title: Investigating the Regulation of Hypopharyngeal Gland Activity in Honeybees Under Nutrition and Brood Pheromone Conditions through RNA-seq Transcriptomics

status: Public on Aug 06 2015

city: Tai'an

first: Lanting

last: Ma

state: Shandong

address: Daizong street, No. 61

institute: Shandong Agricultural University

summary: The hypopharyngeal gland (HG) is the main site of the synthesis and secretion of royal jelly protein (RJP), and shows high plasticity. To identify differentially expressed genes (DEGs) that affect the development of HG and the synthesis and secretion of RJP, we performed a digital gene expression analysis of 9 d Apis mellifera under different conditions of nutrition and exposure to brood pheromone.Six RNA-seq libraries were generated using RNA extracted from 9 d bee HGs. A total of 2801 DEGs were identified on the basis of at least one pairwise comparison, among which 205, 1617 and 2328 genes were differentially expressed in comparisons between the Pollen group and the Honey group, the Brood group and Pollen group and the Brood group and Honey group respectively. The Brood group exhibited the highest number of DEGs, suggesting that brood pheromone plays a key role in the HG ontogeny. A total of 1991 genes were mapped to 129 canonical signaling pathways found in the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the pathways associated with ribosome function and protein processing were significantly enriched.

overall_design: Hypopharyngeal gland mRNA profiles of 9-day old honeybees under three conditions (one control and two treatments) were generated by deep sequencing, in duplicate, using Illumina Hiseq 2500 platform.

first: Ying

first: Baohua

last: Xu


title: A discrete chromatin loop in the murine Tcra/Tcrd locus shapes the TCRδ and TCRα repertoires

status: Public on Aug 10 2015

city: Durham

first: Zachary

last: Carico

state: North Carolina

address: 207 Research Drive

department: Immunology

country: USA

institute: Duke University

summary: The Tcra/Tcrd locus undergoes V(D)J recombination in CD4−CD8− double-negative (DN) thymocytes and CD4+CD8+ double-positive (DP) thymocytes to generate diverse TCRδ and TCRα repertoires, respectively.  Here we reveal a Tcra/Tcrd locus chromatin interaction network in DN thymocytes that is formed by interactions between CTCF-binding elements (CBEs).  Disruption of a discrete chromatin loop encompassing the Dδ, Jδ and Cδ gene segments allows a single Vδ segment to frequently contact and rearrange to Dδ and Jδ segments and dominate the adult TCRδ repertoire.  Disruption of this loop also narrows the TCRα repertoire, which, we believe, follows as a consequence of the restricted TCRδ repertoire.  Hence, a single CTCF-mediated chromatin loop directly regulates TCRδ diversity and indirectly regulates TCRα diversity.

overall_design: Examination of chromatin loops by 4C-seq from 4 viewpoints in two lymphoid cell compartments: CD4-CD8- thymocytes and naïve B splenocytes.

first: Liang

last: Chen

first: Han-Yu

last: Shih

first: Michael

middle: S

last: Krangel


title: hESC-derived liver transcriptome analysis

status: Public on Aug 07 2015

city: La Jolla

first: Maike

last: Sander

state: CA

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

type: Expression profiling by high throughput sequencing

summary: To characterize the transcriptional programs that underlie pancreas differentiation and identity, we have generated genome-scale expression profiles by RNA-seq from human embryonic stem cell derived liver progenitors and human fetal pancreatic tissue (days 54-57 post conception).  These samples were compared to those already published transcriptomes (Xie et al., 2013).  Together, these samples were used to perform principles compotent analysis.  Once this was performed, we were able to identify transcription factors that were important in the identity of each cell type.

overall_design: To generate genome-scale expression profiles by RNA-seq from human embryonic stem cell derived liver progenitors, total RNA was isolated from human embryonic stem cell derived liver progenitors.  Libraries were sequenced and mapped to the hg19 version of the human genome.   Gene expression was determined using Sailfish. These samples were compared to those already published transcriptomes (Xie et al., 2013).  Together, these samples were used to perform principles compotent analysis.

first: Allen

last: Wang

first: Nisha

last: Patel


title: Human fetal pancreas transcriptome analysis

overall_design: To generate genome-scale expression profiles by RNA-seq from human embryonic stem cell derived liver progenitors and human fetal pancreatic tissue (days 54-57 post conception), total RNA was isolated from human embryonic stem cell derived liver progenitors and frozen human fetal pancreas.  Libraries were sequenced and mapped to the hg19 version of the human genome.  Gene expression was determined using Sailfish. These samples were compared to those already published transcriptomes (Xie et al., 2013).  Together, these samples were used to perform principles compotent analysis.

first: Ruiyu

last: Xie


title: Intrahepatic transcriptional signature associated with response to interferon-a treatment in the woodchuck model of chronic hepatitis B

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

summary: To define the intrahepatic cellular and molecular characteristics of the antiviral response to wIFN-alpha in woodchuck, the transcriptional profiles of woodchuck liver were studied by using RNASeq

overall_design: Woodchucks liver samples with chronic woodchuck hepatitis virus (WHV) infection were treated with recombinant woodchuck IFN-alpha or with placebo for 26 weeks

first: Simon

middle: P

last: Fletcher

first: Daniel

middle: J

last: Chin

first: Lore

last: Gruenbaum

first: Hans

last: Bitter

first: Erik

last: Rasmussen

first: Palanikumar

last: Ravindran

first: David

middle: C

last: Swinney

first: Fabian

last: Birzele

first: Stefan

last: Lorenz

first: Erhard

last: Kopetzki

first: Jade

last: Carter

first: Miriam

last: Triyatni

first: Linta

middle: M

last: Thampi

first: Junming

last: Yang

first: Dalal

last: AlDeghaither

first: Marta

middle: G

last: Murredu

first: Paul

last: Cote

first: Stephan

last: Menne


title: SOX9 targets in hESC-derived pancreatic progenitors

first: Maike

last: Sander

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Our lab identified Sox9 as a specific marker and maintenance factor of mouse pancreatic progenitors (Seymour et al., PNAS, 2007).  Here was wanted to identify direct targets of Sox9 in pancreatic progenitors.  However, due to the limited number of pancreatic progenitors in the developing mouse, we used in vitro derived pancreatic progenitors to determine direct targets of Sox9.   We performed ChIP-seq analysis for Sox9 and determined its direct targets in the human genome.  Using pancreatic progenitors that were derived from human embryonic stem cells, we were able to successfully find targets that were pancreas specific as well as those targets that are important in other endodermal lineages.

overall_design: We differentiated CyT49 human embryonic stem cells into pancreatic progenitors as previously described (Kroon et al., 2008; Schulz et al., 2012).   Using a Sox9 antibody, we performed ChIP-seq in the pancreatic progenitors.  We sequenced the samples using the Illumina platform and mapped the reads to the mm9 version of the mouse genome.  Using HOMER analysis software and the UCSC genome browser, we found direct targets of Sox9 in human embryonic stem cell derived pancreatic progenitors.

first: Ruiyu

last: Xie

first: Nisha

last: Patel


title: Dietary selenium levels affect selenoprotein expression and support the interferon-γ and IL-6 immune response pathways in mice [Ribosome Profiling]

city: Salt Lake City

first: Michael

middle: T

last: Howard

state: UT

department: Human Genetics

institute: University of Utah

summary: Mice were fed Se-deficient or Se-adequate diets for 6 weeks. Liver and lung tissue were harvested and processed for RNA-Seq, ribosome profiling, and microarray analysis. From these studies, we identified changes in mRNA levels and translation of selenoprotein genes and genes regulated by interferon-gamma. Cytokine profiles of serum indicated that interferon-gamma and IL-6 levels were increased in the Se-adequate mice relative to Se-deficient mice.

overall_design: Ribosome profiling of liver tissue from mice fed Se-deficient or Se-adequate diets

first: Petra

last: Tsuji

first: Dolph

last: Hatfield

first: Bradley

last: Carlson


title: Transcriptome analysis of TNFR2-knockout mouse colon

status: Public on Aug 11 2015

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

state: IL

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

summary:
PURPOSE: The goal of this study was to determine the gene expression networks regulated by tumor necrosis factor receptor 2 (TNFR2, or Tnfrsf1b) and to evaluate their potential bearing on immune cell subsets and inflammatory bowel disease (IBD).
METHODS: mRNA-seq was performed on isolated distal colons from TNFR2-knockout and wildtype mice. Differentially expressed transcripts were compared to human ulcerative colitis microarray datasets on Gene Expression Omnibus and to mouse immunological expression datasets at the Immunological Genome Project.
RESULTS: We identified 252 mouse transcripts whose expressions were significantly altered by the loss of TNFR2. The majority of these transcripts (228 of 252, ~90%) were downregulated in TNFR2-/- colons. TNFR2-regulated genes were able to positively discriminate between ulcerative colitis patients and healthy individuals with ~80% accuracy. Many TNFR2-regulated genes were also highly expressed in CD8+ T cells.
CONCLUSIONS: Downregulation of TNFR2 is associated with a gene expression profile that is prominent in IBD and supportive of the role of CD8+ T cells in IBD pathogenesis.
MANUSCRIPT ABSTRACT: Increased tumor necrosis factor (TNF) production has been associated with inflammatory bowel disease (IBD), and anti-TNF therapy is a common therapeutic for this patient population. However, the role of TNF or its receptors (TNFR1 and TNFR2) in the immunopathogenesis of inflammatory bowel disease (IBD) remains unclear. Here we report that TNFR2 is protective in spontaneous (IL-10 knockout) and chemically (azoxymethane/dextran sodium sulfate)-induced mouse models of colitis and colitis-associated cancer. Mechanistically, TNFR2-deficiency in hematopoietic cells significantly increased incidence and severity of colitis and colitis-associated cancer characterized by a selective expansion of CD8+ T cells. We identified TNFR2-regulated genes in the colon that were specific for CD8+ T cells, interacted with multiple IBD risk genes, and are important regulators of CD8+ T cell biology. TNFR2 regulated CD8+ T-cell-specific genes that act as genetic susceptibility modifiers for IBD to mitigate the development of a pro-colitogenic milieu. Antibody-mediated depletion of CD8+ T cells prevented colonic inflammation and significantly reduced pathology in IL10-/-/TNFR2-/- deficient mice. Furthermore, adoptive transfer of TNFR2-/- naïve CD8+ T cells resulted in more severe disease than with wildtype naïve CD8+ T cells. Our findings provide insight into the disease modifier role of TNFR2 in the immunopathogenesis of IBD through the modulation of CD8+ T cell responses and support future investigation of this therapeutic target, especially in the subset of IBD patients with CD8+ T-cell dysfunction.

overall_design: Total RNA from distal colons of 8 week-old male wildtype C57Bl/6 and TNFR2-/- mice (n=3 each) was isolated using the PureLink RNA kit (Ambion, Life Technologies). RNA samples were submitted to the Genomic Services Lab at the HudsonAlpha Institute for Biotechnology (Huntsville, AL) for multiplex library preparation, mRNA enrichment, and sequencing. Sequencing was performed to an average depth of 50M paired-end 50bp reads per sample (HiSeq, Illumina, San Diego, CA). Data files containing raw reads were aligned to the mouse genome using Tophat2/Bowtie2. Alignments were assembled into transcript representations with Cufflinks, and statistical tests for differential expression were performed with Cuffdiff 2. An adjusted P value < 0.05 (q<0.05) from the Cuffdiff 2 output was used as the cutoff for statistical significance.

first: Shivesh

last: Punit

first: Philip

middle: E

last: Dubé

middle: Y

first: Nandini

last: Girish

first: M

middle: K

last: Washington

first: D

middle: B

last: Polk


title: Dietary selenium levels affect selenoprotein expression and support the interferon-γ and IL-6 immune response pathways in mice

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

overall_design: Refer to individual Series


title: Telomerase is essential for zebrafish heart regeneration

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: Unlike human hearts, zebrafish hearts efficiently regenerate after injury. Regeneration is driven by the strong proliferation response of its cardiomyocytes to injury. In this study, we show that active telomerase is required for cardiomyocyte proliferation and full organ recovery, supporting the potential of telomerase therapy as a means of stimulating cell proliferation upon myocardial infarction.

overall_design: Heart transcriptomes of WT and telomerase defective adult zebrafish animals were profiled by RNASeq, in control conditions and 3 days after heart cryoinjury.

first: Ignacio

last: Flores

first: Nadia

last: Mercader

first: Rebeca

last: Álvarez

first: Alberto

last: Benguría

first: Segio

last: Callejas

first: Ana

last: Dopazo

last: Gómez

first: Fernando

last: Martínez

first: Fátima

last: Sánchez-Cabo

first: Carlos

last: Torroja


title: Reprogramming roadblocks are system-dependent

status: Public on Aug 08 2015

city: Edinburgh

first: Keisuke

last: Kaji

address: Edinburgh Bioquarter, 5 Little France Drive

department: MRC Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh

summary: Since the first generation of induced Pluripotent Stem cells (iPSCs), several reprogramming systems have been used to study its molecular mechanisms. However, the system of choice largely affects the reprogramming efficiency, influencing our view on the mechanisms. Here we demonstrate that reprogramming triggered by less efficient polycistronic reprogramming cassettes not only highlights Mesenchymal-Epithelial Transition (MET) as a roadblock, but also faces more severe difficulties to attain a pluripotent state even post-MET. Also, in contrast to previous findings, more efficient cassettes can reprogram both wild type and Nanog-/- fibroblasts with comparable efficiencies, routes and kinetics, rebutting previous studies that Nanog is critical for iPSC generation. We revealed that the 9 amino acids in the N-terminus of Klf4 in polycistronic reprogramming cassettes are the dominant factor causing these critical differences. Our data establishes that some reprogramming roadblocks are system-dependent, highlighting the need to pursue mechanistic studies with close attention to the systems to better understand reprogramming.

overall_design: The aim of the experiment is to compare the reprogramming pathways driven by two different polycistronic cassettes (MKOS and OKMS). We have isolated cells at intermediate stages of both MKOS and OKMS reprogramming and analysed their gene expression profiles. 2N- are CD44- ICAM1-, Nanog-GFP-, 3N- are CD44- ICAM1+, Nanog-GFP-, 3N+ are CD44- ICAM1+, Nanog-GFP+, all from day 10 of reprogramming.  MKOS/OKMS iPSCs are established iPSC clones, TNG an Embryonic Stem Cell line carrying a Nanog-GFP reporter published in Chambers et al. Cell, 113, 643-655, from this line TNG MKOS and OKMS Embryonic Stem Cells were generated after targeting the Sp3 locus with the MKOS or the OKMS cassette respectively,E14 a reference Embryonic Stem Cell line and MEF are Mouse Embryonic Fibroblasts either wild type or generaterd from TNG MKOS or OKMS ESCs. D6 is the D6s4B5 iPSC line published in O'Malley et al. Nature, 499, 88-91.

first: Eleni

last: Chantzoura

first: Stavroula

last: Skylaki

first: Sergio

last: Menendez

first: Kim

last: Shin-Il

first: Anna

last: Johnsson

first: Sten

last: Linnarsson

first: Knut

last: Woltjen

first: Ian

last: Chambers


title: Identification of a hepatocyte stem cell and its niche in liver homeostasis

city: San Francisco

first: Bruce

last: Wang

address: 513 Parnassus Ave

department: Medicine

institute: University of California San Francisco

summary:
Summary: RNAseq analysis of Axin2+ hepatocyte stem cells versus Axin2- mature hepatocytes shows that Axin2+ cells have a distinct gene expression profile compared to Axin2- hepatocytes.
Methods: Hepatocytes were isolated from 8 week old Axin2rtTA;TetO-H2B-GFP mice (n = 3) given doxycycline in drinking water for 7 days. After removal of non-parenchymal cells, the hepatocytes were sorted into GFP+ versus GFP- populations by FACS. mRNA was isolated and RNAseq profiles were generated using Illumina HiSeq 2000. The reads were mapped to the mouse genome (mm10) using TopHat (v2.0.11) and differential gene expression analysis was performed using CuffDiff (v.2.2.2).
Results: We mapped about 60 million sequence reads per sample to the mouse genome (build mm10) and identified more than 30,000 transcripts in the Axin2+ and Axin2- cell populations. Differential gene expression analysis using CuffDiff identified 96 genes with signficantly different expression levels between the two populations. Several of these were confirmed by RNA in situ and qRT-PCR analysis.

overall_design: mRNA profiles of Axin2+ and Axin2- cells from uninjured adult mouse liver were analysed by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: Roel

last: Nusse


title: RAG Represents a Widespread Threat to the Lymphocyte Genome - (ChIP-seq)

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

summary: The RAG1 endonuclease, together with its cofactor RAG2, is essential for V(D)J recombination but is a potent threat to genome stability.  The sources of RAG1 mistargeting and the mechanisms that have evolved to suppress it are poorly understood.  Here, we report the surprising finding that RAG1 binds to thousands of sites in the genome of developing lymphocytes, primarily at active promoters and enhancers.  The genome has responded by reducing the abundance of "cryptic" recombination signals near sites of RAG1 binding. This depletion operates specifically on the RSS heptamer, with nonamers enriched at RAG1 binding sites.  Reversing this RAG-driven depletion of cleavage sites by insertion of strong recombination signals creates an ectopic hub of RAG-mediated V(D)J recombination and chromosomal translocations.  Our findings delineate rules governing RAG binding in the genome, identify areas at risk of RAG-mediated damage, and highlight the evolutionary struggle to accommodate programmed DNA damage in developing lymphocytes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RAG1,RAG2 and H3K4me3 ChIP-seq profiles of human thymocytes, mouse thymocytes and preB cells, and Abelson pre-B cell line treated with STI-571

first: Grace

last: Teng

first: Wolfgang

last: Resch

first: Min

last: Kim

first: Arito

last: Yamane

first: Jason

last: Qian

first: Kyong-Rim

last: Kieffer-Kwon

first: Malay

last: Mandal

first: Yanhong

last: Ji

first: Eric

last: Meffre

first: Marcus

middle: R

last: Clark

first: Lindsay

last: Cowell

first: Rafael

last: Casellas

first: David

last: Schatz


title: RAG Represents a Widespread Threat to the Lymphocyte Genome - (Mnase-seq)

overall_design: MNase-seq profiles of mouse thymocytes


title: Transcriptome and cistrome analysis reveals synergistic roles for Sox9 and Pdx1 in lineage allocation of foregut progenitor cells

first: Maike

last: Sander


title: RAG Represents a Widespread Threat to the Lymphocyte Genome - (RNA-seq)

overall_design: RNA-seq profiles of mouse thymocytes


title: Quantification of RNA editing in the Drosophila Genetic Reference Panel

city: Stanford

first: Gokul

last: Ramaswami

address: 300 Pasteur Drive Alway M305

institute: Stanford University

summary: We report the application of mmPCR-seq to male whole body samples from 131 strains of the DGRP. We quantified RNA editing at 605 different loci using a microfluidic multiplex PCR method coupled with deep sequencing.

overall_design: RT-PCR amplification of 605 loci from 131 fly strains to quantify RNA editing levels.


title: FOXA2 regulates a network of genes involved in critical functions of intestinal epithelia

first: Ann

last: Harris

address: 2430 N Halsted Street Box 211

institute: Lurie Children's Hospital of Chicago Research Center

summary: Background and Aims: The forkhead box A (FOXA) family of pioneer transcription factors is critical for the development of many endoderm-derived tissues including the lung and the liver. Here we investigate the role of FOXA2 in regulating intestinal epithelial cell function. Methods: ChIP-seq was used to identify FOXA2 binding sites genome-wide. Targets of FOXA2 were validated using ChIP-qPCR and siRNA-mediated depletion of FOXA1/2 followed by RT-qPCR.  A luciferase-based assay was used to measure intracellular cAMP after FOXA1/2 modulation.Results: Peaks of FOXA2 occupancy were frequent at loci contributing to gene ontology pathways of regulation of cell migration, cell motion, and plasma membrane function. Depletion of both FOXA1 and FOXA2 led to a significant reduction in the expression of multiple transmembrane proteins including ion transporters. One of the targets was the adenosine A2B receptor, and reduced receptor mRNA levels were associated with a functional decrease in intracellular cAMP. We also observed that 30% of FOXA2 binding sites contained a GATA motif and that FOXA1/A2 depletion reduced GATA-4, but not GATA-6 protein levels. Conclusions: These data show that FOXA2 plays a critical role in regulating intestinal epithelial cell function. FOXA2 depletion affects the expression of ion transporters and other transmembrane proteins, which form a network essential for maintaining normal ion and solute transport. Moreover, we show that the FOXA and GATA families of transcription factors may work cooperatively to regulate gene expression genome-wide.

overall_design: To determine the role of FOXA2 in regulating gene expression in intestinal epithelial cells, ChIP-seq was performed for FOXA2 in Caco2 (colorectal adenocarcinoma) cells.

first: Nehal

last: Gosalia

first: Rui

last: Yang

first: Jenny

middle: L

last: Kerschner


title: Zelda determines chromatin accessibility during the Drosophila maternal-to-zygotic transition

city: Madison

first: Melissa

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

summary: We used FAIRE-seq to perform genome-wide profiling of open chromatin in 2-3 hour Drosophila embryos lacking maternal ZLD (zldM-) and in paired control embryos (yw). We demonstrate that ZLD is required to establish or maintain specific regions of open chromatin. Using single embryo RNA-seq data (from stage 5 yw and zldM- embryos) we show that loci that lose accessibility in zldM- embryos require ZLD for robust expression of associated genes.  By comparing our FAIRE peaks to publicly available ChIP data (Xu et al. 2014) we demonstrate that ZLD is required for binding of the transcription factor Bicoid. To our surprise, not all ZLD-bound loci are less accessible in the mutant, suggesting that these regions rely on additional factors for open chromatin. These constitutively accessible ZLD-bound sites are enriched for the GAGA factor (GAF) binding motif, and we therefore propose that GAF may provide this additional function. We conclude that ZLD functions like a pioneer factor to define the cis-regulatory regions that drive gene expression during the MZT.

overall_design: Open chromatin profiling of 2-3 hour Drosophila embryos: embryos lacking maternal ZLD (zldM-, 3 replicates) and paired control embryos (yw, 2 replicates); Genomic DNA Inputs. Sequencing performed on Illumina HiSeq 2000.

first: Katharine

middle: N

last: Schulz

first: Eliana

last: Bondra

first: Jacqueline

last: Villalta

middle: D

last: Lieb

first: Tommy

last: Kaplan

first: Daniel

last: McKay


title: Transcription Dynamically Patterns the Meiotic Chromosome-Axis Interface

city: Vienna

first: Franz

last: Klein

address: Dr. Bohrg. 9

department: Chromosome Biology

country: Austria

institute: University of Vienna, MFPL

summary: Meiotic chromosomes are highly compacted yet remain transcriptionally active. To understand how chromosome folding accommodates transcription, we investigated the assembly of the axial element, the proteinaceous structure that compacts meiotic chromosomes and promotes recombination and fertility. We found that the axial element proteins of budding yeast are flexibly anchored to chromatin by the ring-like cohesin complex and biased towards small chromosomes by a separate modulating mechanism that requires the conserved axial-element component Hop1. The ubiquitous presence of cohesin at sites of convergent transcription provides well-dispersed points for axis attachment and thus compaction. Axis protein enrichment at these sites directly correlates with the propensity for recombination initiation. Importantly, axis anchoring by cohesin is adjustable and readily displaced in the direction of transcription by the transcriptional machinery. We propose that such robust but flexible tethering allows the axial element to promote recombination while easily adapting to changes in chromosome activity.

overall_design: 7 genome wide meiotic ChIP-seq sets: V5-Red1 DNA interaction (V5-Red1-ChIP),  V5-Red1 DNA interaction in the absence of axis protein Hop1 (V5-Red1-ChIP, hop1delta),  V5-Red1 DNA interaction in the absence of another two axis proteins Hop1 and Rec8 (V5-Red1-ChIP, hop1delta rec8delta), Rec8-HA DNA interaction (Rec8-HA-ChIP), Rec8-HA DNA interactionin the absence of Red1 (Rec8-HA-ChIP, red1delta), and 2 untagged control (V5-untagged-ChIP, HA-untagged-ChIP) (corresponding to the main Figure5)

first: Xiaoji

last: Sun

first: Lingzhi

last: Huang

first: Tovah

last: Markowitz

first: Hannah

last: Blitzblau

first: Doris

last: Chen

first: Andreas

last: Hochwagen


title: Global identification of the gene networks and cis-regulatory elements of the cold response in zebrafish

city: Shanghai

first: Peng

last: Hu

address: Huchenghuan Road 999

country: China

institute: Shanghai Ocean University

summary: The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold-responsive transcriptional patterns have been determined in fishes, the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures, ranging from normal (28°C) to mild (18°C) and severe (10°C) cold, using RNA-seq. The tissues varied in the number of cold-responsive genes, of which the kidney appeared to be most sensitive, whereas the brain was the least. Fuzzy k-means clustering revealed 34 gene clusters of distinct expression patterns, demonstrating diverse tissue-specific responses in conjunction with multiple aspects of ubiquitous cross-tissue responses to cold. Thirty-one GO terms were over-represented upon cold treatment. These terms are involved in basic cellular processes, such as RNA splicing and proton transport, as well tissue-specific processes, such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis-regulatory elements governing the concerted cold responses, the promoters of the genes that demonstrated strong co-regulation were analyzed using an enriched motif discovery program, DREME. Eleven motifs, 6 known and 5 novel, were identified. These motifs belong to the genes corresponding to the 16 over-represented GO terms identified above. Some motifs, such as the AP-1 and STAT1 binding sites, are known to be stress responsive. By integrating comprehensive cold-induced transcriptional changes with a cis-motif identification tool, we identified genome-wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts.

overall_design: Examination of gene expression of 24 samples (eight tissues at three temperatures)

first: Liangbiao


title: Characterization of gene expression involved in pig reproduction

city: Jokioinen

first: Anu

last: Sironen

address: Myllytie 1

department: Biotechnology and Food Research

country: Finland

institute: Agrifood Research Finland

summary:
Purpose: Recent development in high-throughput sequencing techniques (RNA-seq) has enabled large scale analysis of genetic variations and gene expression in different tissues and species, but gene expression patterns and genetic variations in livestock have not yet been well characterized. In this study we have used high-throughput transcriptomic sequencing of the Finnish Yorkshire to identify gene expression patterns within the breed in the testis and oviduct.
Methods: The Solid 4 reads were mapped against the pig genome build 10.2 using the colorspace alignment tool provided by Applied Biosystems and distributed with the instrument (LifeScope v2.1). Reads associated with ribosomal RNA, transfer RNA, repeats and other uninformative reads were filtered out during the process as well as reads with more than 10 potential alignments. After alignment to the reference genome, low mapping quality reads were discarded (mapQV(<10)) and unique reads were associated with known genes based on UCSC annotations, and the number of reads aligned within each gene was counted. FPKM values were calculated for normalization of the data to remove variation between samples caused by non-biological reasons using the Cufflinks software v2.0.2.
Results: The analysis of gene expression differences between the testis and oviduct highlighted 1,234 genes up-regulated in the testis and 1,501 in the oviduct.
Conclusions: The RNA-seq technology used in this study provides novel information about transcript expression and differential gene expression in the testis and oviduct. The produced data will assist in the identification of candidate genes based on association mapping results within the pig population and provides insights into the expression of genes in the two reproductive organs studied.

overall_design: Testis and oviduct mRNA profiles of adult WT and immotile short tail sperm (ISTS) affected Finnish Large White pigs were generated by deep sequencing using Solid 4 platform.

last: Fischer

first: Asta

last: Laiho

first: Attila

last: Gyenesei


title: Function and regulation of Cph2 in Candida albicans [ChIP-Seq]

status: Public on Aug 05 2015

city: Irvine

first: Haoping

last: Liu

address: Med. Sci. I, Rm D234

department: Dept. of Biological Chemistry

institute: University of California

summary: Candida albicans is associated with humans as both a harmless commensal organism and a pathogen. Cph2 is a transcription factor whose DNA binding domain is similar to mammalian sterol response element binding proteins (SREBPs). SREBPs are master regulators of cellular cholesterol levels, and are highly conserved from fungi to mammals. However, ergosterol biosynthesis is regulated by the zinc finger transcription factor Upc2 in C. albicans and several other yeasts. Cph2 is not necessary for ergosterol biosynthesis, but important for colonization in the murine gastrointestinal tract. Here we demonstrate that Cph2 is a membrane-associated transcription factor that is processed to release the N-terminal DNA binding domain like SREBPs; but its cleavage is not regulated by cellular levels of ergosterol or oxygen. ChIP-Seq shows that Cph2 binds to the promoters of HMS1 and other components of the regulatory circuit for GI tract colonization. In addition, 50% of Cph2 targets are also bound by Hms1 and other factors of the regulatory circuit. Several common targets function at the head of the glycolysis pathway. Thus, Cph2 is an integral part of the regulatory circuit for GI colonization that regulates glycolytic flux. RNA-seq shows a significant overlap in genes differentially regulated by Cph2 and hypoxia, and Cph2 is important for optimal expression of some hypoxia-responsive genes in glycolysis and the citric acid cycle. We suggest that Cph2 and Upc2 regulate hypoxia-responsive expression in different pathways, consistent with a synthetic lethal defect of the cph2 upc2 double mutant in hypoxia.

overall_design: Genome binding/occupancy profiling by high throughput sequencing. ChIP-seq of Cph2 was carried out in a wild-type strain carrying N-terminal myc-tagged Cph2 under the MAL2 promoter (MAL2-myc-Cph2N). IP and INPUT samples from 2 independent experiments, as well as a sample of untagged wild-type control, were sequenced.

first: Shelley

last: Lane

first: Pietro

last: Di Lena

first: Pierre

last: Baldi


title: Dietary selenium levels affect selenoprotein expression and support the interferon-γ and IL-6 immune response pathways in mice [RNA-Seq]

first: Michael

last: Howard

overall_design: RNA-Seq analysis of liver tissue from mice fed Se-deficient or Se-adequate diets

first: Petra

last: Tsuji

first: Dolph

last: Hatfield

first: Bradley

last: Carlson


title: Expression analysis of leafy spurge crown buds during seasonal dormancy transitions.

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

summary: This submission contains the RNAseq data from a study of leafy spurge crown buds transitioning through a seasonal dormancy time course where buds transitioned from paradoprmancy to endodormancy and then to ecodormancy. The sequences in this study were mapped to an assembled transcriptome built from sequences from this study along with sequences from : 1) A study of leafy spurge crown buds through a time course for paradormancy release induced by excision of the aerial portion of the shoot (Series GSE71317). 2) A study identical to this study but where leafy spurge plants were first treated with glyphosate (Series GSE71406). 3) A previously submitted study of leafy spurge shoots following treatment with glyphosate was also used to assemble the transcriptome (Series GSE56509).

overall_design: This crown buds transitioning through a seasonal dormancy time course study has 4 biological replicates collected at each of the three dormancy states (paradormant, endodormant, and ecodormant).

first: Münevver

last: Doğramacı

first: James

middle: V

last: Anderson

first: Wun

last: Chao

first: Alvaro

last: Hernandez

middle: A

last: Mikel

last: Foley


title: Expression analysis of leafy spurge crown buds during seasonal dormancy transitions after glyphosate treatments.

summary: This submission contains the RNAseq data from a study of leafy spurge crown buds transitioning through a seasonal dormancy time course following glyphosate treatments where buds transitioned from paradoprmancy to endodormancy and then to ecodormancy. The sequences in this study were mapped to an assembled transcriptome built from sequences from this study along with sequences from : 1) A study of leafy spurge crown buds through a time course for paradormancy release induced by excision of the aerial portion of the shoot (Series GSE71317). 2) A study identical to this study but where leafy spurge plants were not treated with glyphosate (Series GSE71321). 3) A previously submitted study of leafy spurge shoots following treament with glyphosate was also used to assemble the transcriptome (Series GSE56509).

overall_design: This crown buds transitioning through a seasonal dormancy time course following a glyphosate treatment study has 4 biological replicates collected at each of the three dormancy states (paradormant, endodormant, and ecodormant).

middle: P

first: Jame

middle: S


title: The microRNA signature of mouse spermatozoa is dynamically modified during epididymal maturation

city: Callaghan

first: Bettina

last: Mihalas

state: NSW

address: Level 4 Life Science Building, University Drive

department: Life Sciences

country: Australia

institute: University of Newcastle

type: Non-coding RNA profiling by high throughput sequencing

summary: In recent years considerable effort has been devoted to understanding the epigenetic control of sperm development leading to an increased appreciation of the importance of RNA interference pathways, and in particular microRNAs (miRNAs), as key regulators of spermatogenesis and epididymal maturation. It has also been shown that sperm are endowed with an impressive array of miRNA that have been implicated in various aspects of fertilization and embryo development. However, to date there have been no reports on whether the sperm miRNA signature is static or whether it is influenced by their prolonged maturation within the male reproductive tract. To investigate this phenomenon we employed next generation sequencing to systematically profile the miRNA signature of maturing mouse spermatozoa. In so doing we have provided the first evidence for the dynamic post-testicular modification of the sperm miRNA profile under normal physiological conditions. Such modifications include the apparent loss and acquisition of an impressive cohort of some 113 and 115 miRNAs, respectively between the proximal and distal epididymal segments. Interestingly, the majority of these changes occur late in maturation and include the uptake of novel miRNA species in addition to a significant increase in many miRNAs natively expressed in immature sperm. Since sperm are not capable of de novo transcription these findings identify the epididymis as an important site in establishing the sperm epigenome with the potential to condition the peri-conceptual environment of the female reproductive tract, contribute to the inheritance of acquired characteristics, and/or alter the developmental trajectory of the resulting offspring.

overall_design: Examination of the microRNA expression profile in sperm thoughout the mouse epididymis and mouse using next generation sequencing in duplicate.

first: Brett

last: Nixon

first: Simone

middle: J

last: Stanger

first: Jackson

last: Reilly

first: Amanda

first: Sonika

last: Tyagi

first: Janet

last: Holt

first: Eileen

last: McLaughlin


title: H3K27ac ChIP-Seq in ALL-SIL

city: Ghent

first: Kaat

last: Durinck

address: Corneel Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Center for Medical Genetics

summary: The T-cell leukemia homeobox 1 (TLX1, HOX11) transcription factor is critically involved in the multistep pathogenesis of T-cell acute lymphoblastic leukemia (T-ALL) and often cooperates with NOTCH1 activation during malignant T-cell transformation. However, the exact molecular mechanisms by which these T-cell specific oncogenes cooperate during transformation remain to be established. Here, we used an integrative genomics approach to show that the oncogenic properties of TLX1 are mediated by genome-wide interference with the ETS1 and RUNX1 transcription factors. Partial disruption of ETS1 and RUNX1 activity by ectopic TLX1 expression in immature thymocytes drives repression of T-cell specific super-enhancers and mediates an unexpected transcriptional antagonism with NOTCH1 signaling. These phenomena coordinately trigger a TLX1 driven pre-leukemic phenotype in human thymic precursor cells, which corresponds with the in vivo thymic regression observed in murine TLX1 tumor models, and creates a strong genetic pressure for acquiring activating NOTCH1 mutations as a prerequisite for full leukemic transformation. In conclusion, our results uncover a functional antagonism between cooperative oncogenes during the earliest phases of tumor development and provide novel insights in the multistep pathogenesis of TLX1 driven human leukemia.

overall_design: ChIP-sequencing data was generated for H3K27ac in the T-ALL cell line ALL-SIL.

first: Joni

last: Van der Meulen

first: Wouter

last: Van Loocke

first: Maté

last: Ongenaert

first: Pieter

last: Rondou

first: Frank

last: Speleman

last: Van Vlierberghe


title: DNA methylation in mammalian placentas

city: Davis

first: Janine

last: LaSalle

address: Medical Microbiology and Immunology

institute: UC Davis

type: Methylation profiling by high throughput sequencing

summary: Over the last 20-80 million years the mammalian placenta has taken on a variety of morphologies through both divergent and convergent evolution.  Recently we have shown that the human placenta genome has a unique epigenetic pattern of large partially methylated domains (PMDs) and highly methylation domains (HMDs) with gene body DNA methylation positively correlating with level of gene expression.  In order to determine the evolutionary conservation of DNA methylation patterns and transcriptional regulatory programs in the placenta, we performed a genome-wide methylome (MethylC-seq) analysis of human, rhesus macaque, squirrel monkey, mouse, dog, horse, and cow placentas as well as opossum extraembryonic membrane.  We found that, similar to human placenta, mammalian placentas and opossum extraembryonic membrane have globally lower levels of methylation compared to somatic tissues.  However, not all species have clear PMD/HMDs in their placentas.  Instead what is conserved is higher methylation over the bodies of genes involved in mitosis, vesicle-mediated transport, protein phosphorylation, and chromatin modification compared with the rest of the genome.  As in human placenta, high gene body methylation is associated with higher gene expression across species.  Analysis of DNA methylation in mouse and cow oocytes shows the same pattern of gene body methylation over many of the same genes as in the placenta, suggesting that this conserved pattern of active gene body methylation of the placenta may be established very early in development.

sample_organism:
Macaca mulatta
Homo sapiens
Canis lupus familiaris
Equus caballus
Bos taurus
Mus musculus
Monodelphis domestica
Saimiri boliviensis

overall_design: MethylC-seq on placentas of 7 mammals, trophoblasts of rhesus, brains of 3 mammals, oocytes of cow, and human cordblood

first: Diane

middle: I

last: Schroeder

middle: M


title: TLX1 ChIP-Seq in ALL-SIL

overall_design: ChIP-sequencing data was generated for TLX1 in the T-ALL cell line ALL-SIL.


title: High-throughput sequencing of mouse liver transcriptome in Clock mutant animals

city: Philadelphia

first: Nicholas

last: Lahens

state: PA

address: Smilow Center for Translational Research 10-110 3400 Civic Center Blvd, Bldg 421

department: ITMAT

institute: University of Pennsylvania

summary: Circadian profile of polyA RNA by RNA-Seq, collected from ClockΔ19 mouse liver at CT22, CT28, CT34, CT40. RNA from three livers pooled per time point.

overall_design: 4 Clock mutant samples with no replicates

middle: F

first: Michael

last: Hughes

first: Heekyung

last: Hong

first: Gregory

last: Grant

first: Brian

last: Gregory

first: Joe

last: Takahashi

first: John

last: Hogenesch


title: High-throughput sequencing of mouse liver transcriptome.

summary: Circadian profile of polyA RNA by RNA-Seq, collected from mouse liver at CT23, CT29, CT35, CT41, CT47, CT53, CT59, CT65. RNA from three livers pooled per time point.

overall_design: 8 wildtype samples with no replicates.


title: Hematopoietic differentiation is required for initiation of acute myeloid leukemia [ATAC-seq]

status: Public on Aug 04 2015

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: Leukemia initiating cells (LICs) of acute myeloid leukemia (AML) may arise from self-renewing hematopoietic stem cells (HSCs) and from committed progenitors. However, it remains unclear how leukemia-associated oncogenes instruct LIC formation from cells of different origins and if differentiation along the normal hematopoietic hierarchy is involved. Here, using murine models with the driver mutations MLL-AF9 or MOZ-TIF2, we found that regardless of the transformed cell types, myelomonocytic differentiation to the granulocyte macrophage progenitor (GMP) stage is critical for LIC generation. Blocking myeloid differentiation through disrupting the lineage-restricted transcription factor C/EBPa eliminates GMPs, blocks normal granulopoiesis, and prevents AML development. In contrast, restoring myeloid differentiation through inflammatory cytokines “rescues” AML transformation. Our findings identify myeloid differentiation as a critical step in LIC formation and AML development, thus guiding new therapeutic approaches.

overall_design: Examination of chromatin accessibility in Cebpa knock-out and control conditions.

first: Min

last: Ye

first: Daniel

middle: G

last: Tenen


title: Drosophila Larval Brain RNA sequencing of ablation versus activation of E347 neurons

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

summary: RNA sequencing data for replicates of E347 driver control, E347 neuronal ablation per Shi dominant-negative expression and activation per NachBac expression to identify differences in RNA abundancy

first: Tânia

last: Reis


title: RNA-seq of control and foxo3b MO zebrafish cells.

city: Beijing

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

institute: Beijing Institute of Genomics

summary: Gata1+ cells isolated from control and foxo3b MO zebrafish at 24 and 48hpf were subjected to RNA-seq and related analyses.

overall_design: Gata1-GFP zebrafish stran was utilized, embryos were injected with foxo3b MO and standard MO at one-cell stage. Gata1+ cells were selected by FACS at 24 and 48hpf and submitted to RNA-seq and related analyses.

first: Xiangdong

last: Fang


title: RAG Represents a Widespread Threat to the Lymphocyte Genome

first: Yaakov

last: Maman

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

overall_design: Refer to individual Series


title: Notch1 dose modulates endothelial gene expression

city: Cincinnati

first: Raphael

last: Kopan

state: Ohio

address: 3333 Burnet Avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital

summary:
Purpose: To use RNA-Seq analysis of endothelial cell in various Notch1 alllels in order to determine transcrptional differencesas a consequence of Notch dose.
Methods: Using a FACS sorting  we generated high-throughput RNA-SEQ data of endothelials in various Notch1 alleles during development
Results: Notch1 dose can alter gene expression in a subset of endothelial genes

overall_design: RNA-Seq was performed on endothelial cells isolated at e9.5 from embryos with various Notch1 alleles including N1+/+, N1+/-, N1+/vg, N112/vg, N112/-

first: Liu

last: Zhenyi

first: Eric

middle: W

last: Brunskill


title: Ground state conditions induce rapid reorganization of core pluripotency factor binding that precede global epigenetic reprogramming

city: Munich

first: Michael

middle: Johannes

last: Ziller

address: Kraepelinstrasse 2-10

department: Translational Psychiatry

country: Germany

institute: Max Planck Institute of Psychiatry

summary: Mouse embryonic stem cells (mESCs) cultured under serum/LIF conditions exhibit heterogeneous expression of pluripotency-associated factors that can be overcome by two inhibitors (2i) of the MEK and GSK3 pathway, respectively. Several studies have shown that the  “ground state” induced by 2i is characterized by global hypomethylation and specific transcriptional profiles, but little is known about the contributing effectors. Here we show that 2i conditions rapidly alter the global binding landscape of OCT4, SOX2 and NANOG. The dynamic binding influences enhancer activity and shows enrichment for regulators linked to Wnt and Erk signaling. Epigenomic characterization provided limited insights to the immediate transcriptional dynamics suggesting these are likely more secondary effects. Likewise, knock-out of the PRC2 component EED to prevent H3K27me3 deposition had minimal effect on the transcriptome, rendering it largely dispensable for continued repression of bivalent genes and de novo silencing in 2i.

overall_design: ChIP-Seq for Oct4, Sox2,Nanog, H3K4me3, H3K27me3 and RNA-Seq in mouse embryonic stem cells cultured serum and 2i conditions

first: Alex

last: Meissner


title: Expression analysis of leafy spurge crown buds during dormancy transitions and release.

first: David

last: Horvath

summary: This submission contains the RNAseq data from one (just the study on paradormancy release) of several studies used to assemble the leafy spurge tranacriptome. These assembled transcrptome was built from 1) A study of leafy spurge crown buds through a time course for paradormancy release induced by excision of the aerial portion of the shoot (this study). 2) A study of leafy spurge crown buds through a seasonal dormancy time course where buds transitioned from paradoprmancy to endodormancy and then to ecodormancy (Series GSE71321). 3) A study identical to #2 above but where leafy spurge plants were first treated with glyphosate (Series GSE71406). 4) A previously submitted study (Series GSE56509) of leafy spurge shoots following treament with glyphosate was also used to assemble the transcriptome.

overall_design: The paradormancy study (#1) contained 4 time points (0hr, 6h, 1d, 3d) with 3 biological replicates at 0hr and 4 biological replicates at each of the other time points.

first: James

last: Anderson

first: Wun

last: Chao

first: Münevver

last: Doğramacı

middle: E

last: Foley

first: Alvaro

last: Hernandez

last: Mikel


title: Liver transcriptome analysis of the large yellow croaker under fasting or temperature treatment by RNA-seq

city: Taizhou

first: Baoying

last: Qian

state: Zhejiang

address: 1139 Shifu Road, Jiaojiang, Taizhou, Zhejiang 318000, P. R. China

department: School of life science

institute: Taizhou University

summary: We sequenced mRNA from 4 liver samples of the large yellow croaker (Larimichthys crocea) taken from thermal stress treatment fish, normal temperature treatment fish, cold stress treatment fish and fasting stress treatment fish, respectively, to investigate the transcriptome and comparative expression profiles of the large yellow croaker liver undergoing thermal stress, cold stress and fasting.

overall_design: Liver mRNA profiles of control group (LB2A), thermal stress group (LC2A), cold stress group (LA2A) and 21-day fasting group (LF1A) were generated by RNA-seq, using Illumina HiSeq 2000.

first: Liangyi

last: Xue


title: ChIP-seq analyses of 10 quorum sensing regulators in Pseudomonas aeruginosa

city: Hong Kong

first: Xin

last: Deng

address: To Yuen Building

department: Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: The Pseudomonas aeruginosa quorum-sensing (QS) systems contribute to bacterial homeostasis and pathogenicity. Although many regulators have been characterized to control the production of virulence factors and QS signaling molecules, its detailed regulatory mechanisms still remain elusive. Here, we performed chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) on 10 key QS regulators. The direct regulation of these genes by corresponding regulator has been confirmed by Electrophoretic mobility shift assays (EMSAs) and quantitative real-time polymerase chain reactions (qRT-PCR). Binding motifs are found by using MEME suite and verified by footprint assays in vitro. Collectively, this work provides new cues to better understand the detailed regulatory networks of QS systems.

overall_design: ChIP-seq of 10 QS regulators in Pseudomonas aeruginosa


title: Epigenetic profiling of well differentiated and dedifferentiated liposarcoma identifies H3K9me3 and Kruppel-like factor 6 (KLF6) as determinants of aggressiveness in sarcoma

city: Houston

first: Kadir

middle: Caner

last: Akdemir

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center


title: Transcriptional regulation of Tet1 during development

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

country: Italy

institute: University of Torino

summary: 5-hydroxymethylcytosine (5hmC) is a recently discovered epigenetic modification that is lost in human cancers. Formation of 5hmC is catalysed by the Ten eleven translocation (TET) proteins that mediate the sequential oxidation of 5-methylcytosine (5mC) to 5hmC, leading to eventual DNA demethylation. Several mechanisms can lead to loss of 5hmC in cancers, including mutations in IDH or TET2 genes. However, little is known about the role of TET proteins and 5hmC in adult cells. Here, we report that TET1 downmodulation is required to permit adult cells to proliferate. TET1 is rapidly downmodulated in proliferating primary cells and in regenerating liver. TET1 silencing accelerates cell cycle progression while its constitutive expression inhibits cell growth. TET1 is a negative regulator of cell proliferation and it is regulated during development in tissue specific manner. These findings enlarge our knowledge on how one epigenetic modification such as the DNA hydroxymethylation mediated by TET1 is a key player on the control of cell proliferation.

overall_design: Examination of 5hmC in MEF at passage 0 and at passage 5.

first: Salvatore

last: Oliviero


title: Epigenetic profiling of well differentiated and dedifferentiated liposarcoma identifies H3K9me3 and Kruppel-like factor 6 (KLF6) as determinants of aggressiveness in sarcoma (ChIP-seq)

summary: Little is known about the epigenomics of liposarcoma (LPS).  Here, we profiled the global expression of 9 epigenetic marks in well differentiated (WD) and dedifferentiated (DD) LPS from 151 patients and found increased H3K9me3 among DDLPS tumors.  We performed ChIP-seq and gene expression profiling of patient derived cell lines to discover functionally significant regions of differential H3K9me3 enrichment between WDLPS and DDLPS associated with concomitant gene expression changes.

overall_design: We performed genome-wide transcriptional profiling of H3K9me3 in dedifferentiated liposarcoma DDLPS and well differentiated liposarcoma WDLPS cell lines.

middle: C

first: Emily

middle: Z

last: Keung

first: Lynda

last: Chin


title: Development of gene expression signatures

first: Kaat

last: Durinck


title: Alterations in serum microRNA in humans with alcohol use disorders impact cell proliferation and cell death pathways and predict structural and functional changes in brain [rat miRNA-Seq]

city: Syracuse

first: Frank

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: We performed a global analysis of extracellular miRNAs in the serum of human subjects diagnosed with Alcohol Use Disorder (AUD) to identify robust biomarkers of early brain damage or dysfunction. This was performed in a set of 20 AUD subjects and 10 age-matched controls. They were subjected to comprehensive medical, neuropsychological and neuroimaging tests, followed by comparison of miRNA levels found in peripheral blood serum. The levels of miRNAs were quantified using two independent high-throughput methods: Affymetrix microarray and Illumina next-generation RNA-sequencing. Cross-species validation was performed using rat drinking models and mouse neural stem cell culture models, with tissue specificity of the serum miRNAs examined using additional RNA-sequencing of serum and body tissues in untreated rats. This data series includes the rat brain and body tissue miRNA data obtained from RNA-sequencing only and is part of a larger SuperSeries (GSE71579) now being curated at GEO

overall_design: A total of 20 RNA-sequencing libraries were run on small RNA obtained from untreated (control) postnatal day 35 male Long Evans Hooded rats. These libraries were derived from 16 different tissues including an entire brain hemisphere, hindlimb muscle, lung, heart, kidney, thymus, pancreas, subcutaneous abdominal fat, stomach, testes, liver, skin, spleen, large intestine and small intestine.  Tissues were dissected and stored in RNAlater (Sigma), and subsequently homogenized prior to miRNA purification. The miRNAs from 3 different rats were pooled together to generate a specific miRNA profile for each tissue, except for the brain hemispheres and serum samples which were run individually.

first: Cherry

last: Ignacio

first: Steven

middle: D

last: Hicks

first: Patrick

last: Burke

first: Lambert

last: Lewis

first: Zsuzsa

last: Szombathyne-Meszaros


title: Stickleback embryos use ABC transporters as a buffer against exposure to maternally derived cortisol

status: Public on Aug 03 2015

city: Urbana

first: Alison

last: Bell

state: Illinois

address: Justin Smith Morrill Hall, 505 S Goodwin Ave #393

department: Animal Biology

institute: University of Illinois at Urbana Champaign

summary:
Purpose: Offspring from females that experience stressful conditions during reproduction often exhibit altered phenotypes and many of these effects are thought to arise due to increased exposure to maternal glucocorticoids. Here we used RNAseq to test whether the embryonic transcriptional response to increased levels of cortisol was similar to the transcriptional response to maternal stress in sticklebacks
Methods: Eggs were treated by immersing eggs for 30 mins in water that contained 0, 5, or 10 ug/L, which represented baseline, predator induced, and super physiological levels of maternally derived cortisol. To isolated enough RNA for RNAseq, 10 embyros from each clutch/treatment were pooled prior to RNA extraction for a total of 18 pools (6 clutches x 3 treatments).
Results: Analysis of genome-wide transcriptional profiles suggests that 17251 (genes which survived a cut-off of having cpm more than 1 in at least two samples; and had a significant likelihood ratio calculated in edgeR) genes out of the possible 22,456 genes in the stickleback genome were expressed in 72-hour embryos. However, we did not detect any differences in gene expression between embryos that were treated with cortisol compared to the control group.

overall_design: mRNA profiles of egg clutches treated with 0, 5, or 10 ug/L are compared, which represented baseline, predator induced, and super physiological levels of maternally derived cortisol.

first: Ryan

middle: T

last: Paitz

first: Syed

last: Bukhari


title: Transcriptome dynamics of developing photoreceptors in 3-D retina cultures recapitulates temporal sequence of human cone and rod differentiation revealing cell surface markers and gene networks

city: Bethesda

first: Matthew

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: To define molecular mechanisms underlying rod and cone differentiation, we generated H9 human embryonic stem cell line carrying a GFP reporter that is controlled by the promoter of cone-rod homeobox (CRX) gene, the first known marker of post-mitotic photoreceptor precursors. CRXp-GFP reporter in H9 line replicates endogenous CRX expression when induced to form self-organizing 3-D retina-like tissue. We define temporal transcriptome dynamics of developing photoreceptors during the establishment of cone and rod cell fate. Our studies provide an essential framework for delineating molecules and cellular pathways that guide human photoreceptor development and should assist in chemical screening and cell-based therapies of retinal degeneration.

overall_design: Undifferentiated CRXp-GFP HP hES cells and 3D-neural retina were collected at days 37, 47, 67 and 90 and dissociated into single cells. Cells were sorted at 4°C and by FACSAria (Becton Dickinson). GFP+ and GFP- cells were separately collected. Total RNA was extracted by RNA purification kit (Norgen Biotek) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: 7.7-9.2) was subjected to libraries construction using 40-60 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.

first: Rossukon

last: Kaewkhaw

first: Koray

last: Kaya

first: Kohei

last: Homma

first: Jizhong

last: Zou

first: Vijender

last: Chaitankar

first: Mahendra

last: Rao

first: Anand

last: Swaroop


title: Genome-wide mapping of Collier in vivo binding sites highlights its hierarchical position in different transcription regulatory networks

city: Toulouse

first: Yannick

last: Carrier

address: 118, route de narbonne

country: France

institute: CNRS

summary: Collier, the single Drosophila COE (Collier/EBF/Olf-1) transcription factor, is required in several developmental processes, including head patterning and specification of muscle and neuron identity during embryogenesis. To identify direct Collier (Col) targets in different cell types, we used ChIP-seq to map Col binding sites throughout the genome, at mid-embryogenesis. In vivo Col binding peaks were associated to 415 potential direct target genes. Gene Ontology analysis revealed a strong enrichment in proteins with DNA binding and/or transcription-regulatory properties. Characterization of a selection of candidates, using transgenic CRM-reporter assays, identified direct Col targets in dorso-lateral somatic muscles and specific neuron types in the central nervous system. These data brought new evidence that Col direct control of the expression of the transcription regulators apterous  and eyes-absent (eya) is critical to specifying neuronal identities. They also showed that cross-regulation between col and eya in muscle progenitor cells is required for specification of muscle identity, revealing a new parallel between the myogenic regulatory networks operating in Drosophila and vertebrates. Col regulation of eya, both in specific muscle and neuronal lineages, may illustrate one mechanism behind the evolutionary diversification of Col biological roles.

overall_design: Fixed nuclear extract of stage 13-14 whole drosophila embryo were submit to Chromatine Immunoprecipitation with a mix of three COL monoclonal antibodies. As control a non relevent antibody (anti-HA) was used. Precipitated DNA was submit to Illumina high-throughput sequencing.

first: Mathilde

last: de Taffin

first: Laurence

last: Dubois

first: Laetitia

last: Bataillé

first: Anaïs

last: Painset

first: Stéphanie

last: Le Gras

first: Bernard

last: Jost

first: Michèle

last: Crozatier

first: Alain

last: Vincent


title: Widespread association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova


title: Allelome.PRO A pipeline to define allele-specific genome features

city: Vienna, Austria

first: Daniel

last: Andergassen

address: Lazarettgasse 14, AKH BT 25.3

institute: CeMM Research Center for  Molecular Medicine of the  Austrian Academy of Sciences

summary: We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results.

overall_design: Defining allele-specific genome features from F1 E12.5 mouse embryonic fibroblasts

first: Christoph

last: Dotter

first: Quanah

last: Hudson

first: Florian

last: Pauler


title: Widespread association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth [ChIP-Seq]

summary: The goal of this study was to identify YAP/TAZ direct transcriptional targets and transcriptional partners, through ChIP-sequencing and gene expression profiling.

overall_design: ChIP-seq analysis of YAP, TAZ, TEAD4 and JUN in MDA-MB-231 cells. Two independent replicates were analysed for each TF, as well as for negative controls.

first: Mattia

last: Forcato

first: Francesca

last: Zanconato

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo


title: Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

status: Public on Aug 20 2015

city: Stanford

first: Fabian

last: Grubert

address: 300 Pasteur Drive

institute: Stanford University

summary: Deciphering the impact of genetic variants on gene regulation is fundamental to understanding human disease. Although gene regulation often involves long-range interactions, it is unknown to what extent non-coding genetic variants influence distal molecular phenotypes. Here, we integrate chromatin profiling for three histone marks in lymphoblastoid cell lines (LCLs) from 75 sequenced individuals with LCL-specific Hi-C and ChIA-PET-based chromatin contact maps to uncover one of the largest collections of local and distal histone quantitative trait loci (hQTLs). Distal QTLs are enriched within topologically associated domains and exhibit largely concordant variation of chromatin state coordinated by proximal and distal non-coding genetic variants. Histone QTLs are enriched for common variants associated with autoimmune diseases and enable identification of putative target genes of disease-associated variants from genome-wide association studies. These analyses provide insights into how genetic variation can affect human disease phenotypes by coordinated changes in chromatin at interacting regulatory elements.

overall_design: To identify genetic variants underlying chromatin variability in humans we mapped quantitative trait loci for three different histone marks (H3K4me3, H3K4me1 and H3K27ac) in lymphoblastoid cell lines (LCL) derived from 76 individuals. These individuals have been extensively genotyped by the 1000 genomes project as part of the Yoruban population (YRI). We integrated previously published RNA and DNase data for these individuals to elucidate the interplay between chromatin variation and gene expression. Additionally we performed chromatin interaction assays (HiC and ChIA-PET) in one individual to investigate the contribution of 3D proximity to genetic regulation.

first: Judith

middle: B

last: Zaugg

first: Maya

last: Kasowski

first: Oana

last: Ursu

first: Damek

middle: V

last: Spacek

first: Alicia

middle: R

last: Martin

first: Peyton

last: Greenside

first: Rohith

last: Srivas

first: Doug

middle: H

last: Phanstiel

first: Aleksandra

last: Pekowska

first: Nastaran

last: Heidari

first: Ghia

last: Euskirchen

first: Wolfgang

last: Huber

first: Jonathan

middle: K

last: Pritchard

first: Carlos

last: Bustamante

first: Lars

last: Steinmetz

first: Anshul

last: Kundaje

first: Michael

last: Snyder


title: BAF250a regulates nucleosome occupancy and histone modification in priming embryonic stem cell differentiation

city: Ann Arbor

first: Paul

last: Tang

state: MI

address: 2800 Plymouth Road

department: Cardiac surgery

institute: University of Michigan

summary: BAF complex is one major group of chromatin remodeling factors in mammals. However, how BAF regulated nucleosomes and other histone modifications is not clear. Here we delete BAF250a, a major component in esBAF to study the nucleosome and histone changes in ESCs. We find that deletion of BAF250a leads to nucleosome occupancy increase in TSS regions and non-pioneer transcription factor binding sites. BAF250a deletion also cause overall decrease of H3K27me3 modification. Collectively, these results reveals how BAF complex coordinates nucleosome, histone modification to control ESC function.

overall_design: Sample 1-4: Nucleosome profiles in WT and BAF250a KO ESCs. Sample 5-10: profiling of H3K4me3 and H3K27me3 in WT and BAF250 KO ESCs.

first: Ienglam

last: Lei

first: Jason

last: West

first: Xiaolin

last: Gao

first: Peng

last: Fang

last: Dennis

first: Robert

last: Kingston

first: Zhong

last: Wang


title: HP1β has distinct subnuclear localizations, chromatin binding features and functions in embryonic stem cells and differentiating cells

status: Public on Aug 02 2015

city: Jerusalem

first: Eran

last: Meshorer

address: Givat Ram

institute: The Hebrew University of Jerusalem


title: Stromal Fat4 acts non-autonomously with Dachsous1/2 to restrict the nephron progenitor pool

status: Public on Aug 01 2015

city: Toronto

first: Qun

last: Pan

address: 160 College St.

country: Canada

institute: University of Toronto

summary: Regulation of the balance between progenitor self-renewal and differentiation is critical to development. In the mammalian kidney, reciprocal signaling between three lineages (stromal, mesenchymal and ureteric) ensures correct nephron progenitor self-renewal and differentiation. Loss of either the atypical cadherin Fat4 or its ligand Dachsous1 (Dchs1) results in expansion of the mesenchymal nephron progenitor pool, called the condensing mesenchyme (CM). This has been proposed to be due to misregulation of the Hippo kinase pathway transcriptional co-activator YAP. Here, we use tissue-specific deletions to prove that Fat4 acts non-autonomously in the renal stroma to control nephron progenitors. We show that loss of Yap from the CM in a Fat4-null background does not reduce the expanded CM, indicating Fat4 regulates the CM independent of YAP. Analysis of Six2-/-;Fat4-/- double mutants demonstrates that excess progenitors in Fat4 mutants are dependent on Six2, a critical regulator of nephron progenitor self-renewal. Electron microscopy reveals that cell organization is disrupted in Fat4 mutants. Gene expression analysis demonstrates that the expression of  Notch and FGF pathway components are altered in Fat4 mutants. Finally, we show that Dchs1, and its paralog Dchs2 function in a partially redundant fashion to regulate the number of nephron progenitors. Our data supports a model in which FAT4 in the stroma binds to DCHS1/2 in the CM to restrict progenitor self-renewal.

overall_design: A total of 3 Fat4-/- mutant embryos and 3 wildtype (Fat4+/+) control embryos were examined. Two kidneys from each embryo was used thereby yielding a total of 6 Fat4-/- mutant kidneys and 6 Fat4+/+ wildype kidneys. All kidneys examined were at E13.5.

first: Mazdak

last: Bagherie-Lachidan

first: Antoine

last: Reginensi

first: Hitisha

middle: P

last: Zaveri

first: Daryl

middle: A

last: Scott

first: Benjamin

middle: J

last: Blencowe

first: Françoise

last: Helmbacher

first: Helen

last: McNeill


title: HP1β has distinct subnuclear localizations, chromatin binding features and functions in embryonic stem cells and differentiating cells [ChIP-seq]

summary: In recent years, several chromatin-related proteins have been shown to regulate ESC pluripotency and/or differentiation, although the role of the major heterochromatin proteins in pluripotency remains largely unknown. Here we identify heterochromatin protein 1-beta (HP1β) to be differentially localized and associated with chromatin in pluripotent and differentiated cells, to be essential for proper ESC differentiation as well as for the maintenance of the pluripotent state. Microscopy analysis supported by biochemical fractionations and chromatin immunoprecipitation (ChIP) experiments demonstrate that unlike its prominent localization in heterochromatic chromocenters in differentiated cells, HP1β is diffuse in the ESC nucleoplasm, poorly bound to chromatin, and highly expressed. The fraction of HP1β that does associate with chromatin in ESCs is highly enriched in genic regions. HP1β-knockout ESCs but not HP1α knockout ESCs exhibit a loss of the morphological and proliferative characteristics of embryonic pluripotent cells. HP1β depletion in ESCs results in reduced expression of pluripotency factors and aberrant differentiation. In contrast, HP1β depletion in differentiated cells perturbs the maintenance of differentiation, and facilitates reprogramming to induced pluripotent stem cells. Our results demonstrate a dual role for HP1β, in ESCs it is essential for pluripotency maintenance, and in differentiated cells for proper differentiation.

overall_design: ChIP-Seq of HP1β in mouse embryonic stem cells.

first: Jan

last: Mallm

first: Karsten

last: Rippe


title: Genome-wide analysis of wild type and gemin2 mutant plants [cold exposure]

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

summary: The goal of this study was to compare the transcriptional profile (RNA-seq) of wild type and gemin2 Arabidopsis mutants plants exposed to 10ºC for 0, 1 and 24 hours.

overall_design: WT and gemin2 mutant plants were grown for nine days under continuous white light at 22 degrees centigrades or exposed for 1 or 24 h to 10ºC on the 9th day, before harvesting. Then the transcriptional profile of these plants was analyzed using RNA-seq.

first: Ruben

last: Schlaen


title: Postnatal epigenetic development of mouse intestinal stem cells

status: Public on Aug 25 2015

first: Lanlan

last: Shen

address: 1100 Bates Ave.

institute: Baylor College of Medicine

summary: We used unbiased whole genome bisulfite sequencing (WGBS) to identify DNA methylation changes in the intestinal stem cells (ISCs) or their progeny during the suckling period of mouse colon development.

overall_design: Lgr5-EGFP mice were used to identify ISC populations in the colons. WGBS were performed using EGFP labeled Lgr5+ ISCs and epithelial cell adhesion molecule (EpCAM) labeled epithelial cells isolated at the beginning and end of the suckling period (postnatal day 0-P0 and P21).


title: Generation of low passage high grade serous ovarian cancer cell lines from primary tumors

city: Los Angeles

first: Sanaz

last: Memarzadeh

state: CA

address: 610 Charles E Young Dr East

department: Obstetrics and Gynecology

institute: UCLA

summary: High grade serous ovarian cancers (HGSC) are deadly malignancies that relapse despite carboplatin chemotherapy.  Many commercially ovarian cancer cell lines are not good models for HGSC. Here we demonstrate that 3 low passage cell lines derived from HGSC have similar transcriptomes to their parental bulk tumors. These cell lines recapitulated tumor characteristics of the primary cancer and had responded to therapy in the same manner as primary HGSC cells, demonstrating they are accurate models for HGSCs.

overall_design: mRNA profiles of low passage high grade serous tumor cell lines and their parental tumors, generated by next generation sequencing, were compared.

first: Jing

last: Lu

first: Deanna

middle: M

last: Janzen


title: Comparison of poly(A) and capture RNA-seq: controlled degradation in vitro

first: Marcin

middle: Piotr

last: Cieslik

state: Michigan

address: 500 S State St

department: Pathology

summary: We compare the performance of two library preparation protocols (poly(A) and exome capture) in in vitro degraded RNA samples

overall_design: VcaP cell were grown, and treated with MDV3100 (enzalutamide) or DHT (dihydrotestosterone), intact RNA was isolated and samples were prepared in technical triplicates using two library preparation protocol. Also cells were subject to in vitro degradation through incubation of the whole cell lysate in 37C for increasing amounts of time. Following incbation paired capture and poly(A) libraries were prepared.

first: Arul

last: Chinnaiyan


title: Genome-wide analysis of gemin2 mutant transcriptome

summary: The goal of this study was to compare the transcriptional profile (RNA-seq) of gemin2 Arabidopsis mutant with wild type plants grown under continous light conditions

overall_design: WT and gemin2 mutant plants were grown for nine days under continuous white light at 22 degrees centigrades and the transcriptional profile of these plants was analyzed using RNA-seq.


title: Apoptosis enhancing drugs overcome innate platinum resistance in CA125 negative tumor initiating populations of high grade serous ovarian cancer

summary: High grade serous ovarian cancers (HGSC) are deadly malignancies that relapse despite carboplatin chemotherapy. Here we show that 16 independent primary HGSCs contain a CA125 negative population enriched for carboplatin resistant cancer initiating cells. Transcriptome analysis reveals up-regulation of homologous recombination DNA repair and anti-apoptotic signals in this population. While treatment with carboplatin enriches for CA125 negative cells, co-treatment with carboplatin and birinapant eliminates these cells in HGSCs expressing high levels of the inhibitor of apoptosis protein cIAP in the CA125 negative population. Birinapant sensitizes CA125 negative cells to carboplatin by mediating degradation of cIAP causing cleavage of caspase-8 and restoration of apoptosis. This co-therapy significantly improved disease free survival in vivo compared to either therapy alone in tumor-bearing mice. These findings suggest that therapeutic strategies that target CA125 negative cells may be useful in the treatment of HGSC.

overall_design: mRNA profiles of CA125 positive and negative populations, generated by next generation sequencing of populations FACS isolated from 10 independent dissociated primary human high grade serous ovarian cancers, were compared.


title: Genome-wide analysis of wild type and gemin2 mutant plants exposed to cold

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

overall_design: Refer to individual Series


title: Noncanonical Genomic Imprinting Effects In Offspring

city: Salt Lake City

first: Christopher

last: Gregg

state: Utah

address: 323 Wintrobe Bldg 530, 20 North 1900 East

department: Neurobiology & Anatomy

institute: University of Utah

summary: We report genomic imprinting effects in the arcuate nucleus, dorsal raphe nucleus, liver and muscle of adult female mice

overall_design: Examination of allele-specific gene expression hybrid mice generated from reciprocal crosses of CastEiJ x C57BL/6J mice


title: Comparative transcriptome profiling of Arabidopsis lyrata and Arabidopsis thaliana

city: Olomouc - Holice

first: Ales

last: Pecinka

address: Slechtitelu 31

department: Centre of Plant Structural and Functional Genomics

country: Czech Republic

institute: Institute of Experimental Botany

summary:
Arabidopsis thaliana and Arabidopsis lyrata are two closely related Brassicaceae species, which are used as models for plant comparative biology. They differ by lifestyle, predominant mating strategy, ecological niches and genome organization. In order to explore molecular basis of specific traits, we performed RNA-sequencing of vegetative rosettes from both species. Additionally, we sequenced apical meristems and inflorescences of A. lyrata that allow for intra-specific transcriptome comparison in several major developmental stages.

Please view also related dataset GSE69077 (RNA-sequencing of heat stressed A. lyrata  and A. thaliana plants).

sample_organism:
Arabidopsis thaliana
Arabidopsis lyrata subsp. lyrata

overall_design: Arabidopsis lyrata and Arabidopsis thaliana aerial tissues were collected from mock treated plants, total RNA isolated and poly-A RNA populations sequenced

first: Ahmed

last: Abdelsamad

first: Björn

last: Pietzenuk

first: Vimal

last: Rawat

first: Korbinian

last: Schneeberger


title: Transcriptomic measurements of Nannochloropsis oceanica CCMP1779 through a light:dark cycle

city: East Lansing

first: Eric

middle: Robert

last: Poliner

address: 612 Wilson Road

country: USA

institute: Michigan State University

summary: Nannochloropsis oceanica CCMP1779 is a marine unicellular stramenopile and an emerging reference species for basic research on oleogenic microalgae with biotechnological relevance. We investigated its physiology and transcriptome under light/dark cycles. We observed oscillations in lipid content and a predominance of cell division in the first half of the dark phase. Globally, more than 60% of the genes cycled in N. oceanica CCMP1779, with gene expression peaking at different times of the day. Interestingly, the phase of expression of genes involved in certain biological processes was conserved across photosynthetic lineages. Furthermore, in agreement with our physiological studies we found the processes of lipid metabolism and cell division enriched in cycling genes. For example, there was tight coordination of genes involved in the lower part of glycolysis, fatty acid synthesis and lipid production at dawn preceding lipid accumulation during the day. Our results suggest that diel lipid storage plays a key role for N. oceanica CCMP1779 growth under natural conditions making this alga a promising model to gain a basic mechanistic understanding of triacylglycerol production in photosynthetic cells. Our data will help the formulation of new hypotheses on the regulation transcriptional control of cell growth and metabolism in Nannochloropsis.

overall_design: Nannochloropsis oceanica CCMP was entrained to 12:12 light:dark cycles and biological replicates collected every 3 hours for a cycle for a total of 16 samples.

first: Nicholas

last: Panchy

first: Linsey

last: Newton

first: Guangxi

last: Wu

first: Andrew

last: Lapinsky

first: Blair

last: Bullard

first: Agnieszka

last: Zienkiewicz

first: Christoph

last: Benning

first: Shin-Han

last: Shiu

first: Eva

last: Farré


title: Dnmt3l-knockout donor cells improve somatic cell nuclear transfer reprogramming efficiency

city: Taipei City

first: Shau-Ping

last: Lin

state: select a state

address: 4F, No. 81, Chang-Xing St.,

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

summary: We found that Dnmt3l-KO donor cells display decreased levels of H3K9me3 and H3K27me3 accumulation, higher level of active histone mark H3K27ac and increased cytoplasmic localization of HDAC1, implicating a permissive epigenetic state beneficial for nuclear reprogramming.

overall_design: To investigate the gene expression profiles of MEFs and to find out the potential genes responsible for the improvement of Dnmt3l-KO cloned embryos.

first: Hung

middle: F

last: Liao

first: Chu

last: Mo

first: Shinn

first: Dai

last: Cheng

first: Chih

middle: Y

last: Yu

first: Kai

middle: W

last: Chang

first: Tzu

last: Kao

first: Chia

last: Lu

first: Marina

last: Pinskaya

first: Antonin

last: Morillon

first: Shih

middle: S

first: Winston

first: Deborah

last: Bourchis

first: Timothy

last: Bestor

first: Li

last: Sung

first: Shau


title: RNA Proximity Ligation to Resolve Intramolecular RNA Structures in situ

city: San Francisco

first: Vijay

last: Ramani

state: California

department: Biochemistry & Biophysics

institute: UCSF

summary: Proof-of-concept of a new method involving the limited digestion and subsequent ligation of intramolecular RNA structures in situ followed by deep sequencing

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens

overall_design: Proof-of-concept of RPL in S. cerevisiae and H. sapiens tissue culture

first: Jay

last: Shendure


title: RNA-sequencing in OS-RC-2 cells under the knockdown of Arkadia or ESRP2

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

country: Japan

institute: University of Tokyo

summary: Tumor-specific alternative splicing is implicated in the progression of cancer, including clear cell renal cell carcinoma (ccRCC). Using ccRCC RNA-sequencing data from The Cancer Genome Atlas, we found that epithelial splicing regulatory protein 2 (ESRP2), one of the key regulators of alternative splicing in epithelial cells, is expressed in ccRCC. ESRP2 mRNA expression did not correlate with the overall survival rate of ccRCC patients, but the expression of some ESRP-target exons correlated with the good prognosis and with the expression of Arkadia (also known as RNF111) in ccRCC. Arkadia physically interacted with ESRP2, induced polyubiquitination, and modulated its splicing function. Arkadia and ESRP2 suppressed ccRCC tumor growth in a coordinated manner. Lower expression of Arkadia correlated with advanced tumor stages and poor outcomes in ccRCC patients. This study thus reveals a novel tumor-suppressive role of the Arkadia-ESRP2 axis in ccRCC.

overall_design: Expression of mRNA in a ccRCC cell line OS-RC-2 under the knockdown of Arkadia or ESRP2. Knock-down of ESRP2 was confirmed by RT-PCR because of low expression of ESRP2 which resulted in non-quantitative FPKM value.

first: Anna

last: Mizutani

first: Hiroyuki

last: Seimiya

first: Kohei

last: Miyazono


title: Dysregulation of Endometrial Inflammation Precedes the Development of Cytological Endometritis [mRNA]

city: Dunsany

first: Kieran

middle: Gerard

last: Meade

state: Co. Meath

address: Grange

department: Animal Bioscience Research Department

country: Ireland

institute: Teagasc

summary: The regulation of endometrial inflammation has important consequences for the resumption of bovine fertility post-partum. All cows experience bacterial influx into the uterus after calving; however a significant proportion fail to clear infection leading to the development of cytological endometritis (CE) and compromised fertility. We hypothesised that early immunological changes could not only act as potential prognostic biomarkers for the subsequent development of disease but also shed light on the pathogenesis of endometritis in the post-partum dairy cow. Here, next-generation sequencing from endometrial biopsies taken at 7 days post-partum (DPP) identified significant expression of inflammatory genes in all cows. Despite the common inflammatory profile and enrichment of the Toll-like receptor, NFκB and TNF signalling pathways, 73 genes and 31 miRNAs differentiated between healthy cows (HC, n=9) and cows which subsequently developed CE at 7 DPP (n=6, FDR<0.1). In healthy cows, 4197 differentially expressed genes between 7 and 21 DPP whereas only 31 genes were differentially expressed in samples from cows with CE. At 21 DPP, a further 1167 genes were differentially expressed between HC cows and cows diagnosed with CE (FDR<0.1). These changes in host gene expression reflected culture-independent microbiological analysis which showed significant differences in uterine bacterial profiles between groups. Inflammatory activity was not confined to the uterus; decreased circulating granulocytes and increased Acute Phase Protein (SAA and HP) plasma expression levels were detected at 7 DPP in cows that developed CE. In conclusion, our data suggests that the major inflammatory cascade activated early post-partum is resolved thereby restoring homeostasis in healthy cows by 21 DPP, but this transition fails to occur in cows which develop CE. Despite a common inflammatory profile, differential expression of specific immune genes may identify cows at risk of prolonged inflammation and the development of CE post-partum.

overall_design: Sixteen Holstein Friesian cows, of mixed parity, within the same university dairy herd were sampled 7 and 21 days postpartum (DPP) in the morning after milking, over an eight week period.

first: Cathriona

last: Foley

first: Aspinas

last: Chapwanya

first: John

last: Callanan

first: Ronan

last: Whiston

first: Raul

last: Miranda-CasoLuengo

first: Wim

middle: G

last: Meijer

first: Junnan

first: David

last: Lynn

first: Cliona

last: O’ Farrelly


title: The Cushing's disease adipose gene expression profile reveals effects of long term glucocorticoids on adipose tissue lipid, protein and glucose metabolism

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

institute: St. Jude Children's Research Hospital

summary: Glucocorticoids have major effects on adipose tissue metabolism. To study tissue mRNA expression changes induced by chronic elevated endogenous glucocorticoids, we performed RNA sequencing on subcutaneous adipose tissue from patients with Cushing’s disease (n=5) compared to patients with non-functioning pituitary adenomas (n=11). We found higher expression of transcripts involved in several metabolic pathways, including lipogenesis, proteolysis and glucose oxidation as well as decreased expression of transcripts involved in inflammation and protein synthesis. To further study this in a model system, we subjected mice to dexamethasone treatment for 12 weeks and analyzed their inguinal (subcutaneous) fat pads, which led to similar findings.  Additionally, mice treated with dexamethasone showed drastic decreases in lean body mass as well as increased fat mass, further supporting the human transcriptomic data. These data provide insight to transcriptional changes that may be responsible for the co-morbidities associated with chronic elevations of glucocorticoids

overall_design: DESIGN: Patients with cushing's (n=5) or non-functioning pituitary adenoma (n=11) were prospectively observed from March 2011 to June 2012.

middle: T

first: Dave

last: Bridges


title: Dysregulation of Endometrial Inflammation Precedes the Development of Cytological Endometritis [miRNA]

last: Lu


title: Reversal of microRNA-150 silencing disadvantages crizotinib-resistant NPM-ALK-positive cell growth.

city: toulouse

first: Coralie

last: Hoareau-Aveilla

address: 2 avenue Hubert Curien

department: CRCT

institute: INSERM

summary: We used bisulfite conversion and Illumina sequencing to analyse miR-150 DNA methylation pattern lost in cells treated with decitabine, a demethylating agent, Crizotinib, an inhibitor of  of ALK activity or siALK

overall_design: Targeted bisulfite conversion and Illumina sequencing in two cell lines bearing the t(2;5)(p23;q35)

first: F

last: Meggetto

first: C


title: Effect of OVO-like 1 knockdown on global transcript expression in differentiated BeWo trophoblast cells

city: London

first: Stephen

last: Renaud

state: Ontario

address: 1151 Richmond St, MSB428

institute: University of Western Ontario

summary: We had previously discovered that the transcription factor OVO-like 1 (OVOL1) was highly induced during trophoblast differentiation. In this study, we used an lentiviral shRNA strategy to decrease OVOL1 expression in BeWo trophoblast cells. Control cells were transduced with shRNAs targeting no known mammalian transcript (shCont). Following stimulation of differentiation (48h exposure to 8-bromo-cyclic adenosine monophosphate), a RNA-seq approach was used to determine global transcript differences in OVOL1-knockdown cells compared to control cells.

overall_design: Trophoblast cells transduced with control shRNAs were used as controls. Cells transduced with shRNAs targeting OVOL1 were used as treatment. All cells received 250 uM 8-bromo-cyclic adenosine monophosphate to stimulate differentiation. Three independent replicates of control and treatment groups were analyzed.

first: Michael

last: Soares


title: Dysregulation of Endometrial Inflammation Precedes the Development of Cytological Endometritis

first: Kieran


title: Antagonistic interaction between androgen signaling and vitamin D signaling in prostate cancer [ChIP-Seq]

city: Chicago

first: Yuwen

last: Liu

state: IL

address: 900 East 57th Street. KCDB building. Room 10250

department: Human Genetics

institute: University of Chicago

summary: Vitamin D induces anti-proliferative and differentiating effects in prostate cancer. Thus calcitriol, the hormonally active form of Vitamin D, and its analogs have been extensively studied in prostate cancer cells. Yet despite its importance, relatively little is known about the genome-scale mechanisms by which Vitamin D, through its cognate nuclear vitamin D receptor (VDR), exerts its regulatory functions at the genomic level. In this study, we defined VDR transcriptional networks in the LNCaP prostate cancer cell line by mapping the genomic binding sites of VDR and by identifying differentially expressed genes upon calcitriol treatment. We found that VDR and androgen receptor (AR) antagonistically regulate a subset of cell cycle-related genes that are over-expressed in prostate cancer tumors. The expression balance of these genes is partially regulated through the competition dynamics between AR and VDR binding to shared cis-regulatory elements. On such shared elements, we found that FOXA1 mediates this competition by serving as a pioneering factor for both AR and VDR binding. We also found significant enrichment of AR-, VDR-, and AR/VDR overlapping binding sites in prostate cancer-associated single-nucleotide polymorphism (SNP) intervals identified from genome-wide association studies (GWAS), providing genetic evidence to link AR, VDR and their crosstalk to prostate cancer susceptibilities. In particular, we found that in a cis-regulatory element of the RFX6 gene implicated in prostate cancer progression, an allelic variant increases prostate cancer risk by switching the antagonism between AR and VDR into a synergistic interaction.

overall_design: Examination of AR, VDR, and FOXA1 binding in LNCaP cells, in biological replicates

first: Kevin

last: White


title: RNA-sequencing in HEK293T cells under the knockdown of Arkadia or ESRP2

first: Daizo

last: Koinuma

summary: We evaluated the role of Arkadia and ESRP2 in HEK293T cells

overall_design: Expression of mRNA in HEK293T cells under the knockdown of Arkadia or ESRP2

first: Anna

last: Mizutani

first: Kohei

last: Miyazono


title: Subsets of NFkappaB-dependent genes are differentially regulated after combined treatment with hyperthermia and cytokine

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

summary: Heat shock transcription factor 1 (HSF1) is responsible for triggering stress-induced activation of the HSP genes. HSF1 is also involved in the regulation of many other genes associated with multiple cellular processes including cell signaling, development, fertility, cell death and metabolism, e.g. NFkappaB transcription factor. Here we aimed to establish a global picture for the association between hyperthermia-modulated expression of NFkappaB-dependent genes and HSF1 binding in regulatory regions of target genes. The global pattern of HSF1 binding was analyzed after 10 and 20 minutes of hyperthermia using the ChIP-Seq approach. The analysis revealed about 25,000 HSF1 binding sites in chromatin of control untreated U-2 OS cells, which nearly doubled in cells subjected to hyperthermia. The presence of hyperthermia-induced HSF1 binding was established in regulatory regions of hyperthermia-affected genes and in TNF-affected genes. In most cases hyperthermia pre-conditioning inhibited cytokine-mediated activation of NF-κB-dependent genes. However, our results also revealed novel gene subsets that included TNFalpha-regulated and hyperthermia-unaffected genes, as well as genes (co)repressed, (co)stimulated, or antagonized by both types of stimuli.

overall_design: On Illumina platform we sequenced DNA immunoprecipitated from U-2 OS cells using anti-HSF1 antibody. Cells were either untreated (control) or heat shocked for 10 and 20 minutes. Two PCR-verified ChIP replicates were collected per each sample.

first: Patryk

last: Janus

first: Stokowy

last: Tomasz

first: Widlak

last: Piotr


title: Characteristics of Long Non-coding RNAs in the Brown Norway Rat and Alterations in the Dahl Salt-Sensitive Rat

city: Shanghai

first: Feng

last: Wang

address: 600 Yishan Road

department: Nephrology

institute: Shanghai Jiao Tong University Affiliated Sixth People's Hospital

summary: Using poly(A)-independent and strand-specific RNA-seq, we identified approximately 1,500 to 1,800 lncRNAs expressed in each of the following tissues of Brown Norway rats: the renal cortex, renal outer medulla, liver, cardiac left ventricle, adrenal gland, and hypothalamus.

overall_design: Examination of several tissues of BN rats

first: Mingyu

last: Liang


title: Antagonistic interaction between androgen signaling and vitamin D signaling in prostate cancer


title: A comprehensive microRNA expression profile related to hypoxic adaptation in Tibetan pig

status: Public on Jul 31 2015

city: Beijing

first: Bo

last: Zhang

address: No. 2 Yuanmingyuan West Road, College Animal Science & Technology, China Agriculture University, Beijing

institute: China Agricultural University

summary: In this study, miRNA-seq technique was used to identify differentially expressed miRNAs (DE miRNAs) in cardiac muscle of the Tibetan pig (TP) and Yorkshire pig (YP), which were both raised in highland environments. We obtained 108 M clean reads and 372 unique miRNAs that included 210 known pre-miRNAs and 162 novel pre-miRNAs. In addition, 20 DE miRNAs, including 10 upregulated and 10 downregulated miRNAs, were identified by comparing TP and YP. Based on the expression abundance and differentiation between the two populations, we predicted their targets, and KEGG pathway analyses suggested that DE miRNAs between the Tibetan pigs and Yorkshire pigs are involved in hypoxia-related pathways, such as the MAPK, mTOR, and VEGF signaling pathways, cancer-related signaling pathways, etc. Five DE miRNAs were randomly selected to validate the veracity of miRNA-seq using real-time PCR. The results showed that the expression corresponds to the trend in miRNA-seq, hence the deep-sequencing methods were feasible and efficient. This study expanded the number of hypoxic-adaptation-related miRNAs in pig and indicated that the expression patterns of hypoxia-related miRNAs are significantly altered in the Tibetan pig. DE miRNAs may play important roles in hypoxic adaptation after migration to hypoxic environments.

overall_design: mRNA profiles of 6-month old Tibetan pig (TP) and Yorkshire pig (YP) were generated by deep sequencing, in duplicate, using Hiseq 2000.

first: Hao