title: Renal cortex microRNA expression differences between hypertensive and normotensive patients

status: Public on Oct 15 2011

city: Sydney

middle: J

last: Morris

address: Anderson Stuart Building, room N452, University of Sydney

department: Physiology

institute: University of Sydney

summary: Identification of renal cortex microRNAs whose expression differs between male individuals with high blood pressure and normal blood pressure using  Agilent Human miRNA Microarrays (V3, release 12.0).

overall_design: The Silesian Renal Tissue Bank, a collection of tissues which aimed to investigate candidate genes in human cardiovascular disease, was used to analyze the miRNA expression in hypertensive and normotensive patients. Approximately 1 cm3 of tissue from the healthy (unaffected by cancer) pole of the kidney was obtained immediately after surgery and transferred into containers with RNAlater (Ambion) and preserved at 70°C before mRNA extraction, which used a commercially available assay (RNeasy, Qiagen). Medulla and cortex were separated and individual RNA was obtained for each of them. No pooling was performed. After extraction of RNA, cRNA was prepared and arrays performed using  Agilent Human miRNA Microarrays (V3, release 12.0)  performed at the Ramaciotti Gene Function Analysis facility, University of New South Wales in Sydney, Australia.

first: Francine

middle: Z

last: Marques

first: Anna

last: Campain

first: Maciej

last: Tomaszewski

first: Ewa

last: Zukowska-Szczechowska

first: Yee

last: Yang

first: Brian

first: Fadi

last: Charchar


title: Renal medulla microRNA expression differences between hypertensive and normotensive patients

state: NSW

country: Australia

summary: Identification of renal medulla microRNAs whose expression differs between male individuals with high blood pressure and normal blood pressure using Agilent Human miRNA Microarrays (V3, release 12.0).

overall_design: The Silesian Renal Tissue Bank, a collection of tissues which aimed to investigate candidate genes in human cardiovascular disease, was used to analyze the miRNA expression in hypertensive and normotensive patients. Approximately 1 cm3 of tissue from the healthy (unaffected by cancer) pole of the kidney was obtained immediately after surgery and transferred into containers with RNAlater (Ambion) and preserved at 70°C before mRNA extraction, which used a commercially available assay (RNeasy, Qiagen). Medulla and cortex were separated and individual RNA was obtained for each of them.  No pooling was performed. After extraction of RNA, cRNA was prepared and arrays performed using Agilent Human miRNA Microarrays (V3, release 12.0) performed at the Ramaciotti Gene Function Analysis facility, University of New South Wales in Sydney, Australia.

middle: E

middle: H


title: A conserved transcriptional regulator governs fungal morphology in widely diverged species

status: Public on Oct 04 2011

city: san francisco

first: Chris

last: Cain

address: 600 16th street

country: USA

institute: UC San Francisco

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: miRNA signatures of multiple endothelial cell types grown in culture

status: Public on Dec 08 2011

city: Baltimore

first: Marc

middle: K

last: Halushka

state: MD

address: 720 Rutland Avenue / Ross Rm 632B

department: Pathology

institute: Johns Hopkins University SOM

summary: This experiment explored what miRNA differences and similarities exist between endothelial cells obtained from different vascular beds.

overall_design: Seven different endothelial cell (EC) types were grown in basal conditions.  RNA was harvested when cells were nearly confluent. miRNAs were evaluated for each EC type in biological replicates.

first: Matthew

middle: N

last: McCall

first: Oliver

middle: A

last: Kent

first: Jianshi

last: Yu

first: Karen

last: Fox-Talbot

first: Ari

middle: L

last: Zaiman


title: Comparative miRNA Expression Profiles in Individuals with Latent and Active Tuberculosis

status: Public on May 10 2011

city: Shanghai

first: qian

last: gao

address: 138, Yi xue yuan Road

department: Shanghai Medical School

country: China

institute: Fudan University

summary: To study the role of miRNAs in the transition from latent to active TB and to discover candidate biomarkers that may help predict TB progression, we have employed miRNA microarray expression profiling as a discovery platform to probe the transcriptome of peripheral blood mononuclear cells (PBMCs) with active TB, latent TB infection (LTBI), and healthy donors.Patients were recruited at the Shanghai Public Health Clinical Centre (Shanghai, China) from December, 2008 to May, 2009. The diagnosis of active TB was based on clinical presentation, chest radiography, and acid-fast stain of sputum smear.All the patients were HIV negative, as diagnosed by the Livzon Anti-HIV1/2 EIA Kit (Livzon Pharmaceutical Group Inc., Guangdong, China). Additional tests were also performed to detect hepatitis B virus (HBV) and hepatitis C virus (HCV) by using the Abbott AxSYM anti-HBsAg and HCV 3.0 antibody assay kit (Abbott Laboratories, Illinois) to exclude HBV- and HCV-positive patients (these 2 diseases are highly prevalent in China). Patients with a diabetes history were also excluded because diabetes could increase the risk of TB. Peripheral venous blood was drawn before treatment. Subjects with LTBI and healthy donors both without a history of clinical TB or other infectious diseases were recruited from the staff at the Shanghai Public Health Clinical Centre. TST and IGRA (T-SPOT®.TB, Oxford Immunuotec, Oxfordshire, U.K) results were used to distinguish the two groups. The LTBI group was TST-positive (TST>10 mm) and IGRA-positive while the healthy donors were TST-negative (TST<5 mm) and IGRA-negative.

overall_design: RNA of PBMC from 6 patients with active TB, 6 donors with Latent TB, and 3 healthy controls (total of 15 biologically independent samples) were used to perform Agilent Human miRNA (version 3) microarray , No replicates were included

first: Chuan

last: Wang

first: Shuayao

first: Qian

last: Gao


title: Lieb JL00006_ZFP1_N2_MXEMB

status: Public on Mar 09 2011

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_2969
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. Our 126 strategically selected targets include 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 and perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins.
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: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Mixed Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Developmental Stage Mixed Embryo; temp (temperature) 20 degree celsius; Antibody JL00006 ZFP1 (target is ZFP-1); Strain N2

first: Morten

last: Jensen

first: Jason

last: Lieb


title: Hypermethylation of CpG Islands and Shores adjacent to mirtron and microRNA genes in bladder cancer

status: Public on Feb 17 2011

city: Sheffield

first: James

middle: W

last: Catto

state: South Yorks

address: Beech Hill Road

department: Institute for Cancer Studies

country: United Kingdom

institute: University of Sheffield

summary: We examined mirtron and miR expression in bladder cancer cell line following DNA Methyltransferase inhibition and normal urothelium using human Agilent microRNA microarrays.

overall_design: Bladder cancer cell lines (EJ, RT4 and RT112) were treated with 5-azacytidine ''Aza'' (2uM) for 5-7 days and normal urothelium (NHU) were subjected for microRNA microarray analysis.  Analysis were performed in triplicates or more.

first: Ewa

last: Dudziec

first: Saiful

last: Miah

first: Hani

middle: M

last: Choudhry


title: Lieb AB3594_H3K79ME2346021_N2_MXEMB

summary:
modENCODE_submission_3204
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. Our 126 strategically selected targets include key histone modifications and histone variants.   We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins.
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: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Mixed Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Mixed Embryo; temp (temperature) 20 degree celsius; Antibody AB3594 H3K79me2:346021 (target is H3K79me2); Strain N2


title: Lieb AB2886_H3K79ME1_361912_N2_L3

summary:
modENCODE_submission_3320
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. Our 126 strategically selected targets include key histone modifications and histone variants.   We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins.
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: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temp (temperature) 20 degree celsius; Antibody AB2886 H3K79me1:361912 (target is H3K79me1); Strain N2


title: Expression Profiling of Inflammatory Breast Cancer Cells Treated with the Novel Histone Deacetylase Inhibitor, CG-1521 (Agilent miRNA v12.0)

status: Public on Apr 12 2011

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary: Studies of gene expression profiles using the whole genomewide microarray analysis of miRNA in SUM149PT cells (ER-, p53mut) and SUM190PT cells (ER-, p53mut) when treated with 5-7.5 µM CG-1521 alone and in combination with 10 nM 17β-Estradiol. Comparisons between each treatment group provides evidence for the dysregulation of miRNA affecting genes associated with the spindle assembly checkpoint.

overall_design: Four independent experiments were carried out in SUM149PT and SUM190PT cells, which were treated with vehicle (ethanol/DMSO), 10nM 17β-Estradiol, 5 or 7.5µM CG-1521, and the combination of 17β-Estradiol and CG-1521. Total RNA was extracted from cell lysates using QIAGEN miRNeasy mini kit after 48h of treatment.

first: Martin

last: Tenniswood

first: Namita

last: Chatterjee


title: Lieb AB3594_H3K79ME2346021_N2_L3

status: Public on Jan 17 2011

summary:
modENCODE_submission_3321
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: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temp (temperature) 20 degree celsius; Antibody AB3594 H3K79me2:346021 (target is H3K79me2); Strain N2


title: Lieb AB2621_H3K79ME3_361576_N2_L3

summary:
modENCODE_submission_3322
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: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temp (temperature) 20 degree celsius; Antibody AB2621 H3K79me3:361576 (target is H3K79me3); Strain N2


title: Lieb AB2621_H3K79ME3361576_N2_MXEMB

summary:
modENCODE_submission_3151
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. Our 126 strategically selected targets include key histone modifications and histone variants.   We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins.
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: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Mixed Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Mixed Embryo; temp (temperature) 20 degree celsius; Antibody AB2621 H3K79me3:361576 (target is H3K79me3); Strain N2


title: Strome DISN147_H4K20ME1001_N2_LTEMB

summary:
modENCODE_submission_3196
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. Our 126 strategically selected targets include key histone modifications and histone variants.   We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins.
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: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Late Embryos; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Late Embryos; temp (temperature) 20 degree celsius; Antibody DISN147 H4K20me1:001 (target is H4K20me1); Strain N2

first: Thea

last: Egelhofer

first: Susan

last: Strome


title: Strome UP07448_H3K27ME124439_N2_EEMB

summary:
modENCODE_submission_3179
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: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Antibody UP07448 H3K27me1:24439 (target is H3K27me1); Strain N2


title: Lieb AB2886_H3K79ME1361912_N2_MXEMB

status: Public on Dec 28 2010

summary:
modENCODE_submission_3202
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Mixed Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Mixed Embryo; temp (temperature) 20 degree celsius; Antibody AB2886 H3K79me1:361912 (target is H3K79me1); Strain N2


title: Strome AB15823_H4K8AC487128_N2_EEMB

summary:
modENCODE_submission_3181
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: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Antibody ab15823-H4K8ac (target is H4K8ac); Strain N2


title: Ahringer UP07448_H3K27ME124439_N2_L3

summary:
modENCODE_submission_3203
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: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temp (temperature) 20 degree celsius; Antibody UP07448 H3K27me1:24439 (target is H3K27me1); Strain N2

first: Anne

last: Canonge

first: Julie

last: Ahringer


title: Expression data of Medicago truncatula skl1-1 roots treated with S. meliloti wild-type or auxin transport inhibitors

status: Public on Mar 26 2011

city: Stanford

first: Adriana

middle: Parra

last: Rightmyer

state: CA

address: 371 Serra Mall

department: Biology

institute: Stanford University

summary: Rhizobium and allied bacteria form symbiotic nitrogen-fixing nodules on legume roots. Plant hormones appear to play a role in nodule formation. We treated Medicago truncatula roots with auxin transport inhibitors (ATIs) N-(1-naphthyl)phthalamic acid (NPA) and 2,3,5-triiodobenzoic acid (TIBA) to induce the formation of pseudonodules. We compared the transcriptional responses of M. truncatula roots treated with ATIs to roots inoculated with Sinorhizobium meliloti. The transcriptional response of M. truncatula roots 1 and 7 days after ATI treatment were opposite to roots treated with S. meliloti.

platform_organism:
Sinorhizobium meliloti
Medicago truncatula

overall_design: Three independent biological replicates were performed for each treatment (buffer, ATI and wild-type bacteria) at 21 days after treatment.

middle: P

first: Sharon

last: Long


title: Genes differentially expressed in wild-type Medicago truncatula plants during nodulation

summary: We used an Affymetrix oligonucleotide microarray consisting of 9,935 tentative consensus (TC)sequences, which are based on cDNA libraries (Mitra et al., 2004 [PMID:15220482]).  We examined gene expression of wild-type M. truncatula plants after inoculation with wild-type S. meliloti at 1 d, 4 d, 7d, 14 d, and 21 d. We chose these time points because they span the range of development of the Rhizobium-legume symbiosis, from initiation of the interaction through nitrogen fixation. The gene expression data for the 1-day time point (Mitra et al., 2004 [PMID 15220482]) and the other time points was previously published (Starker el al., 2006 [PMID 16407449]).

overall_design: Three or five independent biological replicates were performed at each time point (1, 4, 7, 14 and 21 days after treatment) and each treatment (buffer and wild-type bacteria).

first: Colby

middle: G

last: Starker

first: Raka

last: Mitra


title: Expression data of Medicago truncatula Jemalong A17 roots treated with S. meliloti exoA mutant or auxin transport inhibitors

overall_design: Three to five independent biological replicates were performed for each treatment (buffer, exoA bacteria and ATI) at 21 days after treatment.


title: Strome MP07329_H4K16ACDAM1612187_N2_EEMB

first: DCC

last: modENCODE

summary:
modENCODE_submission_3182
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: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Antibody MP07329 H4K16ac:DAM1612187 (target is H4K16ac); Strain N2


title: Ahringer AB9048_H3K36ME1206009_N2_L3

summary:
modENCODE_submission_3205
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: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temp (temperature) 20 degree celsius; Antibody ab9048 H3K36me1:206009 (target is H3K36me1); Strain N2


title: Lieb SDQ4051_LEM2_N2_MXEMB

status: Public on Dec 22 2010

summary:
modENCODE_submission_3166
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: Mixed Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage Mixed Embryo; temp (temperature) 20 degree celsius; Antibody SDQ4051 LEM2 (target is LEM-2); Strain N2

first: Ikegami

last: Kohta

first: Jason

last: Lieb


title: Expression data from Medicago truncatula roots treated with S. meliloti wild-type or exoA mutant bacteria, or auxin transport inhibitors

summary:
Publication title: Pseudonodule formation by wild type and symbiotic mutant Medicago truncatula in response to auxin transport inhibitors

This SuperSeries is composed of the SubSeries listed below.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: Refer to individual Series


title: Lieb SDQ3891_LEM2_VC1317_MXEMB

summary:
modENCODE_submission_3165
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: VC1317; Developmental Stage: Mixed Embryo; Genotype: lem-2(ok1807) II.; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage Mixed Embryo; temp (temperature) 20 degree celsius; Antibody  (target is ); Strain VC1317


title: Lieb SDQ4051_LEM2_SP646_MXEMB_SP646

summary:
modENCODE_submission_3164
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: SP646; Developmental Stage: Mixed Embryo; Genotype: mnT12(IV;X).; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Mixed Embryo; temp (temperature) 20 degree celsius; Antibody  (target is ); Strain SP646


title: Lieb AB46540_NIGG_N2_MXEMB

summary:
modENCODE_submission_3153
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: Mixed Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Mixed Embryo; temp (temperature) 20 degree celsius; Antibody  (target is ); Strain N2


title: Control of expression noise, fitness and gene aggregation by a component of the yeast pheromone response pathway

status: Public on Dec 15 2010

city: San Francisco

first: Hiten

last: Madhani

department: Biochemistry and Biophysics

institute: University of California, San Francisco

summary: Cellular processes are subject to variability, or noise, yet mechanisms that promote cell-to-cell uniformity are poorly understood.  We have identified such a role for Dig1, a redundant (with Dig2) MAPK-responsive inhibitor of the S. cerevisiae mating pathway transcription factor Ste12.  Cells lacking Dig1, but not Dig2, exhibited increased variability in outputs of the mating pathway.  dig1∆ mutants also displayed a Ste12-dependent defect in growth in the absence of mating pheromone and a quantitative defect in the process of mating, itself.  In cells expressing two reporter genes driven by the same promoter, both intrinsic/uncorrelated and extrinsic/correlated noise were found to increase.  Remarkably, the extrinsic noise phenotype in cells lacking Dig1 correlates with the aggregation of target genes: we observed subnuclear foci of Ste12 specifically in dig1∆ cells and, using a newly-developed method to immunoprecipitate a single locus from crosslinked chromatin, we found that Dig1 inhibits long-range interactions between Ste12 target genes in vivo.  Dig1 may shield binding surfaces on Ste12 whose unmasking leads to inappropriate gene associations and increased gene expression noise.  These studies reveal how investigations of variability modulation mechanisms can yield unexpected biological insights.

overall_design: The FUS1 locus is tagged with an array of lac operators.  Wild type and dig1∆ cells containing this tagged FUS1 locus and expressing a mCherry-LacI were grown up for ChIP-chip.  The FUS1 locus was selectively immunoprecipitated using an anti-DsRed antibody.

first: Emma

last: McCullagh

first: Anupama

last: Seshan

first: Hana

last: El-Samad

middle: D


title: Strome HK00013_H3K27ME31E7_N2_EEMB

summary:
modENCODE_submission_3171
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

relation:
SubSeries of: GSE25933
SubSeries of: GSE26186

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Antibody HK00013 H3K27me3:1E7:JL:1 (target is H3K27me3); Strain N2


title: Analysis of the microRNA that involved the tuberculosis or latent TB infection II

status: Public on Nov 18 2010

city: Beijing

first: Zhaogang

last: Sun

state: Beijing

address: No. 97, Machang Road, Tongzhou District

department: Microbiology and Immunology

institute: Beijing Tuberculosis & Thotacic Tumor research Institute

summary: To get to know the different levels of the microRNA among the pulmonary tuberculosis patients, latent-infected individuals and the complete healthy people, we have employed the Agilent miRNA microarray (version 2.0) as a discovery platform to identify microRNA with the potential to diagnose the TB patients and the latent infected persons. The Peripheral Blood Mononuclear Cells (PBMCs) of each group were made up of equally mixed quantity of  3 volunteers. The results showed that several microRNAs were found up- or low regulated in PBMCs of TB patients versus latent-infected individuals and similarly for latent-infected individuals versus complete healthy ones.

overall_design: Each group have 4 volunteers. The PBMCs of each group were made up of equally mixed volumes after being purified.each group was reated three times.

first: Liqun

last: Zhang

first: Weicong

last: Ren


title: Ahringer AB9051_H4K20ME1104513_N2_L3

summary:
modENCODE_submission_2784
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.
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: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temperature 20; Antibody ab9051 H4K20me1:104513 (target is H4K20me1); Strain N2

first: Isabel

last: latorre


title: Ahringer AB8895_H3K4ME1733246_N2_L3

summary:
modENCODE_submission_2775
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.
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: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temperature 20; Antibody ab8895 H3K4me1:733246 (target is H3K4me1); Strain N2


title: Ahringer WA30634849_H3K27AC_N2_L3

summary:
modENCODE_submission_2773
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.
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: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temperature 20; Antibody WA306-34849 H3K27ac (target is H3K27ac); Strain N2


title: Ahringer AB4729_H3K27AC361571_N2_L3

summary:
modENCODE_submission_2771
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.
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: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temperature 20; Antibody ab4729 H3K27ac:361571 (target is H3K27ac); Strain N2


title: Ahringer MP05858_H4DAM1636076_N2_L3

summary:
modENCODE_submission_2768
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.
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: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temperature 20; Antibody H4 (target is H4); Strain N2


title: miRNA expression in bone marrow of an AML patient and CD34 cells of healthy individuals

status: Public on Sep 21 2010

city: St. Louis

first: Daniel

middle: C

last: Link

state: MO

address: 660 S. Euclid, Campus Box 8007

institute: Washington University

summary: miRNA  expression in a patient with AML comparing with pooled CD34 hematopoietic progenitor cells from 5 healthy volunteers

overall_design: RNA from bone marrow of a  patient with AML with more than 90% blast and RNA pooled from 5 volunteers with CD34+ cells selected by automacs from bone marrow

first: Giridharan

last: Ramsingh


title: Strome SDQ3582_CBP1_N2_MXEMB

status: Public on Jul 07 2010

summary:
modENCODE_submission_2767
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Mixed embryos 20dC; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Developmental Stage Mixed embryos 20dC; temperature 20; Antibody SDQ3582 CBP1 (target is CBP-1); Strain N2

first: Kohta

last: Ikegami


title: Ruler Arrays Reveal Haploid Genomic Structural Variation

status: Public on Sep 16 2010

city: Cambridge

first: Alex

last: Rolfe

state: MA

address: 77 Massachusetts Ave, 32-G538

department: CSAIL

institute: Massachusetts Institute of Technology

type: Genome variation profiling by genome tiling array

summary:
A ruler array combines novel sample preparation protocols, tiling genomic microarrays, and a new computational method to turn each probe on a microarray into a ruler that measures the physical distance between defined genomic sequences regardless of the intervening sequence.
The ruler array protocol involves (1) genomic DNA purification (2) digestion with a restriction enzyme (3) ligation of a biotinylated adapter molecule to the cut sites (4) purification on streptavidin beads (5) polymerase extensions from a primer complementary to the adapter using labeled dNTPs and (6) hybridization to a tiling microarray

overall_design: Two replicates of our ruler array experiment to detect insertions and deletions between two genomic samples of strains FY4 and Sigma1278b.

first: P

first: Douglas

last: Bernstein

first: Paula

last: Grisafi

first: Gerald

middle: R

last: Fink

first: David

last: Gifford


title: Strome LPAR109_H4TETRAAC109_N2_EEMB

first: DCC

last: modENCODE

summary:
modENCODE_submission_2766
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temperature 20; Antibody LPAR109 H4tetraac:109 (target is H4tetraac); Strain N2

first: Thea

last: Egelhofer

first: Susan

last: Strome


title: Ahringer AB9045_H3K9ME1291918_N2_L3

summary:
modENCODE_submission_2770
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.
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: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temperature 20; Antibody ab9045 H3K9me1:291918 (target is H3K9me1); Strain N2

first: Julie

last: Ahringer


title: miRNA Profiling of Androgen Receptor and Vitamin D Receptor Mediated Signaling in Prostate Cancer Cells

status: Public on Aug 26 2010

first: Sridar

last: Chittur

summary: Studies of miRNA profiles using Agilent Human miRNA arrays.

overall_design: Four independent experiments were carried out in LNCaP cells, which were treated with ethanol control (no exogenous androgen), 5nM testosterone, 100nM 1,25(OH)2D3, and the combination of testosterone and 1,25(OH)2D3. Total RNA was extracted from cell lysates using QIAGEN miRNeasy mini kit after 48h of treatment. The samples were run on Agilent Human miRNA microarrays that measure the expression levels of 866 human miRNAs from the Sanger database v12.0.

first: Martin

last: Tenniswood

first: Wei-Lin

last: Wang


title: Strome AB4729_H3K27AC361571_N2_EEMB

summary:
modENCODE_submission_2740
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temperature 20; Antibody ab4729 H3K27ac:361571 (target is H3K27ac); Strain N2


title: Expression/miRNA Profiling of Androgen Receptor and Vitamin D Receptor Mediated Signaling in Prostate Cancer Cells

type:
Non-coding RNA profiling by array
Expression profiling by array

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

overall_design: Refer to individual Series


title: Strome AB4441_H3K9AC_N2_EEMB

summary:
modENCODE_submission_2728
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temperature 20; Antibody ab4441 H3K9ac:360927 (target is H3K9ac); Strain N2


title: Strome AB8896_H3K9ME1104560_N2_EEMB

summary:
modENCODE_submission_2739
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temperature 20; Antibody ab8896 H3K9me1:104560 (target is H3K9me1); Strain N2


title: Strome SDQ3891_LEM2_N2_MXEMB

summary:
modENCODE_submission_2729
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Mixed embryos 20dC; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Developmental Stage Mixed embryos 20dC; temperature 20; Antibody SDQ3891 LEM2 (target is LEM-2); Strain N2

first: Jason

last: Lieb


title: Strome SDQ3897_NPP13_N2_MXEMB

summary:
modENCODE_submission_2738
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Mixed embryos 20dC; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Developmental Stage Mixed embryos 20dC; temperature 20; Antibody SDQ4094 NPP13 (target is NPP-13); Strain N2


title: Strome AB8895_H3K4ME1733246_N2_EEMB

summary:
modENCODE_submission_2726
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temperature 20; Antibody ab8895 H3K4me1:733246 (target is H3K4me1); Strain N2


title: Strome AB9051_H4K20ME1104513_N2_EEMB

summary:
modENCODE_submission_2765
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temperature 20; Antibody ab9051 H4K20me1:104513 (target is H4K20me1); Strain N2


title: Strome WA30634849_H3K27AC_N2_EEMB

summary:
modENCODE_submission_3200
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: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Antibody WA306-34849 H3K27ac (target is H3K27ac); Strain N2


title: Strome AB9045_H3K9ME1291918_N2_EEMB

summary:
modENCODE_submission_2646
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temperature 20; Antibody ab9045 H3K9me1:291918 (target is H3K9me1); Strain N2


title: Strome MP07030_H3K4ME2DAM1570816_N2_EEMB

summary:
modENCODE_submission_2645
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temperature 20; Antibody MP07030 H3K4me2:DAM157816 (target is H3K4me2); Strain N2


title: Strome AB9048_H3K36ME1206009_N2_EEMB

summary:
modENCODE_submission_2604
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temperature 20; Antibody ab9048 H3K36me1:206009 (target is H3K36me1); Strain N2


title: Strome OD00079_HCP3_N2_EEMB

summary:
modENCODE_submission_2541
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temperature 20; Antibody OD00001 HCP3 (target is HCP-3); Strain N2


title: Strome WA30834809_H3K4ME2_N2_EEMB

summary:
modENCODE_submission_2445
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; Developmental Stage Early Embryo; Strain N2; Antibody WA308-34809 H3K4me2 (target is H3K4me2); Strain N2; temperature 20


title: Lieb AB2621_H3K79ME3361576_N2_EEMB

summary:
modENCODE_submission_2443
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; Developmental Stage Early Embryo; Strain N2; Antibody AB2621 H3K79me3:361576 (target is H3K79me3); Strain N2; temperature 20

first: Morten

last: Jensen


title: Strome HK00008_H3K9ME26D11_N2_EEMB

summary:
modENCODE_submission_2444
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; Developmental Stage Early Embryo; Strain N2; Antibody HK00008 H3K9me2:6D11 (target is H3K9me2); Strain N2; temperature 20


title: Broad chromosomal domains of histone modification patterns in C. elegans

status: Public on Jan 16 2011

summary:
Chromatin immunoprecipitation identifies specific interactions between genomic DNA and proteins, advancing our understanding of gene-level and chromosome-level regulation. Based on chromatin immunoprecipitation experiments using validated antibodies, we define the genome-wide distributions of 19 histone modifications, one histone variant, and eight chromatin-associated proteins in Caenorhabditis elegans embryos and L3 larvae. Cluster analysis identified five groups of chromatin marks with shared features: two groups correlate with gene repression, two with gene activation, and one with the X chromosome. The X chromosome displays numerous unique properties, including enrichment of monomethylated H4K20 and H3K27, which correlate with the different repressive mechanisms that operate in somatic tissues and germ cells, respectively. The data also revealed striking differences in chromatin composition between the autosomes and between chromosome arms and centers. Chromosomes I and III are globally enriched for marks of active genes, consistent with containing more highly expressed genes, compared to chromosomes II, IV, and especially V. Consistent with the absence of cytological heterochromatin and the holocentric nature of C. elegans chromosomes, markers of heterochromatin such as H3K9 methylation are not concentrated at a single region on each chromosome. Instead, H3K9 methylation is enriched on chromosome arms, coincident with zones of elevated meiotic recombination. Active genes in chromosome arms and centers have very similar histone mark distributions, suggesting that active domains in the arms are interspersed with heterochromatin-like structure. These data, which confirm and extend previous studies, allow for in-depth analysis of the organization and deployment of the C. elegans genome 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

This SuperSeries is composed of the SubSeries listed below.

relation:
SuperSeries of: GSE6739
SuperSeries of: GSE10201
SuperSeries of: GSE16621
SuperSeries of: GSE22697
SuperSeries of: GSE22708
SuperSeries of: GSE22710
SuperSeries of: GSE22717
SuperSeries of: GSE22718
SuperSeries of: GSE22719
SuperSeries of: GSE22720
SuperSeries of: GSE22721
SuperSeries of: GSE22728
SuperSeries of: GSE22729
SuperSeries of: GSE22730
SuperSeries of: GSE22731
SuperSeries of: GSE22732
SuperSeries of: GSE22733
SuperSeries of: GSE22737
SuperSeries of: GSE22738
SuperSeries of: GSE22739
SuperSeries of: GSE22740
SuperSeries of: GSE22741
SuperSeries of: GSE22744
SuperSeries of: GSE22746
SuperSeries of: GSE22747
SuperSeries of: GSE22748
SuperSeries of: GSE22750
SuperSeries of: GSE22754
SuperSeries of: GSE22755
SuperSeries of: GSE25353
SuperSeries of: GSE25354
SuperSeries of: GSE25356
SuperSeries of: GSE25357
SuperSeries of: GSE25358
SuperSeries of: GSE26178
SuperSeries of: GSE26179
SuperSeries of: GSE26180
SuperSeries of: GSE26181
SuperSeries of: GSE26182
SuperSeries of: GSE26183
SuperSeries of: GSE26184
SuperSeries of: GSE26185

overall_design: Refer to individual Series.


title: Strome AB3594_H3K79ME2346021_N2_EEMB

summary:
modENCODE_submission_2442
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; Developmental Stage Early Embryo; Strain N2; Antibody AB3594 H3K79me2:346021 (target is H3K79me2); Strain N2; temperature 20


title: Strome AB2886_H3K79ME1361912_N2_EEMB

summary:
modENCODE_submission_2410
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; Developmental Stage Early Embryo; Strain N2; Antibody WA305-34819 H3K4me3 (target is H3K4me3); Strain N2; temperature 20


title: Ahringer AB1791_H3_N2_L3

summary:
modENCODE_submission_2409
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temperature 20; Antibody C. elegans  AB1791 H3 rabbit polyclonal antibody (target is Histone H3); Strain N2

first: Anne

last: Canonge


title: Ahringer AR0144_H3144_N2_L3

summary:
modENCODE_submission_2407
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temperature 20; Antibody C. elegans  AR0144 H3 rabbit serum (target is histone H3); Strain N2


title: Ahringer AR0144_H3144_N2_L3_LM

summary:
modENCODE_submission_2408
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

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temperature 20; Antibody C. elegans  AR0144 H3 rabbit serum (target is histone H3); Strain N2