title: H4K16ac(M).14-16 hr OR embryo.Solexa

summary:
modENCODE_submission_4938
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS sequencing platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody H4K16ac(M) (target is H4K16ac); Developmental Stage Embryo 14-16hr OR


title: H3K9me3 abcam.14-16 hr OR embryo.Solexa

status: Public on May 28 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_4939
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS sequencing platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody H3K9me3 abcam (target is H3K9me3); Developmental Stage Embryo 14-16hr OR

first: Gary

last: Karpen

first: Sarah

last: Elgin

first: Andrey

last: Gortchakov

first: Greg

last: Shanower

first: Michael

last: Tolstorukov

first: Peter

last: Kharchenko

first: Mitzi

last: Kuroda

first: Vincenzo

last: Pirrotta

last: Park

first: Aki

last: Minoda

first: Nicole

last: Riddle

first: Yuri

last: Schwartz

first: Art

last: Alekseyenko

first: Cameron

last: Kennedy


title: H4K20me1 (3rd lot).OR Head Nuclei.Solexa

summary:
modENCODE_submission_4937
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS sequencing platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Mixed Adult; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); tissue (organism part) ; Antibody H4K20me1 (3rd lot) (target is H4K20me); Developmental Stage Mixed Adult


title: The Swi/Snf tumor suppressor complex establishes nucleosome occupancy at target promoters [ChIP-seq]

status: Public on Jun 04 2013

city: Boston

middle: J

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

country: USA

institute: Harvard Medical School

summary: Precise nucleosome-positioning patterns at promoters are thought to be crucial for faithful transcriptional regulation. However, the mechanisms by which these patterns are established and dynamically maintained and subsequently contribute to transcriptional control are poorly understood. The Swi/Snf (Baf) chromatin remodeling complex is a master developmental regulator and tumor suppressor that is capable of mobilizing nucleosomes in biochemical assays. Yet, its role in establishing the nucleosome landscape in vivo is unclear. Here we have inactivated Snf5 and Brg1, core subunits of the mammalian Swi/Snf complex, to evaluate their effects on chromatin structure and transcription levels genome-wide. We find that inactivation of either subunit leads to disruptions of specific nucleosome patterning combined with a loss of overall nucleosome occupancy at a large number of promoters, regardless of their association with CpG islands. These rearrangements are accompanied by gene expression changes that promote cell proliferation. Collectively, these findings define a direct relationship between chromatin-remodeling complexes, chromatin structure, and transcriptional regulation.

overall_design: Profiling Brg1 binding in murine embryonic fibroblasts

middle: Y

first: Courtney

middle: G

last: Sansam

first: Ping

last: Lu

first: Edward

middle: C

last: Koellhoffer

first: Katherine

last: Helming

first: Burak

middle: H

last: Alver

first: Erik

last: Tillman

first: Julia

middle: A

last: Evans

first: Boris

last: Wilson

first: Charles

middle: W

last: Roberts


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

first: DCC

last: modENCODE

summary:
modENCODE_submission_4951
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS sequencing platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

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

first: Gary

last: Karpen

first: Sarah

last: Elgin

first: Andrey

last: Gortchakov

first: Greg

last: Shanower

first: Michael

last: Tolstorukov

first: Peter

last: Kharchenko

last: Kuroda


title: H3K9me1 (new lot).14-16 hr OR embryo.Solexa

summary:
modENCODE_submission_4123
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS sequencing platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody H3K9me1 (new lot) (target is H3K9me1); Developmental Stage Embryo 14-16hr OR

first: Mitzi

first: Vincenzo

last: Pirrotta

last: Park

first: Aki

last: Minoda

first: Nicole

last: Riddle

first: Yuri

last: Schwartz

first: Art

last: Alekseyenko

first: Cameron

last: Kennedy


title: H3K36me1.14-16 hr OR embryo.Solexa

summary:
modENCODE_submission_4196
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina  NGS sequencing platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody H3K36me1 (target is H3K36me1); Developmental Stage Embryo 14-16hr OR


title: GAF.14-16 hr OR embryo.Solexa

summary:
modENCODE_submission_4119
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody GAF (target is GAF); Developmental Stage Embryo 14-16hr OR


title: H3K79Me1.14-16 hr OR embryo.Solexa

summary:
modENCODE_submission_4122
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS sequencing platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody H3K79Me1 (target is H3K79me1); Developmental Stage Embryo 14-16hr OR


title: H3K27Ac.14-16 hr OR embryo.Solexa

summary:
modENCODE_submission_4120
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS sequencing platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody H3K27Ac (target is H3K27ac); Developmental Stage Embryo 14-16hr OR


title: Solexa.Pc.14-16 hr OR embryo

summary:
modENCODE_submission_3957
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody Pc (target is Pc); Developmental Stage Embryo 14-16hr OR


title: Solexa.SU(HW)-HB.14-16 hr OR embryo

summary:
modENCODE_submission_3958
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody SU(HW)-HB (target is SU(HW)); Developmental Stage Embryo 14-16hr OR


title: Solexa.CP190-HB.14-16 hr OR embryo

summary:
modENCODE_submission_3959
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody CP190-HB (target is CP190); Developmental Stage Embryo 14-16hr OR


title: Solexa.Psc.14-16 hr OR embryo

summary:
modENCODE_submission_3960
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody Psc (target is Psc); Developmental Stage Embryo 14-16hr OR


title: Next generation sequencing analysis of microRNAs in brown preadipocytes and in vitro differentiated mature brown fat cells

city: Bonn

first: Franziska

last: Siegel

address: Sigmund-Freud-Str. 25

department: Institute of Pharmacology and Toxicology

country: Germany

institute: University of Bonn

type: Non-coding RNA profiling by high throughput sequencing

summary: We performed a genome-wide deep sequencing analysis of the microRNAs abundant in mesenchymal stem cells (MSCs) derived from murine brown adipose tissue and in in vitro differentiated mature brown adipocytes. Several microRNAs were identified as differentially regulated when comparing datasets from MSCs vs. mature fat cells. These microRNAs may have an implication in the regulation of adipogenesis as well as thermogenesis in brown adipose tissue (BAT).

overall_design:
Examination of BAT-derived MSCs (BAT-MSC; 1 sample) and in vitro differentiated mature brown fat cells (BAT-DIFF; 1 sample)
vertis biotechnologie AG, D-85354 Freising, Germany (library construction and sequencing)

first: Yong

last: Chen

first: Jiayun

last: Zhu

first: Norbert

last: Eichner

first: Alexander

last: Pfeifer


title: Solexa.H3K27me3.14-16 hr OR embryo

first: DCC

last: modENCODE

summary:
modENCODE_submission_3955
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS sequencing platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody H3K27Me3 (Abcam2) (target is H3K27Me3); Developmental Stage Embryo 14-16hr OR

first: Gary

last: Karpen

first: Sarah

last: Elgin

last: Gortchakov


title: Solexa.H3K9me2_antibody2.S2

summary:
modENCODE_submission_3953
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS sequencing platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody H3K9me2 antibody2 (target is H3K9me2)

first: Andrey

first: Greg

last: Shanower

first: Michael

last: Tolstorukov

last: Kharchenko

last: Kuroda


title: Solexa.HP1 wa 191.14-16 hr OR embryo

summary:
modENCODE_submission_3956
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody HP1 wa191 (target is HP1a); Developmental Stage Embryo 14-16hr OR

first: Peter

first: Mitzi

first: Vincenzo

last: Pirrotta

last: Park

last: Minoda

last: Riddle


title: Induction of pluripotency in mouse somatic cells with novel factors

city: Beijing

first: Hongkui

last: Deng

address: 5th Yiheyuan Road

country: China

institute: Peking University

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: H3K9me3 (new lot).OR Head Nuclei.Solexa

summary:
modENCODE_submission_4933
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS sequencing platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Mixed Adult; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); tissue (organism part) ; Antibody H3K9me3 (new lot) (target is H3K9me3); Developmental Stage Mixed Adult

first: Aki

first: Nicole

first: Yuri

last: Schwartz

first: Art

last: Alekseyenko

last: Kennedy


title: Genome-wide mapping of Runx1-bound sites in early B-cell progenitors

status: Public on May 27 2013

city: Hamburg

first: Neele

middle: Margarete

last: Kriebitzsch

address: Martinistraße 52

institute: Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology

summary: The t(12;21) chromosomal translocation, targeting the gene encoding the RUNX1 transcription factor, is observed in 25% of pediatric acute lymphoblastic leukemia (ALL) and is an initiating event in the disease. To elucidate the mechanism by which RUNX1 disruption initiates leukemogenesis, we investigated its normal role in murine B-cell development. Gene expression analysis and genome-wide Runx1-occupancy studies support the hypothesis that Runx1 reinforces the transcription factor network in B-cell progenitors governing early B-cell survival and development .

overall_design: ChIP-seq experiments were performed in the proB-cell line BMiFLT3(15-3), stably transduced with the transcription factor Runx1, to identify Runx1-bound sites in early B-cell progenitors.

first: Birte

last: Niebuhr

first: Malik

last: Alawi

first: Carol

last: Stocking


title: Xenorhabdus nematophila FliZ regulon identification by RNA-Seq

city: Montpellier

first: Sophie

last: Gaudriault

address: case courrier 54, Place Eugène Bataillon

country: France

institute: Université Montpellier 2 - Institut National de la Recherche Agronomique

summary: A fliZ mutant in the entomopathogenic bacterium X. nematophila is attenuated in virulence in the insect. The goal of this study is to compare transcriptomes of the fliZ mutant and wild type strain to identify the FliZ regulon.

overall_design: Two biological replicates of total RNA from exponential cultures of WT strain and fliZ mutant were analysed by deep sequencing, using Illumina HiSeq 2000.

first: Anne

last: Lanois

first: Alain

last: Givaudan

first: Stéphanie

last: Rialle

first: Dany

last: Severac


title: Time course RNA-seq analysis of barley powdery mildew fungus Bgh infecting immunocompromised Arabidopsis thaliana

city: Cologne

first: Emiel

last: Ver Loren van Themaat

address: Carl von linneweg

institute: Max Planck Institute

summary: RNA-seq experiments detected fungal expression patterns during infection of immunocompromised Arabidopsis thaliana

overall_design: 3 biological replicates per condition.  Arabidopsis plants without (pps) or with (B12) the MLA1-HA construct in pen2 pad4 sag101 background were challenged with either Bgh isolate K1 expressing the cognate AVRA1 effector for MLA1 or Bgh isolate A6 expressing other AVRA effectors. Samples were collected at 6, 12, 18, 24 hours post inoculation (hpi) of Bgh.

first: Takaki

last: Maekawa

first: Barbara

last: Kracher

first: Saskia

last: Vernaldi

first: Paul

last: Schulze-Lefert


title: MicroRNA Target Site Identification by Integrating Sequence and Binding Information

status: Public on May 25 2013

city: Aurora

first: Neelanjan

last: Mukherjee

state: CO

department: BMG/RBI

institute: University of Colorado School of Medicine

summary: High-throughput sequencing has opened numerous possibilities for the identification of regulatory RNA-binding events. Cross-linking and immunoprecipitation of Argonaute protein members can pinpoint microRNA target sites within tens of bases, but leaves the identity of the microRNA unresolved. A flexible computational framework that integrates sequence with cross-linking features reliably identifies the microRNA family involved in each binding event, considerably outperforms sequence-only approaches, and quantifies the prevalence of noncanonical binding modes.

overall_design: Ago2 (Argonaute 2) PAR-CLIP and RNA deep sequencing of Epstein-Barr virus B95.8-infected Lymphoblastoid Cell Lines (LCLs)

first: Rebecca

middle: L

last: Skalsky

first: Bryan

middle: R

last: Cullen

first: Uwe

last: Ohler


title: Profiling of differential allelic expression in horse, donkey, mule and hinny placental tissue

status: Public on May 24 2013

city: Ithaca

first: Andrew

last: Clark

address: 227 Biotech Building

institute: Cornell University

summary: The discovery of genomic imprinting through studies of manipulated mouse embryos indicated that the paternal genome has a major influence on placental development.  However, previous research has not demonstrated paternal bias in imprinted genes.  We applied RNA sequencing to trophoblast tissue from reciprocal hybrids of horse and donkey, where genotypic differences allowed parent-of-origin identification of most expressed genes.  Using this approach, we identified a core group of 15 ancient imprinted genes of which 10 were paternally expressed.  An additional 78 candidate novel imprinted genes identified by RNA-seq also showed paternal bias.  Pyrosequencing was used to confirm the imprinting status of six of the novel genes, including the insulin receptor (INSR), which may play a role in growth regulation with its reciprocally imprinted ligand, histone acetyltransferase (HAT1), the first example of an imprinted gene involved in chromatin modification, and LY6G6C, the first imprinted gene to be identified in the major histocompatibility complex.  The 78 novel candidate imprinted genes displayed parent-of-origin expression bias in placenta but not fetus, and most showed less than 100% silencing of the imprinted allele.  Some displayed variability in imprinting status among individuals.  This results in a unique epigenetic signature for each placenta that contributes to variation in the intrauterine environment and thus presents the opportunity for natural selection to operate on parent-of-origin differential regulation.  Taken together, these features highlight the plasticity of imprinting in mammals and the central importance of the placenta as a target tissue for genomic imprinting.

sample_organism:
Equus asinus
Equus caballus
Equus asinus x Equus caballus
Equus caballus x Equus asinus

overall_design: Examine allelic expression from four individual samples of invasive trophoblast tissue of the chorionic girdle from gestation day 33 conceptuses of horse, donkey, mule and hinny.

first: Douglas

last: Antczak


title: Ribosome Profiling over a Zebrafish Developmental Timecourse

status: Public on May 23 2013

city: Cambridge

first: Guo-Liang

last: Chew

address: 16 Divinity Ave BL 1019

department: Dept of Molecular and Cellular Biology

institute: Harvard University

summary: To experimentally-validate the non-coding status of annotated lncRNAs, we performed ribosome profiling over a developmental timecourse that matched our previously-published (Pauli et al. 2012) developmental transcriptome. We find that many previously-annotated lncRNAs appear to be translated, but in a pattern more akin to 5' leaders of coding genes.

overall_design: Ribosome profiling over 8 stages in early zebrafish development: 2-4 cell, 256 cell, 1K cell, Dome, Shield, Bud, 28hpf and 5dpf

first: Andrea

last: Pauli

first: Eivind

last: Valen

first: Alexander

last: Schier


title: Gene expression is a circular process

city: Rehovot

first: Gal

last: Haimovich

address: Belfer bldg. 416

department: Dept. Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: This study involves the role of yeast mRNA decay factors in transcription. The experiment included here are the ChIP-exo results of three decay factors: Xrn1, Dcp2 & Lsm1.

overall_design: Four experiments were made: Xrn1, Dcp2, Lsm1 and control (no-TAP tag), in two replicates.

first: Manuel

last: Garber

first: Mordechai

last: Choder


title: Tissue specific Pol II Chip-Seq in the early fly embryo

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

institute: Stowers Institute for Medical Research

summary: In order to idetify paused promoters in vivo, we performed tissue specific Pol II Chip-seq using mutant embryos for the dorsal gradient. We used two population of cells, either dorsal ectoderm cells (gd7 embryos) or mesodermal cells (Toll10b) embryos.

overall_design: ChIP-seq for Pol II in various Drosophila embryos

first: Mounia

last: Lagha

first: Jacquesf

last: Bothma

first: Emilia

last: Esposito

first: Laura

last: Stefanik

first: Jeff

last: Johnston

first: Chiahao

last: Tsui

first: Kai

last: Chen

first: David

last: Gilmour

first: Mike

last: Levine


title: High throughput gene expression analysis identifies reliable expression markers of human corneal endothelial cells.

city: Singapore

first: Zhenzhi

last: Chng

address: 8A Biomedical Grove #06-06

country: Singapore

institute: Institute of Medical Biology

summary: Considerable interest has been generated for the development through cell-tissue engineering of suitable corneal endothelial graft alternatives, which can potentially alleviate the shortage of corneal transplant material. The advent of less invasive suture-less key-hole surgery options such as Descemet’s Stripping Endothelial Keratoplasty (DSEK) and Descemet’s Membrane Endothelial Keratoplasty (DMEK), which involve transplantation of solely the endothelial layer instead of full thickness cornea, provide further impetus for the development of alternative endothelial grafts for clinical applications. A major challenge for this endeavor is the lack of specific markers for this cell type. To identify genes that reliably mark corneal endothelial cells (CECs) in vivo and in vitro, we performed RNA-sequencing on freshly isolated human CECs (from both young and old donors), CEC cultures, and corneal stroma. Gene expression of these corneal cell types were also compared to that of other human tissue types. Based on high throughput comparative gene expression analysis, we identified a panel of markers that are: i) highly expressed in CECs from both young donors and old donors; ii) expressed in CECs in vivo and in vitro; and iii) not expressed in corneal stroma keratocytes and the activated corneal stroma fibroblasts. These were SLC4A11, COL8A2 and CYYR1. The use of this panel of genes in combination reliably ascertains the identity of the CEC cell type.

overall_design:
A total of 20 donor corneas consisting of 10 single donor corneas and 5 paired donor corneas were used in this study. Donor age ranged from 19 - 76.
This RNA-seq study included 15 pooled corneas (5 each) used form CEC old, CEC young and stroma samples.

first: Gary

middle: S

last: Peh

first: Wishva

middle: B

last: Herath

first: Paul

last: Robson

first: Jodhbir

last: Mehta

first: Alan

last: Colman


title: Architectural protein subclasses shape 3-D organization of genomes during lineage commitment

city: Worcester

first: Jennifer

middle: Elizabeth

last: Phillips-Cremins

address: 364 Plantation Street

department: Program in Systems Biology and Department of Biology

institute: University of Massachusetts Medical School and Emory University

type: Genome variation profiling by high throughput sequencing

summary: Understanding the topological configurations of chromatin can reveal valuable insights into how the genome and epigenome act in concert to control cell fate during development.  Here we generate high-resolution architecture maps across seven genomic loci in embryonic stem cells and neural progenitor cells.  We observe a hierarchy of 3-D interactions that undergo marked reorganization at the sub-Mb scale during differentiation.  Distinct combinations of CTCF, Mediator, and cohesin show widespread enrichment in architecture at different length scales.  CTCF/cohesin anchor long-range constitutive interactions that might form the topological basis for invariant sub-domains.  Conversely, Mediator/cohesin together with pioneer factors bridge short-range enhancer-promoter interactions within and between larger sub-domains.  Knockdown of Smc1 or Med12 in ES cells results in disruption of spatial architecture and down-regulation of genes found in cohesin-mediated interactions.  We conclude that cell type-specific chromatin organization occurs at the sub-Mb scale and that architectural proteins shape the genome in hierarchical length scales.

overall_design: Analysis of higher-order chromatin chromatin architecture in mouse ES cells and ES-derived NPCs.  Analysis of CTCF and Smc1 occupied sites in ES-derived NPCs.

middle: E


title: DNAseq data from human ovarian carcinoma cell lines subjected to shRNA TRC1.0 library

status: Public on May 21 2013

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

institute: National University of Singapore

summary: The hallmark of human cancer is heterogeneity, mirroring the complexity of genetic and epigenetic alterations acquired during oncogenesis.  We extracted DNA of 14 cultured human ovarian carcinoma cell lines subjected to pooled shRNA screen using TRC 1.0 library, and performed DNAseq.

overall_design: 14 ovarian carcinoma cell lines DNAseq data.

first: TZ

first: QH

last: Miow

first: RY

last: Huang

first: Luqman

last: Abdul Hadi

first: JP

last: Thiery

first: Seiichi

last: Mori


title: Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles

city: Baltimore

first: Adam

middle: D

last: Ewing

state: MD

address: 733 N. Broadway, MRB 439

department: Genetic Medicine

institute: Johns Hopkins University

summary: We explored the RNA binding properties of LINE-1 ORF1p, both free and in the L1 RNP, using a recently developed photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation technique (PAR-CLIP) to comprehensively identify ORF1p binding sites in the transcriptome of human cells (HEK293T). Our results show that ORF1p binds to a wide range of cellular mRNAs, with an enrichment for binding at the 3’ UTR. Our data also show that ORF1p binds very strongly with retrotransposable RNA, i.e., L1, Alu and SVA.

overall_design: PAR-CLIP analysis of L1 RNPs and free ORF1p RNA binding profiles, comparison to HuR RNA binding profile

first: Prabhat

middle: K

last: Mandal

first: Dustin

last: Hancks

first: Haig

last: Kazazian


title: Functional Identification of Critical Bmi1 target genes in Neural Progenitor and Malignant Glioma cells

city: Berlin

first: Gaetano

last: Gargiulo

address: Robert-Rössle-Straße 10

department: Molecular Oncology

institute: Max Delbrüch Center

summary: In this study, we combined a genome-wide analysis of the Polycomb protein Bmi1 and an in vivo RNAi screening to identify critical targets whose repression in neural progenitor and Malignant Glioma cells enables normal and aberrant self-renewal.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Bmi1 ChIP-sequencing generated in 2 primary adult mouse Neural Progenitor cell lines, 1 mouse astrocytic cell line, 1 mouse Glioma initiating cell line, and 1 mouse Glioma cell line. In human cell lines, Bmi1 ChIP-seq was performed for foetal Neural Progenitor Cells, and 2 Glioblastoma Stem-like cells. ChIP-seq for AP-1 in one Glioblastoma stem-like cell line. ChIP-sequencing were generated using either Illumina GxII or HiSeq. We have further performed RNA-seq of  adult Ink4a/Arf -/-;BMI1or GFP  dox-inducible shRNA mNPC with a doxycycline inducible shRNA targeting BMI1 or GFP (as control). These cells were either treated with doxyclyine for 48h to ablate BMI1 and GFP expression or further subjected to short-term differentiation using either BMP4 (10ng/ml or 50ng/ml for 3 or 6hrs), or FBS (1 or 10% for 3 or 6hrs). Additional mouse RNA-seq were performed in two biological replica of adult mouse brains (littermate) with either wild-type FVB background or BMI1 -/-. Finally, we performed RNA-seq in human Glioblastoma stem-like cells (most likely belonging to the mesenchymal GBM subtype) treated with BMP7, Arvanil and doxycycline or  EtOH treated as ctrl.

first: Matteo

last: Cesaroni

first: Michela

last: Serresi

first: Cesare

last: Lancini

first: Nienke

last: De Vries

first: Danielle

last: Hulsman

first: Maarten

last: van Lohuizen


title: Bacterial discrimination by Dictyostelid amoebae reveals the complexity of ancient interspecies interactions

status: Public on May 20 2013

city: Houston

first: Gad

last: Shaulsky

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Transcriptional profiling of D. discoideum revealed sets of genes whose expression is enriched in amoebae interacting with different species of bacteria, including sets that appear specific to amoebae interacting with Gram(+), or with Gram(-) bacteria. In a genetic screen utilizing the growth of mutant amoebae on a variety of bacteria as a phenotypic readout, we identified amoebal genes that are only required for growth on Gram(+) bacteria, including one that encodes the cell surface protein gp130, as well as several genes that are only required for growth on Gram(-) bacteria including one that encodes a putative lysozyme, AlyL. These genes are required for parts of the transcriptional response of wild-type amoebae, and this allowed their classification into potential response pathways.

overall_design: Transcriptional profiling of amoebal response to different bacteria.

first: Waleed

last: Nasser

first: Balaji

last: Santhanam

first: Edward

last: Miranda

first: Anup

last: Parikh

first: Kavina

last: Juneja

first: Gregor

last: Rot

first: Chris

last: Dinh

first: Rui

last: Chen

first: Blaz

last: Zupan

last: Kuspa


title: A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription

status: Public on May 22 2013

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

type: Expression profiling by genome tiling array

type: Genome binding/occupancy profiling by genome tiling array

last: van Bakel

first: Kyle

last: Tsui

first: Marinella

last: Gebbia

first: Sanie

last: Mnaimneh

first: Timothy

last: Hughes

first: Corey

last: Nislow


title: Detoxification activity and energy cost is attenuated in the whiteﬂies feeding on Tomato yellow leaf curl China virus-infected tobacco plants

city: Hangzhou

first: Xiaowei

last: Wang

address: 866 Yuhangtang Road

department: Insect Sciences

institute: Zhejiang University

summary: We compared the transcriptional profiles of female adult whiteflies of B. tabaci Middle East-Asia Minor 1 feeding on TYLCCNV-free and TYLCCNV-infected tobacco plants using the next-generation sequencing technique.

overall_design: Culture of B (MEAM1 cryptic species) whitefly was maintained on cotton plants. One thousand of newly emerged adults of whitefly on cotton were released onto the leaves of healthy and viruliferous tobacco plants. After 72 h of oviposition, all the adult whiteflies were discarded, and the progeny allowed to develop to adults. The cultures of MEAM1 on tobacco plants were maintained in climate chambers at 27 ± 1°C, a photoperiod of 14 h light/10 h darkness and 70 ± 10% relative humidity. Approximately 1,000 female adult whiteflies newly emerged from mock-inoculated tobacco plants and 1,000 female adult whiteflies newly emerged from virus-infected tobacco plants were collected and stored at -80°C. The RNA was extracted and sequenced using Illunima Analyzer II.

first: Jun-Bo

last: Luan

first: Shu-Sheng

last: Liu

first: Xiao-Wei


title: Sperm but not oocyte DNA methylome is inherited by zebrafish early embyros

first: Lan

last: Jiang

address: NO.1 Beichen West Road, Chaoyang District

institute: Beijing Institute of Genomics

type: Methylation profiling by high throughput sequencing

summary: 5-methylcytosine is a major epigenetic modification sometimes called "the fifth nucleotide". However, our knowledge of how offspring inherit the DNA methylome from parents is limited. We generated nine single-base resolution DNA methylomes including zebrafish gametes and early embryos. The oocyte methylome is significantly hypo-methylated compared to sperm. Strikingly, the paternal DNA methylation pattern is maintained throughout early embryogenesis. The maternal DNA methylation pattern is maintained until the 16-cell stage. Then, the oocyte methylome is gradually discarded through cell division, and progressively reprogrammed to a pattern similar to that of the sperm methylome. The passive demethylation rate and the de novo methylation rate are similar in the maternal DNA. By the midblastula stage, the embryo?s methylome is virtually identical to the sperm methylome. Moreover, inheritance of the sperm methylome facilitates the epigenetic regulation of embryogenesis. Therefore, besides DNA sequences, sperm DNA methylome is also inherited in zebrafish early embryos.

overall_design:
hMeDIP-seq is performed in sperm,2-cell,16-cell,1k-cell and a input control sample
4 new samples are added to GSE44075. RNA-seq is performed in sperm, egg,1k-cell, germring samples .hMeDIP-seq is performed in sperm,2-cell,16-cell,1k-cell and a input control sample
10 new samples are added to GSE44075. Bisulfite-seq is performed for nine samples : sperm, egg,16-cell,32-cell,64-cell,128-cell,1k-cell , Germring and testis. TAB-seq is performed for one sample , 32-cell.

first: Jiang


title: Transcriptional effects of overexpression of the mtrCDE operon in Neisseria gonorrhoeae due to a cis-acting point mutation

status: Public on May 18 2013

city: Atlanta

first: Gregory

last: Doho

state: GA

address: 1365B Clifton Rd NE

institute: Emory University

summary: A whole transcriptome comparison of N. gonorrhoeae strain FA19, which bears a wild-type mtr locus, and FA19mtr120, which contains a C-to-T transition mutation 120 base pairs upstream of the mtrC start codon that generates a second promoter for mtrCDE transcription, was performed to determine the effects of high-level expression of the mtrCDE efflux pump operon on global transcription within the gonococcus.

overall_design: Examination of the transcriptomes of N. gonorrhoeae wild-type strain FA19 and the isogenic FA19mtr120 mutant to determine the effect of overexpression of mtrCDE on gonococcal cells grown under laboratory conditions.  Illumina HiSeq-2000 next generation sequencing was used to sequence the transcriptomes of each strain.  Reads were mapped against the N. gonorrhoeae FA1090 genome (NCBI accession number NC_002946) because at the time this experiment was run the FA19 genome was incomplete.

first: Elizabeth

last: Ohneck

first: Corinne

last: Rouquette-Loughlin

first: Sandeep

last: Joseph

first: Daniel

last: Golparian

first: Magus

last: Unemo

first: Ann

last: Jerse

first: William

middle: M

last: Shafer


title: The Making of a Slicer: Activation of Human Argonaute-1

city: Cold Spring Harbor

first: Astrid

last: Haase

state: NY

address: One Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: The Argonautes are the central protein component in small RNA silencing pathways. Of the four human Argonautes (hAgo1-4) only hAgo2 is an active slicer. We determined the structure of hAgo1 bound to endogenous copurified RNAs to 1.75 Å resolution and hAgo1 loaded with let-7 miRNA to 2.1 Å. Both structures are strikingly similar to the structures of hAgo2. A conserved DEDH catalytic tetrad within the PIWI domain of hAgo2 is required for its slicing activity. hAgo3, with an intact tetrad, could be activated by swapping in the N domain of hAgo2, without additional PIWI domain mutations. An additional mutation on a loop adjacent to the active site of hAgo1 results in slicer activity that is substantially enhanced by swapping in the N domain of hAgo2. Intriguingly, the elements that make Argonaute an active slicer involve a sophisticated interplay between the active site and more distant regions of the enzyme.

overall_design: RNAsprofiling of small RNAs associated with recombinant protein used for chrystallographic studies

first: Christopher

last: Faehnle

first: Elad

last: Elkayam

middle: J

last: Hannon

first: Leemor

last: Joshua-Tor


title: Runx1 targets in early B-cell progenitors

city: Hamburg

first: Neele

last: Kriebitzsch

address: Martinistraße 52

institute: Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology

summary: The t(12;21) chromosomal translocation, targeting the gene encoding the RUNX1 transcription factor, is observed in 25% of pediatric acute lymphoblastic leukemia (ALL) and is an initiating event in the disease. To elucidate the mechanism by which RUNX1 disruption initiates leukemogenesis, we investigated its normal role in murine B-cell development. Gene expression analysis and genome-wide Runx1-occupancy studies support the hypothesis that Runx1 reinforces the transcription factor network in B-cell progenitors governing early B-cell survival and development .

overall_design: Refer to individual Series


title: H3K23ac.OR Head Nuclei.Solexa

city: Toronto

first: DCC

last: modENCODE

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

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_4960
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS sequencing platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Mixed Adult; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); tissue (organism part) ; Antibody H3K23ac (target is H3K23ac); Developmental Stage Mixed Adult

first: Gary

last: Karpen

first: Sarah

last: Elgin

first: Andrey

last: Gortchakov

first: Greg

last: Shanower

first: Michael

last: Tolstorukov

first: Peter

last: Kharchenko

first: Mitzi

last: Kuroda

first: Vincenzo

last: Pirrotta

last: Park

first: Aki

last: Minoda

first: Nicole

last: Riddle

first: Yuri

last: Schwartz

first: Art

last: Alekseyenko

first: Cameron

last: Kennedy


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and PPARbeta-null mice during liver regeneration

city: sacramento

first: HUIXIN

last: LIU

state: CA

address: 2 quay court apt 98

institute: UCD medical center

summary:
Purpose: The current study tests the hypothesis that peroxisome proliferator-activated receptor β (PPARβ) has a role in liver regeneration due to its effect in regulating energy homeostasis and cell proliferation.
Methods: Wild-type (WT) and PPARβ-null mice (KO) male mice (3-5 month, C57BL/6) were kept in steel microisolator cages at 22°C with a 14-hr/10-hr light/dark cycle. Food and water were provided ad libitum throughout the entire feeding period. Standard PH was performed. All the animal experiments were conducted in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under protocols approved by the University of California Davis Animal Care and Use Committee.Mouse liver RNA was prepared using TRIzol (Invitrogen, Carlsbad, CA). RNA concentration and integrity were determined by the Agilent 2100 Bioanalyzer using a RNA Nano Bioanalysis Chip. RNA-sequencing library preparation and sequencing was carried out by the Genome Sequencing Facility at University of Kansas Medical Center (Kansas City, KS). cDNA libraries were prepared with 2 µg of total RNA using the TruSeq RNA Sample Preparation Kit (Illumina). The libraries were clustered and sequenced on an Illumina HiSeq 2000 instrument with 100 bp paired end reads.
Results: Differential gene expression profiling revealed the inhibition of expression in genes and pathways that are involved in metabolism and proliferation in regenerating KO livers. Specifically, PPARβ deficiency affected the activation of Akt and the expression of E2fs. Pathways that control glycolysis, FA synthesis as well as cell proliferation were de-regulated in regenerating PPARβ KO livers.
Conclusions: The data suggest a role for PPARβ in regulating liver regeneration that is mediated at least in part through Akt and E2f-regulated pathways.

overall_design: mRNA profiles of 3-month old wild type (WT) and PPARbeta mice were generated by deep sequencing, one simple, using Illumina HiSeq 2000 instrument with 100 bp paired end reads

first: HUI-XIN

first: YU-JUI

middle: Y

last: WAN


title: Using RNA-Seq to create sample-specific proteomic databases that enable mass spectrometric discovery of splice junction peptides

status: Public on May 17 2013

city: Madison

first: Gloria

last: Sheynkman

state: WI

address: 1101 University Ave.

department: Chemistry

institute: UW-Madison

summary:
Many new alternative splice forms have been detected at the transcript level using next generation sequencing (NGS) methods, especially RNA-Seq, but it is not known how many of these transcripts are being translated.  Leveraging the unprecedented capabilities of NGS, we collected RNA-Seq and proteomics data from the same cell population (Jurkat cells) and created a bioinformatics pipeline that builds customized databases for the discovery of novel splice-junction peptides.
Results: Eighty million paired-end Illumina reads and ~500,000 tandem mass spectra were used to identify 12,873 transcripts (19,320 including isoforms) and 6,810 proteins. We developed a bioinformatics workflow to retrieve high-confidence, novel splice junction sequences from the RNA data, translate these sequences into the analogous polypeptide sequence, and create a customized splice junction database for MS searching.

overall_design: Jurkat T-cell mRNA was analyzed on an Illumina HiSeq2000.  ~80 million paired end reads (2x200bp, ~350bp lengths) were collected.

first: Lloyd

last: Smith


title: Impairment of Muscle Regeneration in Muscleblind-like 3 Isoform Knockout Mice

city: La Jolla

first: Ranjan

last: Batra

state: California

address: 2880 Torrey Pines Scenic Drive

department: Cellular and Molecular Medicine

institute: University of California San Diego

summary: We have performed an RNA-seq experiment to identify expression and alternative splicing differences between WT and Mbnl3 isoform knockout mice E15 forelimbs. We have also identified and characterized transcriptome wide Mbnl3-binding sites in C2C12 cells and E15 forelimbs.

overall_design: 6 total samples were analyzed: E15 forelimbs from 3 WT and 3 MBNL3 ΔE2/ΔE2 female mice (15dpc). For HITS-CLIP, 3 samples each of C2C12 cells, WT E15 forelimbs and Mbnl3 ?E2 forelimbs were analyzed for Mbnl3 binding site analysis.

first: Batra

last: Ranjan

first: Zhang

last: Chaolin


title: Single-cell transcriptomics reveals widespread heterogeneity in gene regulation and RNA processing in stimulated immune cells

status: Public on May 19 2013

city: New York City

first: Rahul

last: Satija

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: Here, we used single-cell RNA-Seq to discover extensive cell-to-cell variability – in transcript expression levels, cell state, circuit usage, and alternative splicing – between stimulated immune cells

overall_design: RNA seq libraries from 18 single cells, 3 populations of 10,000 cells, and 2 zero cells (negative controls) with SMARTer. Three additional single cell libraries with molecular barcodes (MB) using a modified SMARTer protocol.

first: Alex

last: Shalek

first: Hongkun

first: Aviv

last: Regev


title: Transcription Factor Foxo1 Controls Memory CD8+ T Cell Responses To Infection

status: Public on May 16 2013

first: Willey

last: Liao

department: Bioinformatics

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


title: Transcription Factor Foxo1 Controls Memory CD8+ T Cell Responses To Infection [ChIP-Seq]

summary: Memory T cells provide immunity against pathogen reinvasion, but mechanisms of their long-term maintenance is unclear.  Here we show that mice with the deletion of the transcription factor Foxo1 in activated CD8+ T cells had defective secondary but not primary responses to Listeria monocytogenes infection.  Compared to short-lived effector T cells, memory precursor effector T cells expressed higher amounts of Foxo1 that promoted their generation and maintenance.  Gene expression profiling and chromatin immunoprecipitation sequencing experiments revealed the chemokine receptor CCR7 and the transcription factor TCF1 as novel Foxo1-bound target genes with critical functions in memory T cell trafficking and transcriptional regulation.  These findings demonstrate that Foxo1 is selectively incorporated into the genetic program that regulates memory but not effector CD8+ T cell responses to infection.

overall_design: CD8+ T cells were isolated from wild-type or Foxo1tagBirA mice in which Foxo1 is endogenously biotinylated. Foxo1 binding targets in CD8+ cells were identified by using Foxo1 antibody- and Streptavidin- ChIP-Seq approaches.

first: Myoungjoo

middle: V

last: Kim

first: Weiming

last: Ouyang

first: Will

first: Michael

middle: Q

last: Zhang

first: Ming

middle: O

last: Li


title: Nucleotide-resolution, genome-wide transcriptome maps of Propionibacterium acnes (cultured with and without potassium downshift)

status: Public on May 15 2013

city: Leeds

first: David

last: Romero A.

state: West Yorkshire

address: Woodhouse lane

country: United Kingdom

institute: University of Leeds

summary: This data contained within this entry was produced as part of a study that included differential RNA-sequencing and microarray analysis.  The results of the latter two have also been deposited in GEO

overall_design: Duplicate cultures of Propionibacterium acnes strain KPA171202 were grown exponentially in Holland Synthetic Medium (Holland et al.1979. J Appl Bacteriol 47: 383), which supports reproducible anaerobic growth. Samples were taken following subculture with and without potassium downshift (i.e. removal from medium).

first: Yu-fei

last: Lin

middle: A

last: Romero

first: Kenneth

last: McDowall


title: Role of Retinoids x Receptor and Retinoic Acid Receptor in Mouse Liver

city: Sacramento

first: Yuqi

last: He

address: Rm3400, Research III, UC Davis Medical Center, 4645 2nd Ave

institute: UC Davis Medical Center

summary: Genome-wide binding of Retinoids x Receptor and Retinoic Acid Receptor in mouse liver was described

overall_design: Using ChIP-Seq data to clarify the role of RXRa and RARa in liver

first: Yu-Jui

last: Wan

first: Qi

last: Zhan

first: Hui-Xin

last: Liu

first: Yanliu

last: Lu


title: A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription [Nuc-Seq]

first: Harm

last: Bakel

summary: Nucleosomes in all eukaryotes examined to date adopt a characteristic architecture within genes and play fundamental roles in regulating transcription, yet the identity and precise roles of many of the trans-acting factors responsible for the establishment and maintenance of this organization remain to be identified. We profiled a compendium of 50 yeast strains carrying conditional alleles or complete deletions of genes involved in transcriptional regulation, histone biology and chromatin remodeling, as well as compounds that target transcription and histone deacetylases, to assess their respective roles in nucleosome positioning and transcription. We find that nucleosome patterning in genes is affected by many factors including the CAF-1 complex, Spt10 and Spt21, in addition to previously reported remodeler ATPases and histone chaperones. Disruption of these factors or reductions in histone levels led genic nucleosomes to assume positions more consistent with their intrinsic sequence preferences, with pronounced and specific shifts of the +1 nucleosome relative to the transcription start site. These shifts of +1 nucleosomes appear to have functional consequences, as several affected genes in Ino80 mutants exhibited altered expression responses. Our parallel expression profiling compendium revealed extensive transcription changes in intergenic and antisense regions, most of which occur in regions with altered nucleosome occupancy and positioning. We show that the nucleosome-excluding transcription factors Reb1, Abf1, Tbf1, and Rsc3 suppress cryptic transcripts at their target promoters, while a combined analysis of nucleosome and expression profiles identified 36 novel transcripts that are normally repressed by Tup1/Cyc8. Our data confirm and extend the roles of chromatin remodelers and chaperones as major determinants of genic nucleosome positioning and these data provide a valuable resource for future studies.

overall_design: We examined 50 single-gene loss-of-function strains, comprised of gene deletions (del) and temperature-sensitive (ts) or tetracycline promoter-shutoff (tet) alleles. These genes were selected based on their known or potential role in nucleosome biology and include remodeler ATPases and chaperones, histones and histone modifiers, transcription and elongation factors, and components of RNA polymerase I and II. The compendium also includes 4 compounds targeting transcription and histone deacetylases, as well as a histone depletion time course performed with a strain in which H4 gene expression is exclusively under the control of a GAL1 promoter. Genome-wide nucleosome occupancy profiles were generated using Affymetrix Tiling arrays with probes spaced every 4 bp [PMID:16569694], or next-generation sequencing. Identically prepared samples for each strain and treatment were analyzed on the same tiling arrays for strand-specific expression differences. Each compendium condition was compared to a matched wild-type (WT) reference grown in parallel.

last: van Bakel

first: Kyle

last: Tsui

first: Marinella

last: Gebbia

first: Sanie

last: Mnaimneh

first: Timothy

last: Hughes

first: Corey

last: Nislow


title: Characterization of human plasma-derived exosomal RNAs

city: Milwaukee

first: Liang

last: Wang

state: Wisconsin

address: 8701 Watertown Plank Rd.

department: Pathology

institute: Medical College of Wisconsin

summary: Exosomes, endosome-derived membrane microvesicles, contain a specific set of RNA transcripts that are involved in cell-cell communication and hold a great potential as disease biomarkers. To systemically characterize exosomal RNA profiles, we performed RNA sequencing analysis using three human plasma samples and evaluated efficacies of small RNA library preparation protocols from 3 manufacturers.

overall_design: We tested the six samples (A1 and A2, B1 and B2, C1 and C2) using two small RNA library preparation kits: NEBNext Multiplex Small RNA library Prep Set from New England Biolab (NEB) and NEXTflex Small RNA Sequencing Kit from Bioo Scientific (BS). We also tested Illumina’s TrueSeq Small RNA Sample Preparation Kit (ILMN) in sample A1 and A2. Together, we tested these plasma samples by sequencing 14 indexed libraries. This study allowed direct comparison of current small RNA library preparation protocols and identified the most suitable strategy for future exosomal RNA sequencing analysis.

first: Xiaoyi

last: Huang

first: Tiezheng

last: Yuan


title: The genomic landscape of cohesin-associated chromatin interactions

city: New Haven

first: Laura

last: DeMare

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

summary: Cohesin is implicated in establishing tissue-specific DNA loops that target enhancers to promoters, and also localizes to sites bound by the insulator protein CTCF, which blocks enhancer-promoter communication. However, cohesin-associated interactions have not been characterized on a genome-wide scale. Here we performed chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) of the cohesin subunit SMC1A in developing mouse limb. We identified 2,264 SMC1A interactions, of which 1,491 (65%) involved sites co-occupied by CTCF. SMC1A participates in tissue- specific enhancer-promoter interactions and interactions that demarcate regions of correlated regulatory output. In contrast to previous studies, we also identified interactions between promoters and distal sites that are maintained in multiple tissues, but are poised in embryonic stem cells and resolve to tissue-specific activated or repressed chromatin states in the mouse embryo. Our results reveal the diversity of cohesin- associated interactions in the genome and highlight their role in establishing the regulatory architecture of development.

overall_design: Smc1a ChIA-PET, RNA-seq, chromatin state maps (H3K27ac, H3K27me3, H3K4m2), and CTCF and Smc1a binding in mouse embryonic limb bud (E11.5)

first: James

middle: P

last: Noonan


title: Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution

first: Gang

last: Fang

address: 266 Whitney Ave

institute: Yale University

summary: We used deep RNA sequencing to obtain high coverage RNA-Seq data of five C. crescentus cell cycle stages, each with three biological replicates. We found that 1,586 genes (over a third of the genome) display significant differential expression between stages. This gene list, which contains many genes previously unknown for their cell cycle regulation, includes almost half of the genes involved in primary metabolism, suggesting that these "house-keeping" genes are not constitutively transcribed during the cell cycle, as often assumed. Gene and module co-expression clustering reveal co-regulated pathways and suggest functionally coupled genes. In addition, an evolutionary analysis of the cell cycle network shows a high correlation between co-expression and co-evolution. Most co-expression modules have strong phylogenetic signals, with broadly conserved genes and clade-specific genes predominating different substructures of the cell cycle co-expression network. We also found that conserved genes tend to determine the expression profile of their module. We describe the first phylogenetic and single-nucleotide-resolution transcriptomic analysis of a bacterial cell cycle network. In addition, the study suggests how evolution has shaped this network and provides direct biological network support that selective pressure is not on individual genes but rather on the relationship between genes, which highlights the importance of integrating phylogenetic analysis into biological network studies.

overall_design: Examination of 5 typical cell cycle types (5 samples), each with 3 biological replicates

first: Karla

last: Passalacqua

first: Jason

last: Hocking

first: Paula

last: Montero Llopis

first: Mark

last: Gerstein

first: Nicholas

middle: H

last: Bergman

first: Christine

last: Jacobs-Wagner


title: Mechanisms of PU.1 binding site selection in-vivo

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

institute: University Hospital Regensburg

summary: The majority of sequence-specific transcription factors bind genomic DNA only at a fraction of their potential binding sites and the ‘rules’ for binding or not-binding are only partially understood. Here, we studied the binding properties of the myeloid and B-cell specific transcription factor PU.1 in-vivo and in-vitro to unveil basic features of occupied vs. non-occupied consensus sites. In addition to published PU.1 ChIP-seq data we mapped CTCF binding sites in monocytes and macrophages to determine chromatin domain boundaries and performed MCIp-seq in monocytes to reveal DNA methylation patterns across the genome.

overall_design: ChIP-seq of CTCF in human monocytes and human monocyte-derived macrophages as well as MCIp-seq in human monocytes


title: Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs.

city: Heidelberg

first: Georg

last: Stoecklin

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

summary: The degradation of TNFα mRNA is critical for restricting TNFα synthesis and involves a constitutive decay element (CDE) in the 3’ untranslated region of the mRNA. We demonstrate that the active CDE is a stem-loop RNA motif that is recognized by the RNA-binding protein Roquin. Deep sequencing of Roquin-associated mRNAs identified CDE-containing mRNAs as the primary targets of Roquin on a transcriptome-wide scale.

overall_design: Expression profiles of LPS treated Raw264.7 cells (input), after Roquin IP or control IP were generated by deep sequencing, in three biological replicates, using Illumina HiSeq 2000.

first: Kathrin

last: Leppek

first: Johanna

last: Schott

first: Sonja

last: Reitter

first: Fabian

last: Poetz

first: Ming

middle: C

last: Hammond


title: Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples

city: Cambridge

first: Joshua

middle: Z

last: Levin

address: 320 Charles Street

institute: Broad Institute of MIT & Harvard

summary: RNA-Seq is an effective method to study the transcriptome, but can be difficult to apply to scarce or degraded RNA from fixed clinical samples, rare cell populations, or cadavers. Recent studies have proposed several methods for RNA-Seq of low quality and/or low quantity samples, but their relative merits have not been systematically analyzed. Here, we compare five such methods using a comprehensive set of metrics, relevant to applications such as transcriptome annotation, transcript discovery, and gene expression. Using a single human RNA sample, we constructed and deeply sequenced 10 libraries with these methods and two control libraries. We find that the RNase H method performed best for low quality RNA, and can even effectively replace oligo (dT) based methods for standard RNA-Seq. SMART and NuGEN had distinct strengths for low quantity RNA. Our analysis allows biologists to select the most suitable methods and provides a benchmark for future method development.

overall_design: Examination of 9 different RNA-Seq libraries starting from total RNA from 5 distinct methods; also 3 control RNA-Seq libraries

first: Aviv

last: Regev

first: Xian

last: Adiconis


title: miRNA profiling in cytoplasmic male sterile (CMS) and its maintainer fertile (MF) lines of Brassica juncea by deep sequencing

first: Jinghua

last: Yang

address: Yuhangtang 388

institute: Zhejiang University

summary: Here, we employed high-throughput sequencing to identify microRNAs in CMS and its maintainer fertile (MF) lines of Brassica juncea. We identified 197 known and 78 new candidate microRNAs during reproductive development of B. juncea. A total of 47 differentially expressed microRNAs between CMS and its maintainer fertile lines were discovered, according to their sequencing read number.

overall_design: Two samples from floral buds of CMS and MF lines.


title: Steroid-induced changes in gene expression of airway smooth muscle in patients with asthma

city: Amsterdam

first: Ching Yong

last: Yick

address: Meibergdreef 9

department: Respiratory Medicine

country: Netherlands

institute: Academic Medical Center

summary:
Rationale: Steroids are the mainstay of asthma therapy. However, it is unclear whether the benefits of steroids in asthma are merely based on anti-inflammatory properties. Steroids may also alter gene expression of airway smooth muscle (ASM).
Hypothesis and Aims: We hypothesized that the transcriptomic profile of the ASM layer in endobronchial biopsies of atopic asthma patients changes by oral steroid therapy. First, we examined the change in ASM transcriptomic profile in endobronchial biopsies after 14 days of oral steroid therapy. Second, we investigated the association between changes in ASM transcriptomic profile and airway function.
Methods: 12 atopic steroid-free asthma patients were included in this double-blind intervention study. Endobronchial biopsies were taken before and after 14 days of oral prednisolon (n=6) or placebo (n=6). RNA of laser-dissected ASM was sequenced (RNA-Seq) using the GS FLX+ System (454/Roche). Gene networks were identified using Ingenuity Pathway Analysis. RNA-Seq reads were assumed to follow a negative binomial distribution. At the current sample size the estimated false discovery rate was approximately 3%.
Results: 15 genes were significantly changed by 14 days of oral prednisolon. 2 of these genes (FAM129A, SYNPO2) were associated with the methacholine PC20 (r=0.637, p=0.035; r=0.662, p=0.027). Pathway analysis revealed 3 gene networks that were associated with cellular functions including cellular growth, proliferation, and development.
Conclusion: Oral prednisolon changes the gene expression profile of the ASM layer in asthma. This indicates that steroids also exert effects on the transcriptomic level of ASM in addition to their anti-inflammatory properties, which can promote improved airway function.

overall_design: The current randomized, double-blind, parallel, placebo-controlled intervention study comprised 4 visits. At visit 1, asthma patients were screened according to the in- and exclusion criteria prior to enrollment. Additionally, spirometry and methacholine bronchoprovocation test were performed. At visit 2, FEV1 reversibility was measured and endobronchial biopsies were collected during a bronchoscopy. Asthma patients were then prescribed oral prednisolon at a dose of 0.5 mg/kg per day or placebo for 14 consecutive days. The dosage and dosing scheme was based on international recommendations for the treatment of acute exacerbations [1]. On the 11th day after visit 2, the patients visited the lung function laboratory for spirometry and methacholine bronchoprovocation test. Finally, at visit 4 (15th day after visit 2) FEV1 reversibility was measured and endobronchial biopsies were collected by bronchoscopy. Airway smooth muscle was collected from the biopsies by laser capture microdissection and total RNA isolated. cDNA was prepared using the Ovation RNA-Seq System (NuGEN). RNA-Seq was performed using the GS FLX+ instrument (454/Roche). Sequence reads were mapped against the human genome (hg19; UCSC). Comparison of the numbers of reads per gene between the prednisolon and placebo study group was carried out with the R package DESeq.

first: Ching


title: Polymerase-IV occupancy at RNA-directed DNA methylation sites requires SHH1

status: Public on May 13 2013

city: Seattle

first: Christopher

middle: Joel

last: Hale

state: WA

address: 1959 NE Pacific St., HSC H-458

institute: University of Washington

summary: DNA methylation is an epigenetic modification that plays critical roles in gene silencing, development, and the maintenance of genome integrity. In Arabidopsis, DNA methylation is established by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) and is targeted by 24 nt small interfering RNAs (siRNAs) through a pathway termed RNA-directed DNA methylation (RdDM)1. This pathway requires two plant-specific RNA polymerases: Pol-IV, which functions to initiate siRNA biogenesis and Pol-V, which functions in the downstream DNA methyltransferase targeting phase of the RdDM pathway to generate scaffold transcripts that recruit downstream RdDM factors1,2. To understand the mechanisms controlling Pol-IV targeting we investigated the function of SAWADEE HOMEODOMAIN HOMOLOG 1 (SHH1)3,4, a Pol-IV interacting protein3. Here we show that SHH1 acts upstream in the RdDM pathway to enable siRNA production from a large subset of the most active RdDM targets and that SHH1 is required for Pol-IV occupancy at these same loci. We also show that the SHH1 SAWADEE domain is a novel chromatin binding module that adopts a unique tandem Tudor-like fold and functions as a dual lysine reader, probing for both unmethylated K4 and methylated K9 modifications on the histone 3 (H3) tail. Finally, we show that key residues within both lysine binding pockets of SHH1 are required in vivo to maintain siRNA and DNA methylation levels as well as Pol-IV occupancy at RdDM targets, demonstrating a central role for methyl H3K9 binding in SHH1 function and providing the first insights into the mechanism of Pol-IV targeting. Given the parallels between methylation systems in plants and mammals1,5, a further understanding of this early targeting step may aid in our ability to control the expression of endogenous and newly introduced genes, which has broad implications for agriculture and gene therapy.

overall_design: For wild type plants (ecotype Columbia) and RdDM mutants whole-genome small RNA (sRNA-seq) and bisulfite sequencing (BS-seq) was performed. The Col and nrpe1 BS-seq libraries were previously reported (GSE39247) and so are not part of this submission. In addition, two replicates of whole genome chromatin immunoprecipitation (ChIP-seq) was performed on wild type (ecotype Columbia) plants as a negative control with experimentals consiting of nrpd1 mutant plants carrying a C-terminally epitope tagged (3XFLAG) NRPD1. Whole-genome bisulfite sequencing and small RNA sequencing was also performed on shh1 mutant plants transformed with the wild-type SHH1 protein-coding construct as well as multiple constructs containing point mutations. For these complementation libraries a separate shh1 mutant and Col control line were sequenced (“complementation replicates”).


title: In vivo live imaging of RNA polymerase II transcription factories in primary cells

city: Oxford

first: Supat

last: Thongjuea

address: Headington

department: MRC Molecular Haematology Unit

institute: The Weatherall Institute of Molecular Medicine

summary: Transcription steps are marked by different modifications of the C-terminal domain of RNA polymerase II (RNAPII). Phosphorylation of Ser5 and Ser7 by cyclin-dependent kinase 7 (CDK7) as part of TFIIH marks initiation, whereas phosphorylation of Ser2 by CDK9 marks elongation. These processes are thought to take place in localized transcription foci in the nucleus, known as ‘‘transcription factories,’’ but it has been argued that the observed clusters/foci are mere fixation or labeling artifacts. We show that transcription factories exist in living cells as distinct foci by live-imaging fluorescently labeled CDK9, a kinase known to associate with active RNAPII. These foci were observed in different cell types derived from CDK9-mCherry knock-in mice. We show that these foci are very stable while highly dynamic in exchanging CDK9. Chromatin immunoprecipitation (ChIP) coupled with deep sequencing (ChIP-seq) data show that the genome-wide binding sites of CDK9 and initiating RNAPII overlap on transcribed genes. Immunostaining shows that CDK9- mCherry foci colocalize with RNAPII-Ser5P, much less with RNAPII-Ser2P, and not with CDK12 (a kinase reported to be involved in the Ser2 phosphorylation) or with splicing factor SC35. In conclusion, transcription factories exist in living cells, and initiation and elongation of transcripts takes place in different nuclear compartments.

overall_design: Examination of genome occupancy of CDK9 and RNAPII that was performed by ChIP-seq in the MEL cell line as described (Soler et al. 2010, 2011) using  CDK9 C20 antibody (Santa Cruz Biotechnology, C20, sc-484) and RNA Pol II antibody (Santa Cruz Biotechnology, N20, sc899),

first: Alireza

last: Ghamari

first: Mariëtte

last: van de Corput

first: Wiggert

last: van Cappellen

first: Wilfred

last: van IJcken

first: Jeffrey

last: van Haren

first: Eric

last: Soler

first: Dirk

last: Eick

first: Boris

last: Lenhard

first: Frank

last: Grosveld


title: Analysis of the Equine Transcriptome by mRNA Sequencing

city: Fort Collins

first: Stephen

last: Coleman

address: 1682 Campus Delivery

department: MIP

institute: Colorado State University

overall_design: Refer to individual Series


title: Next Generation Sequencing of HM1, HP1a-/-, and HP1b-/- ESC transcriptomes

city: Vancouver

first: Patrick

last: Plettner

state: BC

address: 100-570 West 7th Avenue

institute: BC Cancer Agency GSC

summary: HM1, HP1a-/-, and HP1b-/- ESC transcriptomes were generated to determine whether depletion of these HP1 proteins influences gene and/or retroelement expression

overall_design: mRNA profiles of HP1a and HP1b Knockouts and its corresponding wildtype

first: Matthew

last: Lorincz

first: Mohammad

last: Karimi


title: HP1 wa191.D.mel 3rd Instar Larvae Nuclei.Solexa

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_4936
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: 3rd Instar Larvae; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody HP1 wa191 (target is HP1a); Developmental Stage 3rd Instar Larvae

first: Gary

last: Karpen

first: Sarah

last: Elgin

first: Andrey

last: Gortchakov

first: Greg

last: Shanower

first: Michael

last: Tolstorukov

first: Peter

last: Kharchenko

first: Mitzi

last: Kuroda

first: Vincenzo

last: Pirrotta

last: Park

first: Aki

last: Minoda

first: Nicole

last: Riddle

first: Yuri

last: Schwartz

first: Art

last: Alekseyenko

first: Cameron

last: Kennedy


title: Snyder_LSY-2_GFP_L2

status: Public on May 11 2013

summary:
modENCODE_submission_4812
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP240(official name : OP240 genotype : unc119(ed3);wgIs240(lsy-2::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The LSY-2::EGFP fusion protein is expressed in the correct lsy-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LSY-2 transcription factor. made_by : Unknown ); Developmental Stage: L2; Genotype: unc119(ed3);wgIs240(lsy-2::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene lsy-2; Strain OP240(official name : OP240 genotype : unc119(ed3);wgIs240(lsy-2::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The LSY-2::EGFP fusion protein is expressed in the correct lsy-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LSY-2 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Slightam

first: Stuart

last: Kim

first: John

last: Murray

first: Robert

last: Waterston

first: Mark

last: Gerstein

first: Wei

last: Niu

first: Judi

last: Janette

first: Debasish

last: Raha

first: Ashish

last: Agarwal

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: Snyder_CEH-28_GFP_L4

first: DCC

last: modENCODE

summary:
modENCODE_submission_4800
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP241(official name : OP241 genotype : unc119(ed3);wgIs241(ceh-38::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The CEH-38::EGFP fusion protein is expressed in the correct ceh-38 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-38 transcription factor. made_by : Unknwon ); Developmental Stage: L4; Genotype: unc119(ed3);wgIs241(ceh-38::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene ceh-38; Strain OP241(official name : OP241 genotype : unc119(ed3);wgIs241(ceh-38::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The CEH-38::EGFP fusion protein is expressed in the correct ceh-38 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-38 transcription factor. made_by : Unknwon ); temp (temperature) 20 degree celsius


title: Snyder_LSY-2_GFP_L4

summary:
modENCODE_submission_4813
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP240(official name : OP240 genotype : unc119(ed3);wgIs240(lsy-2::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The LSY-2::EGFP fusion protein is expressed in the correct lsy-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LSY-2 transcription factor. made_by : Unknown ); Developmental Stage: L4; Genotype: unc119(ed3);wgIs240(lsy-2::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene lsy-2; Strain OP240(official name : OP240 genotype : unc119(ed3);wgIs240(lsy-2::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The LSY-2::EGFP fusion protein is expressed in the correct lsy-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LSY-2 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius


title: Snyder_ZTF-4_GFP_L1

summary:
modENCODE_submission_4798
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP322(official name : OP322 genotype : unc-119(ed3); wgIs322(ztf-4::TY1 EGFP FLAG; unc119(+)) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The spatio-temporal expression pattern of ZTF-4::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-4 transcription factor. made_by : Bob Waterston's lab from UW ); Developmental Stage: L1 26dC; Genotype: unc-119(ed3); wgIs322(ztf-4::TY1 EGFP FLAG; unc119(+)); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L1 26dC; Target gene ztf-4; Strain OP322(official name : OP322 genotype : unc-119(ed3); wgIs322(ztf-4::TY1 EGFP FLAG; unc119(+)) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The spatio-temporal expression pattern of ZTF-4::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-4 transcription factor. made_by : Bob Waterston's lab from UW ); temp (temperature) 20 degree celsius


title: Snyder_CEH-28_GFP_L3

summary:
modENCODE_submission_4801
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP241(official name : OP241 genotype : unc119(ed3);wgIs241(ceh-38::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The CEH-38::EGFP fusion protein is expressed in the correct ceh-38 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-38 transcription factor. made_by : Unknwon ); Developmental Stage: L3; Genotype: unc119(ed3);wgIs241(ceh-38::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene ceh-38; Strain OP241(official name : OP241 genotype : unc119(ed3);wgIs241(ceh-38::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The CEH-38::EGFP fusion protein is expressed in the correct ceh-38 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-38 transcription factor. made_by : Unknwon ); temp (temperature) 20 degree celsius