title: RNA-Sequencing of lean, intermediate, and obese pigs

status: Public on Jan 15 2015

city: Kongens Lyngby

first: Haja

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

summary: We sequenced mRNA from subcuteneous adipose tissue of 36 pigs (12 Low, 12 Mean and 12 High) to investigate expression profiling of obesity (porcine model). Uploaded RNAseq data on the first 12 samples (from titles 1_SusScrofa to 12_SusScrofa) are LOW obese pigs, the middle 12 samples (from titles 13_SusScrofa to 24_SusScrofa) are MEDIUM obese pigs and the last 12 samples (from titles 24_SusScrofa to 36_SusScrofa) are HIGH obese pigs. These 3 categories based on an aggregate Obesity Index (OI) values and calculated using a multi-trait Estimated Breeding Value (EBV) and Selection Index methods combining nine obesity and obesity-related (OOR) phenotypes into a single value representative of the genetic predisposition to obesity. in Human studies, this is somewhat equivalent to combined multi-trait, weighted Polygenic Risk Scores (PRS) for obesity. That is, they are predicted based on genetic / genomic information and several correlated phenotypes using Mixed Models / BLUP.  For more information on Obesity Index, refer to Frontiers in Genetics (2014), Sec. Systems Biology,  Vol. 5.  https://doi.org/10.3389/fgene.2014.00214

overall_design: Examination of mRNA levels in different  "genetically" categorized obese states in a porcine model for human obesity

first: Lisette

last: Kogelman


title: seq-WA30532379_H3K4me3_10001_N2_Eemb

status: Public on Aug 10 2013

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
modENCODE_submission_5166
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-seq 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

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

first: Susan

last: Strome

first: Thea

last: Egelhofer

first: Andreas

last: Rechtsteiner


title: seq-SDQ3520_LIN61_N2_L3

status: Public on Jul 26 2013

summary:
modENCODE_submission_5979
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-seq 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

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temp (temperature) 20 degree celsius; Strain N2; Antibody LIN-61 SDQ3520 (target is LIN-61)

first: Julie

last: Ahringer

first: Isabel

last: Latorre

first: Anne

last: Canonge


title: The mammalian germline corrects deleterious effects of endocrine disruptors

status: Public on Feb 18 2015

city: Grand Rapids

first: Piroska

middle: E

last: Szabo

state: MI

address: 333 Bostwick Ave. NE

department: Center for Epigenetics

country: USA

institute: Van Andel Research Institute

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: seq-WA30634849_H3K27ac_8002_N2_Eemb

summary:
modENCODE_submission_5159
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-seq 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

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Strain N2; Antibody WA306-34849 H3K27ac (target is H3K27ac)


title: seq-HK00013_H3K27me3_1E7_N2_Eemb

summary:
modENCODE_submission_5163
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-seq 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

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


title: mRNA profiling and clinical outcomes in human osteosarcoma (biopsies)

status: Public on Jan 22 2013

city: Boston

first: Katherine

last: Hill

state: MA

address: 330 Brookline Avenue, DA-679

department: Medicine

institute: Beth Israel Deaconess Medical Center

summary: Osteosarcoma is a malignancy with variable outcomes that are not tightly aligned with chemotherapy response. Previous work has suggested a possible role for microRNAs (miRNAs) in determining the susceptibility of osteosarcomas to treatment but formal miRNA-based outcome models have not been reported. Formalin-fixed, paraffin-embedded (FFPE) specimens may be a unique approach for such studies in a rare malignancy. We used supervised principal components analysis and logistic regression to study survival and chemoresponse endpoints, and miRNA activity and gene set analysis algorithms to study miRNA regulatory networks using mRNA data. Our study also creates a paradigm for FFPE-based miRNA clinical biomarker research in rare tumors.

overall_design: 37 unique diagnostic biopsy specimens were profiled. Samples with paired surgical resection specimens (not included in this submission) are denoted in the Sample 'characteristics' field.

first: Andrew

last: Kelly


title: mRNA profiling and clinical outcomes in human osteosarcoma (biopsy/resection pairs)

overall_design: 5 unique pairs of diagnostic biopsy and surgical resection specimens were profiled. Paired samples are denoted in the Sample 'characteristics' field.


title: microRNA- and mRNA-based studies in paraffin-archived human osteosarcoma specimens reveal profiles with reproducible and independent prognostic value

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


title: Identification of differentially expressed genes in Sfmbt1-knockdown C2C12 myoblasts

status: Public on Jan 28 2013

city: Gainesville

first: Lizi

last: Wu

state: FL

address: 2033 Mowry Road

institute: University of Florida

summary: Gene expression profiling was performed to identify Sfmbt1-dependent regulation in myogenic programs. To establish the magnitude of the Sfmbt1 effect on muscle cells, we have compared gene expression profiles of C2C12 cells transduced with lentiviruses expressing scramble shRNA control or shSfmbt1. Our analysis suggested that Sfmbt1 critically confers transcriptional silencing of muscle genes in myogenic progenitor cells.

overall_design: Two biological replicates for each sample group: C2C12 cells stably transduced with pLKO.1 expressing scramble shRNA control and C2C12 cells transduced with pLKO.1 shSFMBT1. Samples were independently cultured and RNAs were then harvested for microarray analysis.

first: Jian

middle: L

last: Li


title: microRNA profiling and clinical outcomes in human osteosarcoma (biopsies)

overall_design: 65 unique diagnostic biopsy specimens were profiled. Samples with paired surgical resection specimens (not included in this submission) are denoted in the Sample 'characteristics' field.


title: seq-ab8898_H3K9me3_339901_N2_Eemb

summary:
modENCODE_submission_5155
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-seq 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

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Strain N2; Antibody AB8898 H3K9ME3:339901 (target is H3K9me3)


title: Gene expression profiling of multiple myeloma patients included in the HOVON65/GMMG-HD4 trial

status: Public on Jun 27 2010

city: Rotterdam

first: Mark

last: van Duin

address: Wytemaweg 80

country: Netherlands

institute: Erasmus MC

summary: In order to identify relevant, molecularly defined subgroups in Multiple Myeloma (MM), gene expression profiling (GEP) was performed on purified CD138+ plasma cells of 320 newly diagnosed myeloma patients included in the Dutch-Belgian/German HOVON-65/ GMMG-HD4 trial using Affymetrix GeneChip U133 plus 2.0 arrays. Hierarchical clustering identified 10 distinct subgroups. Using this dataset as training data, a prognostic signature was built. The dataset consists of 282 CEL files previously used in the hierarchical clustering study of Broyl et al (Blood, 116(14):2543-53, 2010) outlined above. To this set 8 CEL-files/gene expression profiles were added. Using this set of 290 CEL-files, a prognostic signature of 92 genes (EMC-92-genesignature) was generated by supervised principal components analysis combined with simulated annealing (Kuiper et al.).

overall_design: Bone marrow plasma cell samples were obtained from 320 newly diagnosed multiple myeloma patients included in a large multicenter, prospective, randomized phase III trial (HOVON65/GMMG-HD4). Purified myeloma plasma cells samples with a monoclonal plasma cell purity > 80% were used for analysis. To  the original set of 320 samples which were used for the hierarchical clustering analysis,  8 CEL-files were added. Out of 328 CEL-files, 290 CEL-files were linked to survival data and were used to generate the 92 gene survival signature. GCRMA was performed on 290 CEL-files to give the values given for the additional 8 CEL-files. The values of the original 320 CEL-files are left unchanged (i.e. GCRMA on the original 320 CEL-files) to allow optimal comparison to the original paper by Broyl et al.

first: Annemiek

last: Broyl

first: Dirk

last: Hose

first: Rowan

last: Kuiper

first: Yvonne

last: de Knegt

first: Hartmut

last: Goldschmidt

first: Pieter

last: Sonneveld


title: seq-SDQ3891_LEM2_N2_MXemb

status: Public on Sep 21 2010

city: Chapel Hill

first: Everett

last: Zhou

state: NC

address: 1000 Manning Dr.

institute: UNC

summary:
modENCODE_submission_3168
Although C. elegans was the first multicellular organism with a completely sequenced genome, how this genome is arranged within the nucleus is not known. By chromatin immunoprecipitation of the nuclear transmembrane protein LEM-2, we determined the regions of the C. elegans genome associated with the nuclear membrane. We found that large regions of several megabases on the left and right arms of each autosome were associated with the nuclear membrane. The center of each autosome was free of such interactions, suggesting these regions are largely looped out from the nuclear membrane. The X chromosome, unlike the autosomes, was associated with the nuclear membrane only at its left end. At a finer scale, these large membrane-associated domains consist of smaller subdomains of LEM-2 associations. These subdomains are characterized by a high density of repetitive sequences, a low density of genes, and high levels of H3K27 trimethylation. The subdomains were punctuated by gaps containing genes with high transcriptional activity. Finally, we found that a chromosome arm translocated to the center of a chromosome retained its association with the nuclear membrane, although there was a decrease of association up to 400 kb from the fusion point. This indicates that local chromatin properties are the main determinant of interaction with the nuclear membrane, but the degree of association can be modulated by position along the chromosome. Our data provide the foundation for a model of the spatial arrangement of C.elegans chromosomes within the nucleus. Supplemental materials are available online at http://www.genome.org . Microarray and high-throughput sequencing data are available online at modENCODE Data Coordinating Center website, http://206.108.121.120/submit/public/list .

overall_design:
These dataset are designed to confirm ChIP-chip experiments. The three experiments listed consist of: (1) LEM-2 ChIP-seq (seq-SDQ3891_LEM2_N2_MXemb_1_A_EE8_KI021); (2) control IgG ChIP-seq (seq-AB46540_NIgG_N2_MXemb_2_A_EE1432); and (3)Input-seq (seq-NA_N2_MXemb_3_A_EE1432)

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

first: Kohta

last: Ikegami

first: Jason

last: Lieb


title: microRNA profiling and clinical outcomes in human osteosarcoma (biopsy/resection pairs)

overall_design: 26 unique pairs of biopsy and surgical resection specimens were profiled. Paired samples are denoted in the Sample 'characteristics' field.


title: Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2

status: Public on Dec 22 2010

first: DCC

last: modENCODE

type: Genome binding/occupancy profiling by genome tiling array

type: Expression profiling by genome tiling array

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

This SuperSeries is composed of the SubSeries listed below.

relation:
SuperSeries of: GSE22720
SuperSeries of: GSE22723
SuperSeries of: GSE22740
SuperSeries of: GSE22746
SuperSeries of: GSE22750
SuperSeries of: GSE24241
SuperSeries of: GSE24318
SuperSeries of: GSE26180
SuperSeries of: GSE26200
SuperSeries of: GSE26201
SuperSeries of: GSE26202
SuperSeries of: GSE26203
SuperSeries of: GSE26204
Affiliated with: GSE42741


title: Genome wide DNA methylation analysis in NSCLC

status: Public on Nov 26 2012

city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

department: Medicine I

country: Austria

institute: Medical University of Vienna

summary: DNA methylation is an important mechanism for gene silencing in lung cancer. In this study we identified a large number of tumor specifically methylated genes in NSCLC patients by methylome profiling.

overall_design:
Genomic DNA was extracted from tumor and matching non-malignant lung tissue samples from 101 NSCLC patients and genome wide DNA methylation was analyzed using the MeDIP-chip technology as described previously (Weber et al., 2005).
Genomic DNA was extracted from NSCLC cell lines and genome wide DNA methylation was analyzed using the MeDIP-chip technology as described previously (Weber et al., 2005).

first: Sabine

last: Zöchbauer-Müller