. Use of this data requires permission from its producers.
Keywords: ChIP-chip

overall_design: DNA from immunoprecipitated chromatin using Pol II antibody (N-20) or normal rabbit IgG was hybridized to a Nimblegen ENCODE tiling array containing overlapping 50nt oligonucleotide probes. Samples are three biological replicates.

first: Mi-Young

last: Hong


title: STAT1 (Interferon-alpha) ChIP-ChIP from HeLaS3 Cells using the NimbleGen ENCODE Array

summary:
STAT1 ChIP DNA was isolated from HeLaS3 cells following Interferon-alpha stimulation for 30 min and from HeLaS3 cells left untreated. These two STAT1 ChIP DNA samples were combined and compared in the ENCODE regions on NimbleGen ENCODE arrays.
Keywords: ChIP-chip

overall_design: Cultures of HeLaS3 cells were divided in half and were either stimulated with Interferon-alpha for 30 min. or left untreated. STAT1-ChIP DNA was isolated from both halves of the culture, labeled and then combined and hybridized to a NimbleGen ENCODE tiling array that contains overlapping 50nt oligonucleotide probes. The series is comprised of three biological replicates, hybridized separately to three arrays.

first: Ghia

last: Euskirchen


title: ENCODE ChIP-chip for RNA Polymerase II using polyclonal antibody (N-20) on HeLaS3 Cells [unpublished]

summary:
RNA Polymerase II ChIP-chip using polyclonal antibody (N-20) performed on HeLaS3 cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts). Goal was to identify Pol II-binding regions.  Use of this data requires permission from its producers.
Keywords: ChIP-chip


title: ENCODE ChIP-chip for RNA Polymerase II using monoclonal antibody (8WG16) on HeLaS3 Cells [unpublished]

summary:
RNA Polymerase II ChIP-chip using monoclonal antibody (8WG16) performed on HeLaS3 Cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts). Goal was to identify Pol II-binding regions.  Use of this data requires permission from its producers.
Keywords: ChIP-chip


title: ChIP-chip analysis of Dosage Compensation complex members SDC-3 and DPY-27 in C elegans wild type embryos.

status: Public on Feb 11 2007

first: Jason

last: Lieb

address: 408 Fordham Hall, CB# 3280

institute: University of North Carolina at Chapel Hill

summary:
Among organisms with chromosome-based mechanisms of sex determination, failure to equalize expression of X-linked genes between the sexes is typically lethal. In C. elegans, XX hermaphrodites halve transcription from each X chromosome to match the output of XO males1. Here, we mapped the binding location of the condensin homolog DPY-27 and the zinc finger protein SDC-3, two components of the C. elegans dosage compensation complex (DCC)2,3. Strong foci of DCC binding were observed on X, around which broader regions of localization were centered. Binding foci, but not adjacent regions of localization, were distinguished by clusters of a stereotypic 10-bp DNA sequence, suggesting a recruitment-and-spreading mechanism for X recognition. In contrast to the Drosophila DCC, the C. elegans DCC was bound preferentially upstream of genes, suggesting modulation of transcriptional initiation and transcription-coupled spreading. A mechanism for tuning DCC activity at specific loci was indicated by stronger DCC binding upstream of genes with high transcriptional activity. These data provide a basis for understanding how proteins involved in higher-order chromosome dynamics can regulate transcription at individual loci.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
Keywords: ChIP-chip dosage compensation complex

overall_design:
For extract preparations, N2 adults were grown in standard S-liquid media and embryos were obtained by bleaching25. Embryos were fixed with 2% formaldehyde for 30 minutes at room temperature and washed with 100 mM Tris pH 7.5 once, M9 buffer twice and 10 ml FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) with protease inhibitors (Calbiochem) and frozen at -80ºC. 500 ul of packed embryos were thawed and resuspended in 2 ml of FA buffer and dounce homogenized on ice with 30 strokes. Samples were sonicated with a Branson sonifier at 30% amplitude for 7 cycles of 12 pulses (0.9 sec on, 0.1 sec off) and were cooled in dry ice/ethanol bath for 2 seconds between cycles. Cellular debris was removed by microfuge centrifugation at 13,000 g for 15 minutes at 4ºC. Immunoprecipitation reactions contained approximately 3 mg of total protein with 3-5 ug of purified antibodies in 500 ul total volume, with 1% sarkosyl. Prior to addition of the antibody, 10% of the material was taken as input. Immunocomplexes were collected with Protein A-sepharose beads (Amersham Biosciences) and washed with 1 ml of the following buffers : FA buffer 2 X 5 min, FA-1M NaCl (FA buffer with 1 M NaCl) 5 min, FA-500 mM NaCl 10 min, TEL buffer (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.0) 10 min., TE pH 8.0 2 X 5 min. Complexes were eluted in 1% SDS in TE with 250 mM NaCl at 65ºC 30 minutes. Samples and inputs were treated with Proteinase K for 1 hour and crosslinks were reversed at 65ºC overnight. DNA was purified with Qiagen PCR purification columns and amplified by LM-PCR26.
Microarrays and Data Extraction
The C. elegans genome tiling arrays were designed and constructed by NimbleGen System Inc. using maskless array synthesis technology, with approximately 650,000 oligonucleotides per array27. Two arrays covered the C. elegans genome at ~86-bp spacing with 50mer oligonucleotides. We performed three biologically independent experiments for SDC-3, DPY-27 and No Antibody control ChIPs. Amplified samples were labeled and hybridized to high-resolution microarrays by the NimbleGen Service Laboratory as described previously. Two ChIPs (ChIP 1 and 3) were labeled with Cy5 and the reference materials (Input DNA) were labeled with Cy3, and for one (ChIP 2), the dyes were swapped. Raw intensity data was extracted from scanned images using NimbleScan 2.3 extraction software (NimbleGen Systems Inc.).

first: Sevinc

last: Ercan

first: Paul

last: Giresi

middle: M

last: Whittle

first: Xinmin

last: Zhang


title: Improvements in sample preparation for ChIP-chip assays

status: Public on Sep 01 2006

first: Victor

last: Jin

summary:
We have improved the new protocol for ChIP-chip by using pooling method. The new method has produced reproducible binding patterns and low background signals.
Keywords: ChIP-chip

overall_design: We have performed and compared three methods for ChIP-chip samples: LMPCR, 10 Pooled Samples and WGA.

first: Henriette

last: O'Geen

first: Charles

last: Nicolet

first: Kim

last: Blahnik

first: Peggy

last: Farnham


title: ENCODE ChIP-chip for Tetra-acetylated Histone H4 on HeLaS3 Cells [unpublished]

last: Zhong

summary:
Tetra-acetylated Histone H4 ChIP-chip performed on HeLaS3 Cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts). Goal was to identify Acetylated Histone H4-binding regions.  Use of this data requires permission from its producers.
Keywords: ChIP-chip

first: Chong

last: Shou


title: ENCODE Spike-in ChIP-chip Experiments

status: Public on Aug 08 2006

first: Wei

last: Li

summary:
ENCODE Spike-in ChIP-chip Experiments
Keywords: ChIP-chip comparison

overall_design: ENCODE Spike-in ChIP-chip Experiments


title: Depolarization induced gene from primary cortical neuron

status: Public on Mar 16 2006

city: Seoul

first: Hyun

last: Kim

country: South Korea

institute: College of Medicine, Korea university

summary:
Activation of neurons is one of the fundamental events for the functioning of nervous system. Neuronal activation relays information to next neurons. On the other hand, the activated neurons themselves are also influenced by neuronal activation. Depending on the type and condition of neuronal activation, these activated neurons change their gene expressions, thereby being able to process information more or less efficiently.
We applied the microarray technology to identify hither-to-uncharacterized as activity-dependent genes. Especially, we screened the transcription factors, because early changes in the transcription factors should result in alterations of gene expression profiles and subsequent neuronal properties.
Keywords: duplicated control, duplicated treatment

overall_design: Rat primary cortical neurons with or without KCl treatment were selected for RNA extraction and hybridization on Affymetrix microarrays. To identify the genes whose expression was induced by depolarization, we first compared gene expression profiles in control vs. 4 hr after KCl (25 mM) treated cortical neurons using Affymetrix Genechips specified for neurobiology.  All four hybridizations were analyzed for correlation accuracy between the replicates of the same treatments .Control replicates (control 1, 2) KCl-treated replicates (KCl 1, 2)

first: Woong

last: Sun

first: Sang-Hyun

last: Choi

first: Soon-Kwon

last: Park

first: Soon-Jung

first: Eun-Hae

first: Hyun-Ju


title: IgG control ChIP in HeLa cells

status: Public on Mar 09 2006

first: Mark

last: Bieda

summary:
Control IgG ChIP vs matched total for HeLa cells. Three biological replicates.
Keywords: ChIP-chip

overall_design: ChIP-chip of IgG; look for non-specific binding sites.

first: Shally

last: Xu

first: Michael

last: Singer

first: Roland

last: Green


status: Public on Jun 06 2006

city: Davis

first: Sharon

last: Squazzo

address: 4617 GBSF, 451 E. Health Sci. Dr.

department: Pharmacology

institute: UC Davis Genome Center

summary:
All samples are from the same batch of crosslinked Ntera cells with a matched total produced in parallel.  Amplicons were made from each and hybridized on ENCODE region tiling arrays.  Two color arrays were used; ChIP was red, Total was green.
Keywords: ChIP-chip

overall_design: Goal was determination of Suz12, EZH2, EED1, H3me3K27 binding sites in Ntera cells using ChIP-chip methodology.


title: POLII localization in HeLa cells

summary:
RNA polymerase II (POLR2A; POLII) was localized via ChIP-chip using N20 Ab-mediated pull-down of POLII
Keywords: ChIP-chip

overall_design: Classical design; ChIP-chip of POLII in ENCODE regions


title: E2F1 binding sites in MCF7 cells ENCODE

summary:
E2F1 binding sites in MCF7 cells were determined in the ENCODE regions
Keywords: ChIP-chip

overall_design: Note that both hg16 and hg17 arrays were used in these experiments.


title: Effects of Estrogen and Tamoxifen on Ishikawa cells after 24h and 48h

status: Public on Feb 01 2006

city: Leicester

first: Jerry

last: Styles

state: Leicestershire

address: Robert Kilpatrick Building, Univ. Leicester

department: Cancer Studies and Molecular Medicine

country: United Kingdom

institute: University of Leicester

summary:
Treatment with the breast cancer drug tamoxifen confers a risk of developing uterine tumors or other endometrial pathologies.  Tamoxifen is a selective estrogen receptor modulator, which demonstrates tissue-specific activity although the mechanisms remain poorly understood.  Both estradiol and tamoxifen act as estrogen agonists on the human uterus, and therefore have the potential to promote carcinogenicity.  Estradiol and tamoxifen elicit cellular responses via the estrogen receptors (ER), which are involved in multiple signalling pathways.  The effects at the molecular level are further influenced by the differential recruitment of co-factors and the presence of specific promoter motifs in target genes.

In this study, ER positive (+) Ishikawa cells are used as a model to investigate the overall effect of treatment with either 17b-estradiol or 4-hydroxytamoxifen on the gene expression profiles.
Keywords: Comparison of estradiol and tamoxifen on Ishikawa human uterine cells after 24h or 48h

overall_design: Ishikawa cells were serum-starved for 72 hours prior to treatment with 10-8M 17b-estradiol (E2) or 10-6M 4-hydroxytamoxifen (tam) for 24 or 48 hours.  Cells were collected for total RNA extraction, and the quality and quantity of the RNA was determined spectrophotometrically.  cDNA was prepared from treated (tam or E2) and control (vehicle only) Ishikawa cells, and was both forward and reverse labelled using Cy-3 dUTP/ Cy-5 dUTP and hybridised to oligo microarray slides representing >19,000 human genes (MRC HGMP-RFC).  The data were analysed using GenePix Pro 3.0 software (Axon instruments) and statistical analyses applied to select significant gene changes (p<0.05).

first: Suzanne

last: Johnson

first: Ian

last: White


title: Gene expression evidence for remodeling of lateral hypothalamic circuitry in cocaine addiction

status: Public on Jan 26 2006

first: Lena

middle: Dina

last: van der Stap

address: 10550 N. Torrey Pines Rd.

department: Neuropharmacology

institute: The Scripps Research Institute

summary:
By using high-density oligonucleotide arrays, we profiled gene expression in reward-related brain regions of rats that developed escalated cocaine intake after extended access to cocaine (6 h per day). Rats allowed restricted daily access to cocaine (only 1 h) that displayed a stable level of cocaine intake and cocaine naive rats were used for controls. Four analysis methods were compared: Affymetrix microarray suite 4 and microarray suite 5, which use perfect-match-minus-mismatch models, and dchip and rma, which use perfect-match-only models to generate expression values. Results were validated by RT-PCR in individual animals from an independent replication of the experiment. A small number of genes was associated with escalated cocaine intake (ESC genes). Unexpectedly, of the brain regions examined [prefrontal cortex, nucleus accumbens, septum, lateral hypothalamus (LH), amygdala, and ventral tegmental area], the LH was the most transcriptionally responsive in escalation of cocaine intake. Most of the ESC genes identified are also expressed during synaptogenesis and synaptic plasticity and include genes that code for several presynaptic and postsynaptic proteins involved in neurotransmission. These results suggest that LH intrinsic circuitry undergoes a structural reorganization during escalation of cocaine use. This remodeling of LH circuitry could contribute to the chronic deficit in reward function that has been hypothesized to drive the transition to drug addiction. Results also support the value of using multiple analysis strategies to identify the most robust changes in gene expression and to compensate for the biases that affect each strategy.
Keywords: cocaine addiction

overall_design:
The experimental design for this study comprised three groups of rats (n = 8) with different daily access to a continuous schedule of i.v. cocaine self-administration (0.25 mg per injection): 0 h access per day (drug-naive control rats), 1 h access per day (ShA rats), or 6 h access per day (LgA rats).
 Gene expression profiling was then performed for each dissected brain region by using Affymetrix rat neurobiology arrays.

first: Serge

last: Ahmed

first: Robert

last: Lutjens

first: Dusan

last: Lekic

first: Vincenzo

last: Romano-Spica

first: Marisela

last: Morales

first: George

middle: F

last: Koob

first: Vez

last: Repunte-Canonigo

first: Pietro

last: Sanna


title: ENCODE: PolyA+ RNA from retinoic acid stimulated HL-60 cells at 4 time points (NCBIv35)

status: Public on Dec 13 2005

city: Santa Clara

first: Thomas

middle: R

last: Gingeras

address: 3380 Central Expressway

institute: Affymetrix, Inc.

summary:
PolyA+ RNA from retinoic acid stimulated HL-60 cells at 0, 2, 8, or 32 hours using Affymetrix ENCODE tiling chip with NCBI build 35 annotation.
Keywords: Expression profiling on tiling array

overall_design: PolyA+ RNA from retinoic acid stimulated HL-60 cells at 0, 2, 8, or 32 hours.

first: Edward

last: Sekinger

first: Heather

last: Hirsch

first: Annie

last: Yang

first: Sandeep

last: Patel

first: Victor

last: Sementchenko

first: Philipp

last: Kapranov

first: Dione

last: Kampa


title: ENCODE: PolyA+ RNA from cytosol of HeLa and GM06990 cells (NCBIv35)

summary:
PolyA+ RNA from cytosol of HeLa and GM06990 cells using Affymetrix ENCODE tiling chip with NCBI build 35 annotation.
Keywords: Expression profiling on tiling array

overall_design: PolyA+ RNA from cytosol of HeLa and GM06990 cells.

first: Tom


title: ENCODE: p63ActD & p63_mActD ChIP of retinoic acid-stimulated ME180 cells at 0 h (NCBIv35) - strict analysis parameters

summary:
p63 with and without actinomycin D treatment ChIP from retinoic acid stimulated ME180 Cells at 0 hours using Affymetrix ENCODE tiling chip with NCBI build 35 annotation.
Keywords: ChIP-chip

overall_design: p63_ActD and p63_mActD ChIP from retinoic acid stimulated ME180 Cells, 0 hours.


title: ENCODE: Pol2 ChIP-chip of retinoic acid-stimulated HL60 cells at 4 timepoints (NCBIv35) - strict analysis parameters

summary:
Pol2 ChIP-chip of retinoic acid-stimulated HL60 cells at 0, 2, 8, or 32 hours using Affymetrix ENCODE tiling chip with NCBI build 35 annotation.
Keywords: ChIP-chip

overall_design: Pol2 ChIP-chip of retinoic acid-stimulated HL60 cells at 0, 2, 8, or 32 hours.


title: ENCODE: HisH4 ChIP-chip of retinoic acid-stimulated HL60 cells at 4 timepoints (NCBIv35) - strict analysis parameters

summary:
HisH4 ChIP-chip of retinoic acid-stimulated HL60 cells at 0, 2, 8, or 32 hours using Affymetrix ENCODE tiling chip with NCBI build 35 annotation.
Keywords: ChIP-chip

overall_design: HisH4 ChIP-chip of retinoic acid-stimulated HL60 cells at 0, 2, 8, or 32 hours.


title: ENCODE ChIP-chip for TAF II p250 on Human Hela S3 Cells

status: Public on Oct 19 2005

city: Woodbridge

first: Can

last: Bruce

address: 5 Chestnut Lane

institute: Sciomix

summary:
TAF II p250 ChIP-chip performed on Human Hela S3 Cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts).  Goal was to identify TAF II p250-binding sites.
Keywords = Transcription Factor Binding, TAF II p250, ChIP-chip, Human, Genome Tiling Arrays
Keywords: ChIP-chip

overall_design: DNA from immunoprecipitated chromatin or total genomic DNA was hybridized to a Nimblegen ENCODE tiling array containing overlapping 50 nt oligonucleotide probes.  Samples are two biological replicates.

first: Peter

last: Kraus

first: Ghia

last: Euskirchen

first: Zhengdong

last: Zhang

first: Joel

last: Rozowsky

first: Mark

last: Gerstein

first: Michael

last: Snyder


title: ENCODE: H3K9K14D ChIP-chip of retinoic acid-stimulated HL60 cells at 4 timepoints (NCBIv35) - strict analysis parameters

summary:
H3K9K14D ChIP-chip of retinoic acid-stimulated HL60 cells at 0, 2, 8, or 32 hours using Affymetrix ENCODE tiling chip with NCBI build 35 annotation.
Keywords: ChIP-chip

overall_design: H3K9K14D ChIP-chip of retinoic acid-stimulated HL60 cells at 0, 2, 8, or 32 hours.


title: ENCODE: TFIIB-R ChIP-chip of retinoic acid-stimulated HL60 cells  (NCBIv34)

status: Public on Jun 17 2005

summary:
TFIIB-R ChIP-chip of retinoic acid-stimulated HL60 cells 32 hours.
Keywords: ChIP-chip

overall_design: Study of TFIIB-R binding to ENCODE regions


title: ENCODE spikein, amplified DNA samples, NimbleGen arrays

status: Public on Jan 09 2008

last: Bieda

address: 3330 Hospital Dr NW

institute: University of Calgary

summary:
The goals of the study were to assess array platform performance and analysis algorithm performance.

The most widely used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms, amplification procedures, and signal detection algorithms in a simulated ChIP-chip experiment. Mixtures of human genomic DNA and "spike-ins" comprised of nearly 100 human sequences at various concentrations were hybridized to four tiling array platforms by eight independent groups. Blind to the number of spike-ins, their locations, and the range of concentrations, each group made predictions of the spike-in locations. We found that microarray platform choice is not the primary determinant of overall performance. In fact, variation in performance between labs, protocols and algorithms within the same array platform was greater than the variation in performance between array platforms. However, each array platform had unique performance characteristics that varied with tiling resolution and the number of replicates, which have implications for cost versus detection power. Long oligonucleotide arrays were slightly more sensitive at detecting very low enrichment. On all platforms, simple sequence repeats and genome redundancy tended to result in false positives. LM-PCR and WGA, the most popular sample amplification techniques, reproduced relative enrichment levels with high fidelity. Performance among signal detection algorithms was heavily dependent on array platform. The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated.
Keywords: ChIP-chip, competition, artificial DNA

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

overall_design: DNA samples had spike-in DNA added to simulate peaks in ChIP-chip experiments.  Same DNA samples used in the arrays in this Series; these are technical array replicates.


title: ENCODE: RARecA ChIP-chip of retinoic acid-stimulated HL60 cells at 4 timepoints  (NCBIv34)

summary:
RARecA ChIP-chip of retinoic acid-stimulated HL60 cells at 0, 2, 8, or 32 hours.
Keywords: ChIP-chip

overall_design: Study of RARecA binding to ENCODE regions


title: ENCODE: SIRT1 ChIP-chip of retinoic acid-stimulated HL60 cells at 4 timepoints  (NCBIv34)

summary:
SIRT1 ChIP-chip of retinoic acid-stimulated HL60 cells at 0, 2, 8, or 32 hours.
Keywords: ChIP-chip

overall_design: Study of SIRT1 binding to ENCODE regions


title: ENCODE: PolyA+ RNA from retinoic acid-stimulated HL60 cells at 4 timepoints (II)  (NCBIv34)

summary:
PolyA+ RNA from retinoic acid-stimulated HL60 cells at 0, 2, 8, and 32 hours.
Keywords: time-course

overall_design: Expression profiling of HL60 cells treated with retinoic acid


title: ENCODE: PolyA+ RNA from cytosols of GM06990 and Hela cells  (NCBIv34)

summary:
PolyA+ RNA from cytosols of GM06990 and Hela Cells
Keywords: cell type comparison

overall_design: Expression profiling of GM06990 and Hela cells


title: ENCODE: P300 ChIP-chip of retinoic acid-stimulated HL60 cells at 4 timepoints  (NCBIv34)

summary:
P300 ChIP-chip of retinoic acid-stimulated HL60 cells at 0, 2, 8, or 32 hours.
Keywords: ChIP-chip

overall_design: Study of P300 binding to ENCODE regions


title: ENCODE: PolyA+ RNA from retinoic acid-stimulated HL60 cells at 4 timepoints (I)  (NCBIv34)

status: Public on Jan 31 2005

summary:
Analysis of transcription using Affymetrix genome tiling array.

Examined polyA+ RNA from HL-60 cells stimulated with retinoic acid for 0, 2, 8, or 32 hours.
Keywords: other


title: ENCODE: RNAP transcription factor binding using Affymetrix genome tiling array  (NCBIv34)

summary:
Analysis of RNA Polymerase II transcription factor binding using Affymetrix genome tiling array.

Examined RNA Polymerase II RNAP chromatin immunoprecipitated (ChIP) DNA from HL-60 cells stimulated with retinoic acid for 0, 2, 8, or 32 hours.
Keywords: other


title: ENCODE: Pol2 ChIP-chip of retinoic acid-stimulated HL60 cells at 4 timepoints  (NCBIv34)

summary:
Pol2 ChIP-chip of retinoic acid-stimulated HL60 cells at 0, 2, 8, or 32 hours.
Keywords: ChIP-chip

overall_design: Study of Pol2 binding to ENCODE regions


title: ENCODE: HisH4 ChIP-chip of retinoic acid-stimulated HL60 cells at 4 timepoints  (NCBIv34)

summary:
HisH4 ChIP-chip of retinoic acid-stimulated HL60 cells at 0, 2, 8, or 32 hours.
Keywords: ChIP-chip

overall_design: Study of HisH4 binding to ENCODE regions


title: ENCODE: PU1 ChIP-chip of retinoic acid-stimulated HL60 cells at 4 timepoints  (NCBIv34)

summary:
PU1 ChIP-chip of retinoic acid-stimulated HL60 cells at 0, 2, 8, or 32 hours.
Keywords: ChIP-chip

overall_design: Study of PU1 binding to ENCODE regions


title: ENCODE: CEBPe ChIP-chip of retinoic acid-stimulated HL60 cells at 4 timepoints  (NCBIv34)

summary:
CEBPe ChIP-chip of retinoic acid-stimulated HL60 cells at 0, 2, 8, or 32 hours.
Keywords: ChIP-chip

overall_design: Study of CEBPe binding to ENCODE regions


title: ENCODE: H3K27T ChIP-chip of retinoic acid-stimulated HL60 cells at 4 timepoints  (NCBIv34)

summary:
H3K27T ChIP-chip of retinoic acid-stimulated HL60 cells at 0, 2, 8, or 32 hours.
Keywords: ChIP-chip

overall_design: Study of H3K27T binding to ENCODE regions


title: ENCODE: CTCF ChIP-chip of retinoic acid-stimulated HL60 cells at 4 timepoints  (NCBIv34)

summary:
CTCF ChIP-chip of retinoic acid-stimulated HL60 cells at 0, 2, 8, or 32 hours.
Keywords: ChIP-chip

overall_design: Study of CTCF binding to ENCODE regions


title: ENCODE: Brg1 ChIP-chip of retinoic acid-stimulated HL60 cells at 4 timepoints (NCBIv34)

summary:
Brg1 ChIP-chip of retinoic acid-stimulated HL60 cells at 0, 2, 8, or 32 hours.
Keywords: ChIP-chip

overall_design: Study of Brg1 binding to ENCODE regions


title: 12hr, 1d, 3d, and 5d exposure of beta-amyloid to astrocytes

status: Public on Dec 09 2003

city: Murray

first: William

middle: Clayton

last: Spencer

state: KY

address: P.O. Box 9

department: Department of Biological Sciences

institute: Murray State University

summary:
Cortical type-I astrocytes were cultured on the beta-amyloid peptide 25-35 fragment for 12hr, 1d, 3d, and 5d.
Keywords = amyloid astrocytes rat
Keywords: time-course

first: David

last: Canning