title: Messenger RNA is a functional component of a chromatin insulator complex

city: Bethesda

first: Ryan

last: Dale

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: Chromatin insulators are DNA-protein complexes situated throughout the genome capable of demarcating independent transcriptional domains. Previous studies point to an important role for RNA in gypsy chromatin insulator function in Drosophila; however, the identity of these putative insulator-associated RNAs is not currently known. Here we utilize RNA-immunoprecipitation and high throughput sequencing (RIP-seq) to isolate RNAs stably associated with gypsy insulator complexes. Strikingly, these RNAs correspond to specific sense-strand, spliced, and polyadenylated mRNAs, including two insulator protein transcripts. In order to assess the functional significance of these associated mRNAs independent of their coding function, we expressed untranslatable versions of these transcripts in developing flies and observed both alteration of insulator complex nuclear localization as well as improvement of enhancer-blocking activity. Together these data suggest a novel, noncoding mechanism by which certain mRNAs contribute to chromatin insulator function.

overall_design: RIP-seq of insulator proteins with different library preparations and multiple biological replicates

first: Leah

last: Matzat

first: Elissa

last: Lei


title: RPLII_ab5408.Clone_8.Solexa

status: Public on Aug 02 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_5580
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: Cell Line: CME-W1-Cl.8+; Tissue: dorsal mesothoracic disc; Developmental Stage: third instar larval stage; Sex: Male;  EXPERIMENTAL FACTORS: Cell Line CME-W1-Cl.8+; Antibody RPLII ab5408 (target is RNA polymerase II CTD repeat YSPTSPS)

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: BET Bromodomains Mediate Transcriptional Pause Release in Heart Failure

status: Public on Aug 06 2013

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Small RNA-seq of human granulosa cells reveals miRNAs in FSHR and aromatase genes

status: Public on Aug 05 2013

city: Tallinn

first: Agne

last: Velthut-Meikas

address: Akadeemia tee 15

department: Department of Chemistry and Biotechnology

country: Estonia

institute: Tallinn University of Technology

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing


title: High-throughput RNA sequencing of human preovulatory cumulus and mural granulosa cells (mRNA)

summary: The granulosa cells in the mammalian ovarian follicle respond to gonadotropin signalling and are involved in the processes of folliculogenesis and oocyte maturation. Studies on gene expression and regulation in human granulosa cells are of interest due to their potential for estimating the oocyte viability and IVF success. The current study determined the mRNA profile by deep sequencing of the two intrafollicular somatic cell types: mural and cumulus granulosa cells isolated from women undergoing controlled ovarian stimulation and in vitro fertilization.

overall_design: Paired cumulus and mural granulosa samples were analysed from 3 women participating in IVF procedure. Differential gene expression study was performed. The identified gene expression profile was also used for predicting targets for miRNAs that were also identified from the same samples (GSE46489).

first: Jaak

last: Simm


title: Genomic Interaction Profiles in Breast Cancer Reveal Altered Chromatin Architecture

status: Public on Aug 03 2013

city: La Jolla

first: Ferhat

last: Ay

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary: Gene transcription can be regulated by remote enhancer regions through chromosome looping either in cis or in trans.  Cancer cells are characterized by wholesale changes in long-range gene interactions, but the role that these long-range interactions play in cancer progression and metastasis is not well understood. In this study, we used IGFBP3, a gene involved in breast cancer pathogenesis, as bait in a 4C-seq experiment comparing normal breast cells (HMEC) with two breast cancer cell lines (MCF7, an ER positive cell line, and MDA-MB-231, a triple negative cell line). The IGFBP3 long-range interaction profile was substantially altered in breast cancer.  Many interactions seen in normal breast cells are lost and novel interactions appear in cancer lines. We found that in HMEC, the breast carcinoma amplified sequence gene family (BCAS) 1-4 were among the top 10 most significantly enriched regions of interaction with IGFBP3. 3D-FISH analysis indicated that the translocation-prone BCAS genes, which are located on chromosomes 1, 17 and 20, are in close physical proximity with IGFBP3 and each other in normal breast cells. We also found that epidermal growth factor receptor (EGFR), a gene implicated in tumorigenesis, interacts significantly with IGFBP3 and that this interaction may play a role in their regulation. Breakpoint analysis suggests that the interchromosomal rearrangements seen in the MCF7 cancer cell line involve regions that engage in long-range interactions in normal breast cells.  Overall, our data from multiple lines of evidence suggest an important role for long-range chromosomal interactions in the pathogenesis of cancer.

overall_design: Comparison of IGFBP3 interaction profiles in normal breast tissue and 2 breast tumor subtypes

last: Zeitz


title: RLPII_phospho5_ab5131.Kc.Solexa

first: DCC

last: modENCODE

summary:
modENCODE_submission_5571
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: Cell Line: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female;  EXPERIMENTAL FACTORS: Cell Line Kc167; Antibody RLPII phospho5 ab5131 (target is RNA polymerase II CTD repeat YSPTSPS (phospho S5))

first: Gary

last: Karpen

last: Elgin

last: Gortchakov


title: H4K8ac.L3.Solexa

summary:
modENCODE_submission_5262
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 H4K8ac (target is H4K8ac); Developmental Stage 3rd Instar Larvae

first: Sarah

first: Andrey

last: Shanower

last: Tolstorukov

last: Kharchenko

last: Kuroda


title: Thermotoga maritima transcriptome analysis under multiple growth conditions [RNA-seq]

first: Haythem

last: Latif

state: California

address: 417 Powell-Focht Bioengineering Hall, 9500 Gilman Drive

institute: University of California San Diego

summary:
Investigation of transcripts (boundaries, expression level, etc.) using strand specific, paired-end RNA sequencing for T. maritima under multiple growth conditions.

The new genome annotation has been approved by Genbank [CP004077, pending release of the manuscript].

overall_design: Four distinct growth conditions were sequenced after isolating total RNA on cultures grown in maltose minimal media. Growth conditions included logphase, late exponential, heat shock and hydrogen inhibion.

first: Joshua

middle: A

last: Lerman

first: Vasiliy

last: Portnoy

first: Yekaterina

last: Tarasova

first: Harish

last: Nagarajan

first: Alexandra

middle: C

last: Schrimpe-Rutledge

first: Richard

middle: D

last: Smith

middle: N

last: Adkins

first: Dae-Hee

last: Lee

first: Yu

last: Qiu

first: Bernhard

middle: O

last: Palsson

first: Karsten

last: Zengler


title: H2B-ubiq (NRO3).L3.Solexa

last: modENCODE

summary:
modENCODE_submission_5077
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 H2B-ubiq (NRO3) (target is H2Bubi); Developmental Stage 3rd Instar Larvae

last: Karpen

last: Elgin

last: Gortchakov

first: Greg

first: Michael

first: Peter

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: RLPII_phospho2_ab5095.Kc.Solexa

first: DCC

summary:
modENCODE_submission_5570
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: Cell Line: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female;  EXPERIMENTAL FACTORS: Cell Line Kc167; Antibody RLPII phospho2 ab5095 (target is RNA polymerase II CTD repeat YSPTSPS (phospho S2))

first: Gary

first: Sarah

first: Andrey

last: Shanower

last: Tolstorukov

last: Kharchenko

last: Kuroda


title: H3K27ac (Active Motif).L3.Solexa

summary:
modENCODE_submission_5084
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 H3K27ac (Active Motif) (target is H3K27ac); Developmental Stage 3rd Instar Larvae


title: H4K16ac(M).L3.Solexa

summary:
modENCODE_submission_5260
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 H4K16ac(M) (target is H4K16ac); Developmental Stage 3rd Instar Larvae


title: H3K27me3 (Abcam lot3).L3.Solexa

summary:
modENCODE_submission_5089
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 H3K27me3 (Abcam lot3) (target is H3K27me3); Developmental Stage 3rd Instar Larvae


title: H3K4me3 (ab8580 lot 2).L3.Solexa

summary:
modENCODE_submission_5097
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 H3K4me3 (ab8580 lot 2) (target is H3K4me3); Developmental Stage 3rd Instar Larvae


title: H3K27me1 (Millipore).L3.Solexa

summary:
modENCODE_submission_5085
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 H3K27me1 (Millipore) (target is H3K27me1); Developmental Stage 3rd Instar Larvae


title: H3K79me3 (Abcam ab2621 lot 1).L3.Solexa

summary:
modENCODE_submission_5101
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 H3K79me3 (Abcam ab2621 lot 1) (target is H3K79me3); Developmental Stage 3rd Instar Larvae


title: H3K79me2 (Abcam ab3594 lot 1).L3.Solexa

summary:
modENCODE_submission_5100
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 H3K79me2 (Abcam ab3594 lot 1) (target is H3K79me2); Developmental Stage 3rd Instar Larvae


title: HP1c (MO 462).L3.Solexa

summary:
modENCODE_submission_5112
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 HP1c (MO 462) (target is HP1c); Developmental Stage 3rd Instar Larvae


title: Su(var)3-9-Q2598.L3.Solexa

summary:
modENCODE_submission_5128
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 Su(var)3-9-Q2598 (target is Su(var)3-9); Developmental Stage 3rd Instar Larvae


title: Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8).

status: Public on Aug 01 2013

city: Basel

first: Neha

last: Tiwari

address: Mattenstrasse 28

country: Switzerland

institute: University of Basel

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

overall_design: Refer to individual Series


title: Transcription start site analysis for Thermotoga maritima [RNA-seq]

first: Haythem

last: Latif

summary: Investigation of 5' transcripts using strand specific sequencing for T. maritima under logphase, maltose minimal media growth conditions

overall_design: Two replicate samples were sequenced after isolating total RNA of cultures grown in maltose minimal media. Cells were harvested in logphase growth.

first: Joshua

last: Lerman

first: Vasiliy

last: Portnoy

first: Yekaterina

last: Tarasova

first: Harish

last: Nagarajan

first: Alexandra

last: Schrimpe-Rutledge

first: Richard

last: Smith

last: Adkins

first: Dae-Hee

last: Lee

first: Yu

last: Qiu

first: Bernhard

last: Palsson

last: Zengler


title: Identification of transcript starts in Desulfovibrio alaskensis G20

city: Berkeley

first: Morgan

last: Price

address: 1 Cyclotron Road Mailstop 955-512L

department: Physical Biosciences Division

institute: Lawrence Berkeley National Lab

summary: 5' RNASeq of mRNA from G20 in defined lactate/sulfate media (LS4D)

overall_design: 5' RNASeq of a single sample

first: Adam

middle: M

last: Deutschbauer

first: Jennifer

middle: V

last: Kuehl

middle: P

last: Arkin


title: RLPII_phospho5_ab5131.Clone_8.Solexa

first: DCC

last: modENCODE

summary:
modENCODE_submission_5579
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: Cell Line: CME-W1-Cl.8+; Tissue: dorsal mesothoracic disc; Developmental Stage: third instar larval stage; Sex: Male;  EXPERIMENTAL FACTORS: Cell Line CME-W1-Cl.8+; Antibody RLPII phospho5 ab5131 (target is RNA polymerase II CTD repeat YSPTSPS (phospho S5))

first: Gary

last: Karpen

last: Elgin

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: H3K79me1 (Abcam lot 1).L3.Solexa

summary:
modENCODE_submission_5099
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 H3K79me1 (Abcam lot 1) (target is H3K79me1); Developmental Stage 3rd Instar Larvae

first: Sarah

first: Andrey


title: Arabidopsis circadian regulatory networks

city: Buenos Aires

first: Marcelo

last: Yanovsky

state: Ciudad Autonoma de Buenos Aires

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundación Instituto Leloir. IIBBA- CONICET


title: Acute Genome-Wide Effects of Rosiglitazone on PPARγ Transcriptional Networks in Adipocytes

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Here we report, for the first time, the acute effects of the synthetic PPARγ agonist rosiglitazone on the transcriptional network of PPARγ in adipocytes. Treatment with Rosiglitazone for 1 hour leads to acute transcriptional activation as well as repression of a number of genes as determined by genome-wide RNA polymerase II occupancy. Unlike what has been shown for many other nuclear receptors, agonist treatment does not lead to major changes in the occurrence of PPARγ binding sites. However, rosiglitazone promotes PPARγ occupancy at many preexisting sites, and this is paralleled by increased occupancy of the mediator subunit MED1. The increase in PPARγ and MED1 binding is correlated with an increase in transcription of nearby genes indicating that rosiglitazone, in addition to activating the receptor, also promotes its association with DNA, and that this is causally linked to recruitment of mediator and activation of genes. Notably, both Rosiglitazone-activated and -repressed genes are induced during adipogenesis. However, Rosiglitazone-activated genes are markedly more associated with PPARγ than repressed genes and are highly dependent on PPARγ for expression in adipocytes. By contrast, repressed genes are associated with the other key adipocyte transcription factor CCAAT-Enhancer binding protein (C/EBPα), and their expression is more dependent on C/EBPα. This suggests that the relative occupancies of PPARγ and C/EBPα are critical for whether genes will be induced or repressed by PPARγ agonist.

overall_design: Examination of binding of PPARγ, C/EBPα, RNAPII, CBP and MED1 in mature 3T3-L1 adipocytes treated with 1 μM Rosiglitazone and/or 0.1% DMSO for 1 hour.

first: Anders

middle: K

last: Haakonsson

first: Maria

middle: S

last: Madsen

first: Ronni

last: Nielsen

first: Albin

last: Sandelin


title: ChIP-Seq of Klf4 in NMuMG normal murine mammary gland epithelial cells.

first: Neha

last: Tiwari

summary: Chromatin immunoprecipitation  of Klf4 in NMuMG cells identifies gene promoter sequences that are directly bound by Klf4.

overall_design: Chromatin immunoprecipitation   using a Klf4-specific antibody in NMuMG cells followed by next  generation sequencing (ChIP-Seq).

first: N

first: G

last: Christofori


title: Genome-wide analysis of the rat colon reveals site-specific differences in histone modifications and proto-oncogene expression

city: College Station

first: Karen

last: Triff

state: TX

address: 321 Kleberg Center, 5523 TAMU

institute: Texas A&M University

summary:
Goal: Since disease susceptibility of the intestine exhibits an anatomical bias, we propose that the chromatin landscape, especially the site-specific epigenetic differences in histone modification patterns throughout the longitudinal axis, contributes to a differential response to chemoprotective agents.
Method: We assessed the chromatin structure associated with gene expression profiles in the rat proximal and distal colon by globally correlating chromatin immunoprecipitation next-generation sequencing analysis (ChIP-Seq) with mRNA transcription (RNA-Seq) data. Crypts were isolated from the proximal and distal colonic regions from rats maintained on a semi-purified diet, and mRNA gene expression profiles were generated using RNA-Seq. The remaining isolated crypts were paraformaldehyde-crosslinked and chromatin immunoprecipitated using antibodies against H3K4me3, H3K9me3, and RNA Polymerase II.
Results/Conclusion: Globally, RNA-Seq results indicated that 9,866 genes were actively expressed, of which 540 genes were differentially expressed between the proximal and distal colon. With regard to differentially expressed genes, a high correlation was observed between H3K4me3-Seq and RNA-Seq data, with 96% of the canonical pathways being similarly affected in the H3K4me3-Seq and RNA-Seq data sets. Gene ontology analysis indicated that colonic crypt location significantly impacted both chromatin and transcriptional regulation of genes involved in cell transformation, lipid metabolism, lymphatic development and immune cell trafficking. Gene function analysis indicated that the PI3-Kinase signaling pathway was regulated in a site-specific manner, e.g., pathway proto-oncogenes, c-Jun, c-Fos and ATF, were up-regulated in the distal colon. Middle and long non-coding RNAs (lncRNAs) were also detected in the colon, including select lncRNAs formerly only detected in the rat nervous system. In summary, distinct combinatorial patterns of histone modifications exist in the proximal versus distal colon. These site-specific differences may explain the differential effects of chemoprotective agents on cell transformation in the ascending (proximal) and descending (distal) colon.

overall_design: Examination of mRNA profiles and 2 different histone modifications (H3K4me3 and H3K9me3) in 2 tissue types (proximal and distal colon).

first: Robert

last: Chapkin


title: Genome-wide analysis of LINK1 and LINK2 effects on the Arabidopsis transcriptome

summary: The goal of this study was to compare the transcriptional profile (RNA-seq) of wild type plants with that of link1link2 double mutants grown under continous light or long day (16h light/8 h darkness) conditions.

overall_design: In the first experiment wild-type and link1link2 mutant plants were grown for two weeks under continuous white light conditions at 22 degrees centigrades and the transcriptional profile of these plants was analyzed using RNA-seq. In the second experiment, wild-type and link1link2 mutants were grown under long day conditions (16 h light/8 h darkness), and the transcriptional profile of these plants was analyzed in samples harvested every 4 hours over a 24 hour, starting 2 hourse after the onset of the light period.

first: Detlef

last: Weigel


title: RMST associates with SOX2 to regulate neurogenesis

city: Cambridge

first: Shi Yan

last: Ng

address: 7 Divinity Ave

institute: Harvard University


title: Transcription factors OVOL1 and OVOL2 induce the mesenchymal to epithelial transition in human cancer

city: Ann Arbor

first: Richard

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

summary: This paper shows, for the first time, a novel function of the OVO-like proteins (OVOL1and OVOL2) as critical inducers of mesenchymal to epithelial transition (MET) in human cancer.

overall_design: Examination of the effects of OVOL1 and OVOL2 overexpression in a prostate cancer model.

first: Hernan

last: Roca

first: Ken

last: Pienta


title: Genome-wide identification of microRNA and siRNA responsive to endophytic beneficial diazotrophic bacteria in maize

city: Rio de Janeiro

first: Paulo

last: Ferreira

address: Rua Rodolpho Paulo Rocco s/nº, CCS, Bl.L, Cidade Universitária

country: Brazil

institute: Universidade Federal do Rio de Janeiro

summary: Several reports have described the involvement of miRNAs in abiotic stresses. However, their role in biotic stress or to beneficial microbes has not been fully explored. In order to understand on the epigenetic regulation in plant in response to nitrogen-fixing bacteria association, we analyzed the sRNA regulation in maize hybrids (Zea mays – UENF 506-8) inoculated with the beneficial diazotrophic bacteria (Herbaspirillum seropedicae). Deep sequencing analysis was carried out to identify the sRNAs regulated in maize during association with diazotrophic bacteria. For this analysis, maize plants were germinated in wet paper and put in hydroponic system with Hoagland’s solution and then inoculated with H. seropedicae for seven days.  Mock and inoculated plants were collected and total RNA from a pool of samples was extracted with Trizol reagent. The two sRNA libraries were sequenced by Illumina. The sequences were filtered to remove adaptors and contaminants rRNA and tRNAs, and sequences with 18-28 nt in length were selected. To identify the miRNAs present in these libraries, we used two strategies using the same website (http://srna-tools.cmp.uea.ac.uk): one to identify novel miRNAs using the maize genome (verson 2) and miRCat pipeline; and other to identify conserved miRNAs using the miRBase database (release 13.0, http://microrna.sanger.ac.uk) and miRProf pipeline. We identified 17 novel putative miRNAs candidates and mapped the precursor of these miRNAs in the maize genome. Furthermore, we identified 25 conserved miRNAs families and the differential expressions were analyzed with miRProf pipeline. The bioinformatics analysis of four up-regulated miRNAs (miR397, miR398, miR408 and miR528) in inoculated plant was validated using stem–loop RT-PCR assay. Our findings contribute to increase the knowledge of the molecular relation between plants and endophytic bacteria.

overall_design: Screenning of sRNA transcriptome of maize plants inoculated with Herbaspirillum seropedicae after seven days

first: Flávia

last: Thiebaut

first: Clícia

last: Grativol

first: Cristian

last: Rojas

first: Mariana

middle: R

last: Motta

first: Tauan

middle: G

last: Vieira

first: Laurent

last: Farinelli

first: Adriana

last: Hemerly


title: Genome wide mapping of effects of U6atac knockdown on pre-mRNA splicing

city: philadelphia

first: Ihab

last: Younis

state: PA

address: 415 Curie Blvd

department: Biochemistry and Biophysics

institute: University of Pennsylvania

summary: This project looks into experimentally identifying all minor introns by knocking down the minor spliceosome's catalytic snRNP, U6atac.

overall_design: Knockdown of U6atac by antisense morpholino followed by examining mRNA splicing by RNA-seq

first: Gideon

last: dreyfuss


title: RMST associates with SOX2 to regulate neurogenesis [ChIP-Seq]

summary: We report that knockdown of the lncRNA RMST changes the chromatin binding profile of the transcription factor SOX2.

overall_design: Examination of SOX2 chromatin binding profile under normal and RMST-depleted conditions in differentiating neural stem cells.

first: Shi-Yan

first: Lawrence

last: Stanton


title: Convergent transcription induces dynamic DNA methylation at disiRNA loci

city: Dallas

first: Yunkun

last: Dang

address: 5323 Harry Hines Blvd

department: Physiology

institute: University of Texas Southwestern Medical Center

summary: Cytosine methylation of DNA is an important epigenetic gene silencing mechanism in plants, fungi, and animals. In the filamentous fungus Neurospora crassa, nearly all known DNA methylations occur in transposon relics and repetitive sequences, and DNA methylation does not depend on the canonical RNAi pathway. disiRNAs are Dicer-independent small non-coding RNAs that arise from gene-rich part of the Neurospora genome. Here we describe a new type of DNA methylation that is associated with the disiRNA loci. Unlike the known DNA methylation in Neurospora, disiRNA loci DNA methylation (DLDM) is highly dynamic and is regulated by an on/off mechanism. Surprisingly, some of the DLDM is independent of the known DNA methyltransferase. At least in disi47, disiRNA production appears to rely on pol II directed transcription. Importantly, DLDM is triggered by convergent transcription and enriched in promoter regions. Together, our results establish a new mechanism that triggers DNA methylation.

overall_design: Two small RNA library were generated from Neurospora wild type (FGSC4200) and wc-2 KO mutant

first: Yi

last: Liu


title: Ultra-deep RNA-seq of in vitro and in vivo transcripts by Escherichia coli RNA polymerase

city: Frederick

first: Masahiko

last: Imashimizu

state: MD

department: NCI/CCR

institute: NCI

summary: We report a high-resolution Illumina RNA-seq method that can analyze non-coded base substitutions in mRNA at 10(-4)-10(-5) per base frequencies in vitro and in vivo.

overall_design: The RNA samples were generated by transcription of pPR9 plasmid that contains a  5.7 kb fragment of E. coli rpoBC operon transcribed from a strong lambda phage PR promoter and terminated at an fd phage transcription terminator. The reference transcription reaction was performed in a buffer with 5 mM MgCl2 to determine the standard error rate (barcode 1). To reduce fidelity, we replaced Mg2+ with Mn2+ (barcode 2). To increase fidelity, we added GreA/GreB proteins for proofreading activity (barode 3 and 4). The same transcrit was purified from E. coli cells (barcode 5).


title: Loss of a Conserved tRNA Anticodon Modification Perturbs Cellular Signaling

city: Baltimore

first: Boris

last: Zinshteyn

state: Maryland

address: 725 N Wolfe St, PCTB 714

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: Transfer RNA (tRNA) modifications enhance the efficiency, specificity and fidelity of translation in all organisms. The anticodon modification mcm5s2U34 is required for normal growth and stress resistance in yeast; mutants lacking this modification have numerous phenotypes. Mutations in the homologous human genes are linked to neurological disease. The yeast phenotypes can be ameliorated by overexpression of specific tRNAs, suggesting that the modifications are necessary for efficient translation of specific codons. We determined the in vivo ribosome distributions at single codon resolution in yeast strains lacking mcm5s2U. We found accumulations at AAA, CAA, and GAA codons, suggesting that translation is slow when these codons are in the ribosomal A site, but these changes appeared too small to affect protein output. Instead, we observed activation of the GCN4-mediated stress response by a non- canonical pathway. Thus, loss of mcm5s2U causes global effects on gene expression due to perturbation of cellular signaling.

overall_design: WT yeast and mutants lacking anticodon tRNA modifications were grown in YPD, and subjected to ribosome footprint profiling (ribo-seq) and RNA-seq of poly-A selected RNA. Dataset contains biological replicates for WT, Δncs6 and Δuba4. Technical replicates were also performed for all RNA-seq datasets (using a different poly-A selection method).

first: B

first: W

last: Gilbert


title: IL-33 markedly induces murine eosinophil gene transcription via autocrine IL-4-dependent and -independent mechanisms

city: Cincinnati

first: Mark

last: Rochman

state: OH

address: 3333 Burnett Ave

department: Allergy and Immunology

institute: CCHMC

summary: Eosinophils are major effector cells in type 2 inflammatory responses and become activated in response to IL-4 and IL-33, yet the molecular mechanism remains unclear. We examined the direct effect of these cytokines on eosinophils and demonstrated that murine eosinophils respond to IL-4 and IL-33 by phosphorylation of STAT-6 and NFkB, respectively. RNA sequencing analysis of murine eosinophils indicated that IL-33 regulates 519 genes, whereas IL-4 regulates only 28 genes, including 19 IL-33-regulated genes. Interestingly, IL-33 induced eosinophil activation via two distinct mechanisms, IL-4 independent and IL-4 secretion/auto-stimulation dependent. Anti-IL-4 or anti-IL-4Ra antibody-treated eosinophils, as well as Il4- or Stat6-deficient eosinophils, had attenuated protein secretion of a subset of IL-33-induced genes, including Retnla and Ccl17. However, the induction of most IL-33-regulated transcripts (e.g. Il6 and Il13) was IL-4 independent and blocked by NFkB inhibition. Indeed, IL-33 induced the rapid release of pre-formed IL-4 protein from eosinophils by an NFkB-dependent mechanism. Thus, we have identified a novel activation pathway in murine eosinophils that is induced by IL-33 and differentially dependent upon IL-4. These data suggest that IL-4 plays a critical role in auto-amplification of IL-33-induced eosinophil activation and could be a potential target for therapeutic approaches in IL-33-related eosinophil-associated diseases.

overall_design: Low density bone marrow derived murine eosinophils were generated in culture over the period of 14 days. Eosinophils were activated by either IL-33 or IL-4 at 10 ng/ml for 1hr and 4hr. RNA was collected and subjected to next generation sequencing.

first: Marc

middle: E

last: Rothenberg


title: The Genomic Binding Profile of GAGA Element Associated Factor (GAF) in Drosophila S2 cells

city: Farmington

first: Michael

middle: Joseph

last: Guertin

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

summary: GAGA associated transcription factor (GAF) is a highly abundant and essential protein in Drosophila. GAF recognizes and binds arrays of GA dinucleotides via a zinc finger DNA binding domain to regulate transcription by binding to general TF machinery or recruit nucleosome remodeling factors. We performed GAF ChIP-seq to quantify the intensity of GAF binding at high resolution in S2 cells. In addition, we performed GAF ChIP-seq in S2 cells that were depleted of GAF by RNAi. By quantifying the degree to which all GAF binding sites are susceptible to GAF depletion, we found the cellular degree of depletion does not translate equally to the depletion of GAF at individual chromatin bound sites. For example, some high intensity GAF binding sites were completely unaffected by GAF depletion, while lower affinity binding sites were often ablated upon GAF depletion. These data sets will serve as a valuable resource to others who study the dynamic interplay between GAF and chromatin. We also compared the GAF binding sites to the full set of genomic ChIP data that is available for S2 cells and compared the intensity for each factor and histone modification/variant. Lastly, we investigated the influence that GAF had upon inducible transcription factor binding using the heat shock system.

overall_design: A single mock immunoprecipitation (IP) using non-specific IgG was used as a background dataset for this study (see PMID: 20844575; GSM470838). We performed two independent GAF-ChIP-seq experiments in untreated S2 cells and two replicates in S2 cells that were depleted of GAF by RNAi.

middle: J


title: Gene expression profiling of zebrafish embryos at 5 days post fertilization [Illumina RNA-Seq]

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

summary: We compared Agilent custom made expression microarrays with Illumina deep sequencing for RNA analysis of zebrafish embryos 5 days post fertilization, showing as expected a high degree of correlation of expression of a common set of 15,927 genes for untreated fish. The transcriptomes were also compared for fish injected in the yolk with Mycobacterium marinum

overall_design: This RNA deep sequencing study was designed to determine the gene expression profile of zebrafish embryos 5 days post fertilization. We also have compared expression with embryos that were injected with Mycobacterium marinum in the yolk at 2 hours post fertilization. After injections embryos were transferred into fresh egg water and incubated at 28°C. 150 embryos of mock-injected embryos or 200 embryos injected with 12 CFU bacteria were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.

first: H

first: R

last: Dirks

last: Veneman


title: Identification of chromatin regulatory sites in conditions of basal and increased SF-1 dosage in the H295R adrenocortical tumor cell line

city: Valbonne

first: Enzo

last: LALLI

address: 660 route des Lucioles

department: CNRS UMR 7275

country: France

institute: IPMC

summary: The goal of this study was to identify chromatin regulatory sites by FAIRE-seq under conditions of basal and increased dosage of transcription factor SF-1 in the H295R human adrenocortical tumor cell line.

overall_design: 4 samples: input DNA in basal SF-1 expression conditions - FAIRE-seq in basal SF-1 expression conditions - input DNA in SF-1 overexpression conditions - FAIRE-seq in SF-1 overexpression conditions

last: Lalli


title: Identification of NRSF/REST genomic binding sites in conditions of basal and increased SF-1 dosage in the H295R adrenocortical tumor cell line

summary: The goal of this study was to identify genomic binding sites of the NRSF/REST transcription factor under conditions of basal and increased SF-1 dosage in the H295R human adrenocortical tumor cell line.

overall_design: 4 samples: input DNA (2 replicates) - NRSF/REST ChIP basal SF-1 dosage - NRSF/REST ChIP increased SF-1 dosage


title: affy_sunflower_2010_13-ROS and hormones in sunflower seed dormancy.

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

summary: affy_sunflower_2010_13 - affy_sunflower_2010_13 - It concerns the interaction between ROS and hormones in dormancy release in sunflower seeds. ABA is responsible for dormancy maintenance, while GA and ethylene promote seed germination. Based on our results, ROS could represent good candidate to shift from a hormone signalling to another determining the dormancy state in sunflower seeds.-We aim to understand the mechanisms controlling sunflower seed dormancy at the transcriptomic level, by the application of treatments which maintain dormancy as ABA, or alleviate dormancy as ROS and ethylene. Transcripts comparison will be performed between dormant and non-dormant sunflower embryo imbibed 24h on water, on ABA, on methylviologen, a pro-oxidant compound or on ethylene.

overall_design: 12 arrays - SUNFLOWER; treated vs untreated comparison

first: Stephanie

last: Huguet

first: Hayat

last: Bouteau

first: Christophe

last: Bailly

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Transcription profiling of Arabidopsis plants overexpressing SlHsfA3

city: Harbin

first: jingfu

last: li

address: Mucai street

country: China

institute: Northeast Agricultural University

summary: In order to investigate the possible molecular mechanisms of SlHsfA3 function in plant growth and stress responses, we employed the RNA-seq approach to identify the genes with altered expression levels in the transgenic Arabidopsis overexpressing SlHsfA3. Processing of RNA samples on the Illumina HiSeq 2000 system yielded more than 24 million reads, each 100bp in length, encompassing 2.4Gb of sequence data for each sample which was then mapped to the reference genome. Quantitative analysis of RNA-seq data identified substantial variation in expression profiles among different genotypes, consistent with known functional differences. Transcript abundance obtained from RNA-seq data was indicated as RPKMs and therefore, Up- and down-regulated genes were determined by a greater than 2-fold change of normalized RPKMs in comparison analysis (35S:SlHsfA3 transgenic plants versus Col-0(WT) plants) in both over-expression lines: Q-value < 0.05. The statistical analysis identified a total of 181 differentially expressed genes between OE lines and Col-0(WT) at Q-value < 0.05, among which 114 (63%) were up-regulated and 67 (37%) were down-regulated with fold changes higher than 2.

overall_design: RNA-sequencing was carried out using two independent transgenic lines (35S:SlHsfA3-3 and 35S:SlHsfA3-6). Total RNA was isolated with Trizol reagent (Invitrogen, USA) from the aerial part of the 4-week-old seedlings of 35Spro:SlHsfA3 and Col-0 (WT) plants grown in parallel under unstressed conditions. Materials from 20 plants of each genotype were pooled for RNA isolation.

first: Zhenjun

last: Li

first: Lili

last: Zhang


title: Strand-specific RNA-seq analysis of three streptomycetes

city: Hamilton

first: Matthew

middle: John

last: Moody

state: ON

address: Life Sciences Building Rm 323, McMaster University, 1280 Main St W

department: Biology

institute: McMaster University

summary: We report the mRNA and small RNA transcriptomes of Streptomyces coelicolor, Streptomyces avermitilis, and Streptomyces venezuelae.  We identified dozens of new conserved sRNAs and antisense RNAs, including a prominent group of antisense RNAs termed ‘cutoRNAs’ that result from overlap of the 3′ ends of convergently transcribed mRNAs.  In addition, we observed abundant unique ncRNAs, including many within secondary metabolic gene clusters.

sample_organism:
Streptomyces coelicolor
Streptomyces avermitilis
Streptomyces venezuelae

overall_design: For each of the three species (S. coelicolor, S. avermitilis, S. venezuelae) two libraries were created. The first was a long-read library, where total RNA was depleted of rRNA. The second was a short read library, where total RNA was size selected (40-300 nucleotides) prior to library creation. The long-read library allowed the profiling of mRNAs and asRNAs, while the short-read library was enriched for small RNAs (sRNAs).

first: Marie

last: Elliot

first: Rachel

last: Young

last: Jones


title: Identification of SF-1 genomic binding sites in conditions of basal and increased dosage in the H295R adrenocortical tumor cell line

summary: The goal of this study was to identify genomic binding sites of the SF-1 nuclear receptor under conditions of basal and increased dosage in the H295R human adrenocortical tumor cell line.

overall_design: 14 samples: input DNA (2 replicates) - SF-1 ChIP Millipore antibody basal SF-1 dosage (3 replicates) - SF-1 ChIP Millipore antibody increased SF-1 dosage (3 replicates) - SF-1 ChIP Perseus antibody basal SF-1 dosage (3 replicates) - SF-1 ChIP Perseus antibody increased SF-1 dosage (3 replicates)


title: IkBa associates with histone H2A in human keratinocytes

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

country: Spain

institute: Hospital del Mar

summary: Here, we demonstrate that IkBa displays a predominant and unique nuclear localization in normal basal keratinocytes. This nuclear IkBa binds the chromatin through direct interaction of the ankyrin repeats with histone H2A and associates with the promoter and regulatory regions of several developmental-related genes including HOXA10, HOXB2 and HOXB9. Most importantly, IkBa dictates the competence of these HOX genes to be activated upon TNFa stimulation.

overall_design: Examination of IkBalpha location in keratinocyte cells

first: Abul

last: Islam

first: Maria

last: Mulero

first: Anna

last: Bigas

first: Nuria

last: Lopez-Bigas


title: Expression data from 7 Human Melanomas

city: Glasgow

first: Peter

middle: D.

last: Adams

address: Switchback Rd, Bearsden

country: United Kingdom

institute: University of Glasgow, Beatson Institute for Cancer Research

summary: Melanocytes within benign human nevi are the paradigm for tumor suppressive senescent cells in a pre-malignant neoplasm. These cells typically contain mutations in either the BRAF or N-RAS oncogene and express markers of senescence, including p16. However, a nevus can contain 10s to 100s of thousands of clonal melanocytes and approximately 20-30% of melanoma are thought to arise in association with a pre-existing nevus. Neither observation is indicative of fail-safe senescence-associated proliferation arrest and tumor suppression. We set out to better understand the status of nevus melanocytes. Proliferation-promoting Wnt target genes, such as cyclin D1 and c-myc, were repressed in oncogene-induced senescent melanocytes in vitro, and repression of Wnt signaling in these cells induced a senescent-like state. In contrast, cyclin D1 and c-myc were expressed in many melanocytes of human benign nevi. Specifically, activated Wnt signalling in nevi correlated inversely with nevus maturation, an established dermatopathological correlate of clinical benignancy. Single cell analyses of lone epidermal melanocytes and nevus melanocytes showed that expression of proliferation-promoting Wnt targets correlates with prior proliferative expansion of p16-expressing nevus melanocytes. In a mouse model, activation of Wnt signaling delayed, but did not bypass, senescence of oncogene-expressing melanocytes, leading to massive accumulation of proliferation-arrested, p16-positive non-malignant melanocytes. We conclude that clonal hyperproliferation of oncogene-expressing melanocytes to form a nevus is facilitated by transient delay of senescence due to activated Wnt signaling. The observation that activation of Wnt signaling correlates inversely with nevus maturation, an indicator of clinical benignancy, supports the notion that persistent destabilization of senescence by Wnt signaling contributes to the malignant potential of nevi.

overall_design: We used RNA-Seq to detail the global programme of gene expression in human melanoma cell lines

first: Jeff

last: Pawlikowski

first: Tony

last: McBryan


title: Innate immune pathways in afferent lymph following vaccination with poly(I:C) -containing liposomes

city: Clayton

first: Melissa

last: Burke

state: VIC

address: Wellington Road

country: Australia

institute: Monash University

summary: Many modern vaccines use defined adjuvants to stimulate the innate immune system and shape the adaptive immune response. The exact nature of these innate signals and whether immune differentiation can originate within the periphery is not known. In the present study we used an ovine lymphatic cannulation model to characterise the cellular and transcriptomic profile of the afferent lymph following injection of a liposomal vaccine formulation incorporating diphtheria toxoid and the innate stimulator poly (I:C) over a 78 h period. The response to this vaccine featured an early activation of broad proinflammatory pathways (e.g. TLR signalling and inflammasome pathways) and the transient recruitment of granulocytes into the lymph. At 24hrs a more monocytic cellular profile arose coinciding with a transition to a specific antiviral response characterised by the up-regulation of genes associated with the receptors typical for the viral mimic, poly (I:C) (e.g. TLR3, RIG-I and MDA5). At the latest time points the up-regulation of IL-17A and IL-17F suggested that Th17 cells may participate in the earliest adaptive response to this vaccine. Together these data provide the most comprehensive picture of the cellular and molecular mechanisms that link the periphery to the draining lymph node following vaccination and indicate that the immune response is capable of specialising within the periphery.

overall_design: This study employed an ovine model of pseudoafferent lymphatic cannulation (see de Veer et al. 2010, Vaccine) to characterise the innate immune response within the afferent lymph to vaccination with liposomes+poly (I:C)+ diptheria toxoid. The sheep used in this study had both their pre-femoral lymph nodes removed at 1 year of age. Approximately 1 year after the lymph node removal, a second surgery was performed to insert a 0.96_0.58mm heparin-coated polyvinyl chloride cannula into the pseudoafferent (previous efferent) lymphatic duct of both sides. At least seven days were allowed for healing to occur after surgery before vaccinations were administered and experimental lymph samples were collected. Handling of animals and experimental procedures were all approved by the Monash University Animal Ethics Committee in accordance with the relevant licensing agreement. Vaccinations were injected subcutaneously in the area drained by the prefemoral lymph node. Afferent lymphatic samples were collected prior to vaccination as a control (PRE) and at 4-6, 26-28, 51-53 and 76-78 hours post vaccination with liposomes+poly (I:C)+ diptheria toxoid. Lymphocytes were removed from the afferent lymph using immunomagnetic separation. Next-generation sequencing was performed on RNA derived from the remaining innate immune cells. Samples from three sheep were used at all time points except 4-6 and 26-28 hours, where only two samples yielded sufficient RNA for sequencing.

middle: L

first: Michael

last: de Veer

first: Jill

last: Pleasance

first: Melanie

last: Neeland

first: Martin

last: Elhay

first: Paul

last: Harrison

first: Els

last: Meeusen


title: ChIP-seq data of Epstein-Barr Virus Nuclear Antigen Leader Protein (EBNALP)

status: Public on Jul 31 2013

city: Boston

first: Hufeng

last: Zhou

address: 181 Longwood Ave,

department: Department of Microbiology and Molecular Genetics

institute: Harvard Medical School

summary: Epstein-Barr-Virus (EBV) Nuclear Antigens EBNALP and EBNA2 are   co-expressed in EBV infected B-lymphocytes and are critical for Lymphoblastoid Cell Line (LCL) growth. EBNALP removes NCOR1 and RBPJ repressive complexes from promoter and enhancer sites and EBNA2 mostly activates transcription from distal enhancers. ChIP-seqs found EBNALP at 19,224 LCL sites, which were 33% promoter associated. EBNALP was associated with 10 transcription factor (TF) clusters that included YY1(63%), SP1(62%), PAX5(59%), BATF(50%), IRF4(49%), RBPJ(43%), ETS1(39%), PU.1(37%), RAD21(33%), NF-kB(31%), TBLR1(26%), ZNF143(24%), CTCF(23%), SMC3(21%), and EBF(17%). EBNALP sites had higher H3K4me3, H3K9ac, H3K27ac, H2Az, and RNA Pol II signals than EBNA2 sites and had similar transcription effects. EBNALP co-localized with 29% of 19,845 EBNA2 sites. EBNALP/EBNA2 sites were similar to EBNALP sites in promoter localization, associated cell TFs, Pol II, H3K4me3, H3K9ac, H3K27ac, and H2Az signals. EBNALP and EBNA2 promoter sites were more transcriptionally active than EBNALP or EBNA2 promoter sites. EBNALP was at the enhancer or promoter of myc and MYC affected genes, including cyclin D2, and bcl2. EBNALP at promoters with DNA looping and transcription factors, is positioned to deplete repressors from enhancers and promoters, enable chromatin remodeling, and transcription activation.

overall_design: Two EBNALP ChIP-seq replicates from IB4 LCL are analyzed in this study.

first: Daniel

last: Portal

first: Elliott

last: Kieff


title: Wnt-signaling potentiates nevogenesis.

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

overall_design: Refer to individual Series


title: Genome-wide mapping of CarD, RNAPs, and RNAPb on the Mycobacterium smegmatis genome using Chromatin Immunoprecipitation Sequencing

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: CarD is an essential mycobacterial protein that we had previously shown to bind the RNA polymerase (RNAP) and affect the transcriptional profile of M. smegmatis and Mycobacterium tuberculosis. For this reason, we suspected that CarD was directly regulating transcriptional complexes but we did not know at what stage of CarD was functioning and at which genes CarD interacted with the RNAP. To determine in which stage of the transcription cycle (initiation, elongation, or termination) CarD acts, we used Chromatin Immunoprecipitation sequencing (ChIP-seq) to survey the distribution of CarD throughout the M. smegmatis chromosome. Specific antibodies targeting core RNAPb, RNAPσ, or a hemagglutinin (HA) epitope fused to CarD (CarD-HA) were used to co-immunoprecipitate associated DNA. CarD-HA was immunoprecipitated from the M. smegmatis Mc2155 ΔcarD attB::tetcarD-HA strain and unfused HA was immunoprecipitated from the Mc2155 attB::pmsg431 strain with monoclonal antibodies specific for HA (Sigma). RNAP β and σ were immunoprecipitated from M. smegmatis ΔcarD attB::tetcarD-HA with monoclonal antibodies specific for these subunits (Neoclone, Madison, WI; 8RB13 for β, 2G10 for σ). Co-precipitated DNA was sequenced using a SOLiD sequencer (Life Technologies), which provided sufficient reads for 100-fold coverage of the genome. The number of sequence reads per base pair was normalized to the total number of reads and expressed as a log2 value. The reads per base pair from the HA-alone sample served as the background and was subtracted from the other datasets. We found that CarD was never present on the genome in the absence of RNAP. However, whereas RNAP core enzyme was found throughout transcribed regions of the genome, CarD was primarily associated with promoter regions and highly correlated with RNAPσ. The colocalization of σA and CarD led us to propose that in vivo, CarD associates with RNAP initiation complexes at most promoters and is therefore a global regulator of transcription initiation.

overall_design: The genome sequences associated with M. smegmatis CarD, RNAPb, and RNAPs were determined by ChIP-seq analysis. Samples were done in duplicate, except for RNAPs. And sequencing was performed using a SOLiD sequencer (Life Technologies).

first: Christina

last: Stallings

last: Glickman


title: Default DNA Methylation is Preceded by Broad, Low-Level Transcription in Fetal Male Germ Cells and Is Inversely Patterned by Dynamic H3K4 Methylation (RNA-Seq)

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: To understand what dictates the emerging patterns of de novo DNA methylation, we mapped DNA methylation, chromatin, and transcription changes in purified fetal mouse germ cells using MIRA-chip, ChIP-chip, and strand-specific RNA-seq, respectively. De novo methylation occurred without any apparent trigger from preexisting repressing chromatin marks but was preceded by broad, low-level transcription along the entire genome in prospermatogonia. Only distinct short sequences remained unmethylated, precisely aligned with constitutive or emerging peaks of H3K4me2. Establishment of methylation at differentially methylated regions (DMRs) of imprinted genes, CpG islands, and IAPs followed these same default rules. Transcription run-through occurred at paternal DMRs with no- or diminishing H3K4me2 peaks. Maternal DMRs remained unmethylated among highly methylated DNA at precisely aligned H3K4me2 peaks with transcription initiating at least in one strand. Our results suggest that the pattern of de novo DNA methylation in prospermatogonia is dictated by opposing actions of broad, low-level transcription and dynamic patterns of active chromatin.

overall_design: Strand-specific RNA-seq was done in male and female fetal germ cells and somatic gonadal cells at 15.5 dpc to map transcription.

first: Purnimam

last: Singh

first: Piroska

last: Szabo


title: Default DNA Methylation is Preceded by Broad, Low-Level Transcription in Fetal Male Germ Cells and Is Inversely Patterned by Dynamic H3K4 Methylation

type: Genome binding/occupancy profiling by genome tiling array

type: Methylation profiling by genome tiling array


title: Genetic Programs in Human and Mouse Early Embryos Revealed by Single-Cell RNA-Sequencing

status: Public on Jul 29 2013

city: Los Angeles

first: Kevin

last: Huang

address: Gonda BLDG Rm. 6554, P.O.Box 957088

department: Human Genetics

institute: UCLA

summary: Mammalian preimplantation development is a complex process involving dramatic changes in the transcriptional architecture. Through single-cell RNA-sequencing (RNA-seq), we report here a comprehensive analysis of transcriptome dynamics from oocyte to morula in both human and mouse embryos. Based on single nucleotide variants (SNVs) in blastomere mRNAs and paternal-specific SNPs, we identify novel stage-specific monoallelic expression patterns for a significant portion of polymorphic gene transcripts (25-53%). By weighted gene co-expression network analysis (WGCNA), we find that each developmental stage can be concisely delineated by a small number of functional modules of co-expressed genes. This result indicates a sequential order of transcriptional changes in pathways of cell cycle, gene regulation, translation, and metabolism in a step-wise fashion from cleavage to morula.  Cross-species comparisons reveal that the majority of human stage-specific modules (7 out of 9) are remarkably preserved, only to diverge in developmental specificity and timing in mice. We further identify conserved key members (or hub genes) of the human and mouse networks. These genes represent novel candidates that are likely key players in driving mammalian preimplantation development. Collectively, we demonstrate that mammalian preimplantation development is orchestrated by evolutionarily conserved genetic programs that diverge in developmental timing.  Our results provide a valuable resource to dissect gene regulatory mechanism underlying progressive development of early mammalian embryos.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: single-cell RNA-seq of human and mouse blastomeres

first: Xue

last: Zhigang

first: Guoping

last: Fan


title: Genome wide hydroxymethylation tested using the HELP-GT assay shows redistribution in cancer

status: Public on Jul 30 2013

city: Bronx

first: Yiting

last: Yu

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

type: Methylation profiling by high throughput sequencing

summary: Background: 5-hydroxymethylcytosine (5-hmC) is a recently discovered epigenetic modification that is altered in cancers. Genome wide assays for 5-hmC determination are needed as many of the techniques commonly used to assay 5-methylcytosine (5-mC), including conventional methyl-sensitive restriction digest and bisulfite sequencing, are incapable of distinguishing between 5-mC and 5-hmC.   Results: Glycosylation of 5-hmC residues by beta-Glucosyl Transferase (beta-GT) can make CCGG residues insensitive to digestion by MspI. We used this premise to modify the HELP-tagging assay to identify both 5-mC and 5-hmC loci in the genome. Comparison of sequencing libraries after HpaII, MspI and MspI+ beta-GT conversion resulted in locus specific 5-mC and 5-hmC determination. A custom bioinformatics pipeline was created to identify 5-hmC sites that were validated at global level by LS-MS and the locus specific level by qRT-PCR of 5-hmC pulldown DNA. Hydroxymethylation at both promoter and intragenic locations correlated positively with gene expression. Analysis of pancreatic cancer samples revealed striking redistribution of 5-hmC sites in cancer cells and demonstrated enrichment of this modification at many oncogenic promoters such as GATA6.   Conclusions: The HELP-GT assay allows a high resolution, simultaneous determination of 5-hmC and 5-mC loci from small amounts of DNA with the utilisation of modest sequencing resources. Redistribution of 5-hmC seen in cancer highlights the importance of examining this modification in conjugation with conventional methylome analysis.

overall_design: We did methylation and hydroxymethylation tests for one control and two pancreatic cancer cases

first: S

last: Bhattacharyya

first: A

last: Verma


title: RNA-Seq expression data from the reproductive tracts of WT, Hoxa91011, and Hoxd91011 mutant mice

first: Steve

last: Potter

address: 3333 Burnet Ave.

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Hox genes are key regulators of development. In mammals, the study of these genes is greatly confounded by their large number, overlapping functions, and their interspersed shared enhancers. In this report, we describe a novel recombineering strategy that was used to introduce simultaneous frameshift mutations into the flanking Hoxa9, Hoxa10, and Hoxa11 genes, as well as their paralogs on the HoxD cluster. The resulting mutant mice displayed dramatic homeotic transformations of the reproductive tracts, with uterus anteriorized towards oviduct and the vas deferens anteriorized towards epididymis. The Hoxa9,10,11 mutant mice provided a sensitized genetic background that allowed the discovery of Hoxd9,10,11 reproductive tract patterning function. Both shared and distinct Hox functions were defined. The HoxD genes played a crucial role in the regulation of the uterine immune function. Non-coding nonpolyadenylated RNAs were among the key Hox targets. In addition we observed a surprising anti-dogmatic posteriorization of the uterine epithelium.

overall_design: Reproductive tracts were collected from WT and Hox mutant mice (n=3/genotype) aged 3-7 months in order to characterize the molecular changes caused by mutation of Hoxa9,10,11 and Hoxd9,10,11.  Female mice were staged and collected in diestrus.

first: Anna

last: Raines

first: Mike

last: Adam

first: Bliss

last: Magella

first: Sara

last: Meyer

first: H

last: Grimes

first: Sudhansu

last: Dey


title: PAX5 overexpression is not enough to reestablish the mature B-cell phenotype in classical Hodgkin lymphoma (ChIP-Seq)

city: Berlin

first: Lora

last: Dimitrova

state: Berlin

address: Hindenburgdamm 30

department: Institute of Pathology

country: Germany

institute: Charité-University Medicine Berlin

summary: In lymphomas derived from mature B cells the expression of the transcription factor PAX5 is maintained whereas classical Hodgkin lymphoma displays significantly reduced PAX5 expression despite its derivation from mature B cells. To elucidate the functional role of PAX5 in classical Hodgkin lymphoma, we re-established the PAX5 expression in the Hodgkin cell line L428 with and without epigenetic modulation. To this end, we stably transfected the Hodgkin cell line L428 with an inducible PAX5 expression construct. Although the overexpressed PAX5 was transcriptionally active as demonstrated by synthetic reporter constructs, no induction of the B-cell phenotype was achieved. PAX5 chromatin immunoprecipitation with subsequent next generation sequencing in B-cell lines and the PAX5 overexpressing L428 cell line showed different binding patterns. Since epigenetic restrictions might affect PAX5 binding, combined DNA demethylation and histone acetylation was performed. However, no re-expression of B-cell genes was observed also under these conditions. Thus, PAX5 is not sufficient for the re-activation of the B-cell program in Hodgkin cells despite epigenetic opening of the chromatin. This clearly indicates that the repression of the B-cell identity of the Hodgkin cells is caused and secured by complex molecular mechanisms.

overall_design: Analysis of genome-wide PAX5 binding sites in B-cell lines (Raji, Namalwa) and the PAX5-producing Hodgkin cell line L428-PAX5 by ChIP-Seq

first: Volkhard

last: Seitz

first: Jochen

last: Hecht

first: Dido

last: Lenze

first: Peter

last: Hansen

first: Monika

last: Szczepanowski

first: Liya

last: Ma

first: Elisabeth

last: Oker

first: Anke

last: Sommerfeld

first: Franziska

last: Jundt

first: Wolfram

last: Klapper

first: Michael

last: Hummel


title: Analysis of Unannotated Equine Transcripts Identified by mRNA Sequencing

city: Fort Collins

first: Stephen

last: Coleman

state: CO

address: 1682 Campus Delivery

department: MIP

institute: Colorado State University

summary: Sequencing of equine mRNA (RNA-seq) identified 428 putative transcripts which do not map to any previously annotated or predicted horse genes.  Most of these encode the equine homologs of known protein-coding genes described in other species, yet the potential exists to identify novel and perhaps equine-specific gene structures.  A set of 36 transcripts were prioritized for further study by filtering for levels of expression (depth of RNA-seq read coverage), distance from annotated features in the equine genome, the number of putative exons, and patterns of gene expression between tissues.  From these, four were selected for further investigation based on predicted open reading frames of greater than or equal to 50 amino acids and lack of detectable homology to known genes across species.  Sanger sequencing of RT-PCR amplicons from additional equine samples confirmed expression and structural annotation of each transcript.  Functional predictions were made by conserved domain searches.  A single transcript, expressed in the cerebellum, contains a putative kruppel-associated box (KRAB) domain, suggesting a potential function associated with zinc finger proteins and transcriptional regulation.  Overall levels of conserved synteny and sequence conservation across a 1MB region surrounding each transcript were approximately 73% compared to the human, canine, and bovine genomes; however, the four loci display some areas of low conservation and sequence inversion in regions that immediately flank these previously unannotated equine transcripts.  Taken together, the evidence suggests that these four transcripts are likely to be equine-specific.

overall_design: Examination of 8 equine RNA samples representing 6 distinct tissues

first: James

last: MacLeod


title: Unprecedented alternative splicing and 3 Mb of novel transcribed sequence leads to significant transcript diversity in the transcriptome of the human retina

first: Eric

last: Pierce

state: MA

address: 243 Charles Street

department: Ophthalmology

institute: Massachusetts Eye and Ear Infirmary

summary: The mRNA repertoire is specific to a given tissue type.  This specificity, whether it is in the levels of gene expression or the splicing pattern of the transcripts, is important to study to increase our general knowledge of transcription and alternative splicing, as well as to identify novel coding sequence that can be important for elucidating the mechanisms of disease.  We have performed RNA-Seq on three normal human retinal samples and have found a profound level of novel alternative splicing including novel exons, exon skipping, and 3’ and 5’ alternate splice sites.  Additionally, we have identified hundreds of novel genes.  With so many novel splicing events identified in the retinal transcriptome, we set out to determine if these novel features were indeed real.  We developed a high throughput capture set to target 14,696 of the novel features.  We found that 99% of the novel features do validate, including those initially detected at a depth of coverage as low as one.  These results confirm that the transcripts expressed in the retina are much more diverse than previously identified.  The complete human retinal transcriptome described here will be useful for investigators studying multiple aspects of retinal biology and disease.

overall_design: Characterization of alternative splicing in the normal human retinal transcriptome.

middle: H

last: Farkas

first: Gregory

last: Grant

first: Joseph

last: White

first: Maria

last: Sousa

middle: A


title: Expression data from Uninfected and BRAF600V induced melanocytes

last: Adams

overall_design: We used RNA-Seq to detail the global programme of gene expression in primary human melanocytes which were Uninfected and BRAF600V induced cells

first: Jeff

last: Pawlikowski

first: Tony

last: McBryan

middle: D


title: seq-ab8895_H3K4me1:733246_N2_L3

status: Public on Jul 26 2013

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_5048
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include key histone modifications and histone variants.   We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temp (temperature) 20 degree celsius; Strain N2; Antibody ab8895 H3K4me1:733246 (target is H3K4me1)

first: Julie

last: Ahringer

first: Isabel

last: Latorre

first: Anne

last: Canonge


title: Transcriptome analysis of Thermotoga maritima

city: La Jolla

first: Haythem

last: Latif

state: California

address: 417 Powell-Focht Bioengineering Hall, 9500 Gilman Drive

institute: University of California San Diego

type: Expression profiling by genome tiling array

first: Joshua

last: Lerman

first: Vasiliy

last: Portnoy

first: Yekaterina

last: Tarasova

first: Harish

last: Nagarajan

first: Alexandra

middle: C

last: Schrimpe-Rutledge

first: Richard

last: Smith

middle: N

last: Adkins

first: Dae-Hee

last: Lee

first: Yu

last: Qiu

first: Bernhard

middle: O

last: Palsson

first: Karsten

last: Zengler


title: Sex-biased expression profile of Schistosoma mansoni microRNAs

city: Colchester

first: Antonio

last: Marco

address: Wivenhoe Park

department: School of Life Sciences

institute: University of Essex

summary: Schistosoma mansoni is a dioecious species, that is, it has two differentiated sexes. Interestingly, this sexual species evolved from a hermaphrodite ancestor. Indeed, most Platyhelminthes are hermaphrodites. Here we characterize the microRNAs of S. mansoni and quantify their differential expression between males and females.

overall_design: Mice were infected with Schistosoma mansoni 1-2 weeks prior to dissection. RNA from two independent samples were extracted and sequenced with Illumina MiSeq technology and AB SOLiD 4 technology. Reads were mapped to the reference genome and microRNA detected and analyzed.

first: Jerome

last: Hui

first: Sam

last: Griffiths-Jones

first: Matthew

last: Ronshaugen


title: seq-AB46540_NIgG_N2_Mxemb

first: DCC

last: modENCODE

summary:
modENCODE_submission_6208
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.  We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Mixed Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  EXPERIMENTAL FACTORS: Developmental Stage Mixed Embryo; temp (temperature) 20 degree celsius; Strain N2; Antibody AB46540 NIgG (target is N/A (negative control IgG))

first: Jason

last: Lieb

first: Ikegami

last: Kohta


title: Transcriptomic analysis of zebrafish during development and homeostasis

status: Public on Jul 27 2013

city: Eggenstein-Leopoldshafen

first: olivier

last: armant

address: Hermann-von-Helmholtz-Platz 1

institute: ITG

summary: Sequencing libraries were generated from total RNA samples following the mRNAseq protocol for the generation of single end (16-36 hpf, 5 day larvae, adult head and adult tail) or paired end (24 hpf) libraries (Illumina). Single end reads of 36 nucleotides and paired end reads (2 x 76 nucleotides) were obtained with a GAIIx (Illumina). Gene expression at the different stages/tissu was assessed by cufflinks and HTseq.

overall_design: RNAseq on 5 differents samples:  24hpf embryos, pool of 16 hour to 36 hour embryos, 5 days old larvea, adult head and adult tail

first: Olivier

last: Armant

first: Uwe

last: Straehle

first: Sepand

last: Rastegar


title: seq-ab9051_H4K20me1_N2_Mxemb

summary:
modENCODE_submission_6210
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include key histone modifications and histone variants.   We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Mixed Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  EXPERIMENTAL FACTORS: Developmental Stage Mixed Embryo; temp (temperature) 20 degree celsius; Strain N2; Antibody ab9051 H4K20me1:104513 (target is H4K20me1)


title: seq-HK00009_H3K9me3_2F3_N2_Eemb

summary:
modENCODE_submission_5153
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include key histone modifications and histone variants.   We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Strain N2; Antibody HK00009 H3K9me3:2F3 (target is H3K9me3)

first: Susan

last: Strome

first: Thea

last: Egelhofer

first: Andreas

last: Rechtsteiner


title: Examination of histone H2B ubiquitination in wild type and USP49 knockdown cells [ChIP-Seq]

status: Public on Jul 28 2013

city: Richmond

first: Hengbin

last: Wang

state: VA

address: 401 College Street

department: Massey Cancer Institute

institute: Virginia Commonwealth University

summary: Posttranslational histone modifications play important roles in regulating chromatin structure and function. Histone H2B ubiquitination and deubiquitination have been implicated in transcriptional regulation, but the function of H2B deubiquitination is not well defined, particularly in higher eukaryotes. Here we report the purification of USP49 as a histone H2B specific deubiquitinase and demonstrate that H2B deubiquitination by USP49 is required for efficient co-transcriptional splicing of a large set of exons. USP49 forms a complex with RVB1 and SUG1, and specifically deubiquitinates histone H2B in vitro and in vivo. USP49 knockdown results in small changes in gene expression, but affects the abundance of over 9,000 isoforms.  Exons down-regulated in USP49 knockdown cells show both elevated levels of alternative splicing and a general decrease in splicing efficiency.  Importantly, USP49 is relatively enriched at this set of exons.  USP49 knockdown increased uH2B levels at these exons as well as upstream 3’ and downstream 5’ intronic splicing elements.  Change in H2B ubiquitination level, as modulated by USP49, regulates U1A and U2B association with chromatin and binding to nascent pre-mRNA. Although H3 levels are relatively stable after USP49 depletion, H2B levels at these exons are dramatically increased, suggesting that uH2B may enhance nucleosome stability. Therefore, this study identifies USP49 as a histone H2B specific deubiquitinase and uncovers a critical role for H2B deubiquitination in co-transcriptional pre-mRNA processing events.


title: Examination of gene expression in wild type and USP49 knockdown cells [RNA-Seq]


title: seq-WA30932379_H3K9ac_N2_L3

summary:
modENCODE_submission_3578
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include key histone modifications and histone variants.   We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temp (temperature) 20 degree celsius; Strain N2; Antibody WA30932379 H3K9ac (target is H3K9Acetyl)

first: Julie

last: Ahringer

first: Isabel

last: Latorre

first: Anne

last: Canonge


title: seq-HK72A9_H4K8ac_FEM2_AD

summary:
modENCODE_submission_6009
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include key histone modifications and histone variants.   We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: fem-2(b245); Developmental Stage: Germline containing young adult; Genotype: fem-2(b245)III; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage Germline containing young adult; temp (temperature) 20 degree celsius; Strain fem-2(b245); Antibody HK H4K8ac 72A9 (target is H4K8ac)

first: Abby

last: Dernburg

first: Christina

last: Whittle


title: seq-SDQ2966_MIS12_N2_Mxemb

summary:
modENCODE_submission_6021
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.  We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Mixed Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  EXPERIMENTAL FACTORS: Developmental Stage Mixed Embryo; temp (temperature) 20 degree celsius; Strain N2; Antibody MIS-12 SDQ2966 (target is MIS-12)

first: Arshad

last: Desai

first: Reto

last: Gassmann


title: The role of microRNA-regulating energy metabolism and pollen wall development in male sterility in cotton

city: Anyang

first: Ming ming

last: Wei

address: Huang he road 38

institute: Cotton Research Institute, Chinese Academy of Agriculture Sciences (CAAS)

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

overall_design: Refer to individual Series


title: USP49 deubiquitinates histone H2B and regulates pre-mRNA splicing


title: Canonical Wnt signaling negatively modulates T regulatory cell function

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

summary: Foxp3 is crucial for both the development and function of regulatory T cells (Treg),however the post-translational mechanisms regulating Foxp3 transcriptional output remain poorly defined. Here, we demonstrate that TCF1 and Foxp3 interact in the nucleus of Treg, and that active Wnt-signaling disrupts Foxp3 transcriptional activity. Utilizing a global ChIP-seq comparison we demonstrate considerable overlap between Foxp3 and Wnt target genes in Treg. Activation of Wnt signaling significantly reduces Treg-mediated suppression both in vitro and in vivo, while disruption of Wnt signaling in Treg enhances their suppressive capacity. Activation of effector T cells increases Wnt3a production, and Wnt3a levels were found to be greatly increased in mononuclear cells isolated from synovial fluid versus peripheral blood of arthritis patients. We propose a model in which Wnt produced by activated mononuclear cells under inflammatory conditions represses Treg function allowing a productive immune response, but if uncontrolled could lead to the development of autoimmunity.

overall_design: Beta catenin ChIP-seq in Treg


title: ChIP-Seq for transcriptional regulators and RNA Polymerase II in tumor cells treated with JQ1

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: ChIP-Seq of RNA Polymerase II, and transcriptional regulators in multiple myeloma (MM.1S), glioblastoma (U87-MG), and small cell lung carcinoma (H2171) treated with the BET bromodomain inhibitor JQ1.

overall_design: Cell lines (MM.1S, U87-MG, and H2171) representing multiple myeloma, glioblastoma, and small cell lung carcinoma, were treated with varying concentrations (5nM to 5µM) of the BET bromodomain inhibitor JQ1 followed by ChIP-Seq for RNA Polymerase II and transcriptional regulators.  Other datasets from this series of experiments have been release as a part of GSE42355.

first: Heather

last: Hoke

first: Anders

last: Lars

first: Alla

last: Sigova

first: Ana

last: DAlessio