title: LaSSO, a strategy for genome-wide mapping of intronic lariats and branch-points using RNA-seq

city: London

first: Danny

middle: Asher

last: Bitton

address: Darwin Building, Gower Street

department: Department of Genetics, Evolution & Environment

institute: University College London

summary: Both canonical and alternative splicing of RNAs is governed by intronic sequence elements and produces transient lariat structures fastened by branch-points within introns. To map precisely the location of branch-points on a genomic scale, we developed LaSSO (Lariat Sequence Site Origin), a data-driven algorithm which utilizes RNA-seq data. Using fission yeast cells lacking the debranching enzyme Dbr1, LaSSO not only accurately identified canonical splicing events, but also pinpointed novel, but rare, exon-skipping events, which may reflect aberrantly spliced transcripts. Compromised intron turnover perturbed gene regulation at multiple levels, including splicing and protein translation. Notably, Dbr1 function was also critical for the expression of mitochondrial genes, and for the processing of self-spliced mitochondrial introns. LaSSO showed better sensitivity and accuracy than algorithms used for computational branch-point prediction or for empirical branch-point determination. Even when applied to a human data set acquired in the presence of debranching activity, LaSSO identified both canonical and exon skipping branch-points. LaSSO thus provides an effective, accurate and unbiased approach for defining high-resolution maps of branch-site sequences and intronic elements on a genomic scale. LaSSO should be useful to validate introns and uncover branch-point sequences in any eukaryote, and it could be integrated to RNA-seq pipelines.

overall_design: Interrogation of the S. pombe transcriptome using rRNA depleted strand specific RNA sequencing (Illumina HiSeq 2000) in wild type and dbr1.Δ cultures. A total of 4 samples were analyzed: two biological repeates of wild-type strain and two biological repeats of dbr1.Δ

first: Daniel

middle: C

last: Jeffares

first: Charalampos

last: Rallis

first: Graeme

last: Smith

first: Yuan

middle: Y

last: Chen

first: Sandra

last: Codlin

first: Samuel

last: Marguerat

first: Jürg

last: Bähler


title: miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis [PARE-seq]

status: Public on Mar 18 2014

city: Cold Spring Harbor

first: Kate

middle: M

last: Creasey

state: NY

address: 1 Bungtown Road

department: Plant Sciences

country: USA

institute: Cold Spring Harbor Laboratory

type: Non-coding RNA profiling by high throughput sequencing

summary: Utilizing whole-genome Parallele Analysis of RNA Ends (PARE)-seq to analyze the degradome to assess miRNA-binding of transposons in DNA methylation mutants, and RNAi mutants, compared to wildtype.

overall_design: Genome-wide small RNA profiling was done by Illumina TruSeq sample preparation followed by high-throughput sequencing with Illumina HiSeq 2000 platform.

first: K

first: R

middle: A

last: Martienssen


title: Functional genomic analysis of the periodic transcriptome in the developing Drosophila wing.

status: Public on Mar 15 2014

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: A superseries of gene expression in early craniofacial development in mouse embryos at stages E8.5, E9,5, and E10.5.

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center


title: Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans

status: Public on Mar 14 2014

city: San Francisco

first: Dale

last: Muzzey

state: CA

address: 1700 4th Street BH403

department: Cellular & Molecular Pharmacology

institute: UCSF

summary: Though sequence differences between alleles are often limited to a few polymorphisms, these differences can cause large and widespread allelic variation at the expression level. Such allele-specific expression (ASE) has been extensively explored at the level of transcription but not translation. Here we measured ASE in the diploid yeast Candida albicans at both the transcriptional and translational levels using RNA-seq and ribosome profiling, respectively. Since C. albicans is an obligate diploid, our analysis isolates ASE arising from cis elements in a natural, non-hybrid organism, where allelic effects reflect evolutionary forces. Importantly, we find that ASE arising from translation is of a similar magnitude as transcriptional ASE, both in terms of the number of genes affected and the magnitude of the bias. We further observe coordination between ASE at the levels of transcription and translation for single genes. Specifically, reinforcing relationships—where transcription and translation favor the same allele—are more frequent than expected by chance, consistent with selective pressure tuning ASE at multiple regulatory steps. Finally, we parameterize alleles based on a range of properties and find that SNP location and predicted mRNA-structure stability are associated with translational ASE in cis. Since this analysis probes more than 4,000 allelic pairs spanning a broad range of variations, our data provide a genome-wide view into the relative impacts of cis elements that regulate translation.

overall_design: Two biological replicates of WT Candida albicans ribosome profiling and RNA-seq

first: Gavin

last: Sherlock

first: Jonathan

middle: S

last: Weissman


title: Genome-wide binding of the homeodomain transcription factor Sine oculis (So) in the Drosophila eye imaginal disc

status: Public on Mar 17 2014

city: Houston

first: Feng

last: Wang

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report genome-wide binding of the highly conserved TF Sine oculis (So), which is necessary for Drosophila eye development and has few previously known direct transcriptional targets. Our data identify novel putative targets of So-mediated regulation, including genes involved in multiple aspects of development.

overall_design: 2 biological replicates of ChIP-seq with anti-So antibody on chromatin from D. melanogaster third instar eye-antennal imaginal discs; negative control - same sample and ChIP-seq protocol without anti-So antibody

first: Barbara

last: Jusiak

first: Umesh

last: Karandikar

first: Su-Jin

last: Kwak

first: Hui

first: Rui

last: Mardon


title: Transcriptional comparison of the filamentous fungus Neurospora crassa growing on three major monosaccharides D-glucose, D-xylose and L-arabinose

city: Tianjin

first: Jingen

last: Li

address: Xiqi Dao 32, Tianjin Airport Economic Area

country: China

institute: Tianjin institute of industrial biotechnology,Chinses Academy of Sciences

summary: D-glucose, D-xylose and L-arabinose are three major monosaccharides in the plant cell wall. Complete utilization of all three sugars is still a bottleneck for second-generation cellulolytic bioethanol production, especially for L-arabinose. However, little is known about the gene expression profiles during L-arabinose utilization in fungi at genome-wide level and a comparison of the genome-wide fungal response to these three major monosaccharides has not yet been reported. To better understand the microbial response and utilization of L-arabinose for subsequent microbial engineering for co-fermentation all three sugars, we performed transcriptome analysis of N. crassa grown on L-arabinose, compared with that on D-xylose and D-glucose.

overall_design: RNA was extracted from cultures of N. carassa in early growth stage growing with D-glucose, L-arabinose or D-xylose as carbon source; duplicate cultures were sampled in some conditions.

first: Chaoguang

last: Tian


title: Major and Minor Group Human Rhinovirus Response in Human Macrophages

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

country: Netherlands

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

summary: Major- and minor-group rhinoviruses enter their host by binding to the cell surface molecules ICAM-1 and LDL-R, respectively, which are present on both macrophages and epithelial cells. Although epithelial cells are the primary site of productive HRV infection, previous studies have implicated macrophages in establishing the cytokine dysregulation that occurs during rhinovirus-induced asthma exacerbations. Even though major- and minor-group rhinoviruses are nearly genetically identical, these viruses do not replicate with equal success in monocyte-lineage cell lines. In human primary macrophages, differential mitochondrial activity and signaling pathway activation was observed between major- and minor-group rhinovirus upon initial HRV binding, indicating discordant receptor-dependent response to these rhinovirus types. As well, variances in phosphorylation of kinases (p38, JNK, ERK5) and transcription factors (ATF-2, CREB, CEBP-alpha) were observed between the major- and minor- group HRV treatments. The difference between major- and minor- group HRV activation of signaling pathways was confirmed through RNA-sequencing and observation of differential production of the asthma-relevant cytokines CCL20, CCL2, and IL-10. This is the first report of genetically similar viruses eliciting dissimilar cytokine release, transcription factor phosphorylation, and MAPK activation from macrophages. These results suggest that receptor dependence plays a role in establishing the inflammatory microenvironment initiated in part by monocytic-lineage cells in the human airway upon exposure to rhinovirus.

overall_design: RNA sequencing of monocyte-derived macrophages after mock infection or infection by HRV16 or HRV1A


title: Argonaute-bound small RNAs from promoter-proximal RNA Polymerase II

status: Public on Mar 13 2014

city: LOS ANGELES

first: Jesse

middle: R

last: Zamudio

address: 610 CHARLES E. YOUNG DRIVE EAST BOX 957239

department: MCDB

institute: University of California, Los Angeles

summary: Argonaute (Ago) proteins mediate post-transcriptional gene repression by binding  guide microRNAs (miRNAs) to regulate targeted RNAs. To confidently assess Agobound  small RNAs, we adapted a mouse embryonic stem cell system to express a single  inducible epitope-tagged Ago protein. Here, we report the small RNA profile of Agodeficient  cells and determine Ago-dependent stability is a common feature of mammalian  miRNAs. Considering both in vivo Ago-dependence for stability and Ago2 binding as  defined by immunopurification, we have identified a novel class of non-canonical  miRNAs derived from protein-coding gene promoters, which we name transcriptional  start site miRNAs (TSS-miRNAs). A subset of promoter-proximal RNA polymerase II  complexes produce hairpin RNAs that are processed in a DGCR8/Drosha-independent,  but Dicer-dependent manner. TSS-miRNA activity is detectable endogenously, upon  transfection of a mimic or by mRNA overexpression. Finally, we present evidence of  differential expression and conservation in humans, suggesting important roles in gene  regulation.

overall_design: Examination of Ago immunoprecipitations and mESC without Ago proteins


title: The miRNAome of the postpartum dairy cow liver in negative energy balance

city: Athenry

first: Dermot

middle: G

last: Morris

state: Co. Galway

address: Animal & Grassland Research and Innovation Centre, Mellows Campus

department: Animal Bioscience Research Department

country: Ireland

institute: Teagasc

summary: Negative energy balance (NEB) is an altered metabolic state in high yielding cows that occurs during the first few weeks postpartum when energy demands for lactation and maintenance exceed the energy supply from dietary intake. NEB can, in turn, lead to metabolic disorders and to reduced fertility. Alterations in the expression of more than 700 hepatic genes have previously been reported in a study of NEB in postpartum dairy cows. miRNAs (microRNA) are known to mediate many alterations in gene expression post transcriptionally. To study the hepatic miRNA content of postpartum dairy cows, including their overall abundance and differential expression, in mild NEB (MNEB) and severe NEB (SNEB) short read RNA sequencing was carried out.

overall_design: A NEB dairy cow model developed previously was used. In this model differential feeding and milking regimes were used to produce two groups of Holstein Friesian cows; MNEB and SNEB. Briefly, MNEB cows were fed ad libitum grass silage with 8 kg/day of a 21% crude protein dairy concentrate and milked once daily. SNEB cows were fed 25 kg/day silage with 4 kg/day concentrate and milked thrice daily. All procedures were carried out under license in accordance with the European Community Directive, 86-609-EC. Cows were slaughtered approximately 14 days postpartum (MNEB; 13.6 ± 0.75, range 11–15; SNEB 14.3 ± 0.56, range 13–16 ) and the entire liver was removed within 15 to 30 min.  Samples weighing approximately 1 g were dissected, rinsed in RNase-free phosphate buffer, snap-frozen in liquid nitrogen and stored at -80ºC. Liver tissue samples from 5 SNEB and 3 MNEB animals were used for miRNA library preparation.

first: Attia

last: Fatima

first: David

middle: J

last: Lynn

first: Padraic

last: O'Boyle

first: Cathal

last: Seoighe


title: Transcriptional profiles of experimentally evolved monogamous and polygamous Drosophila melanogaster

city: Columbia

first: Brian

last: Hollis

state: SC

address: 715 Sumter Street

department: Department of Biological Sciences

institute: University of South Carolina


title: Transcriptome sequencing analysis of pepper

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

summary: To facilitate the functional annotation of the pepper genome, we generated 90.84 Gb of RNA-Seq data from 33 libraries representing all major tissue types and developmental stages of Zunla 1, as well as fruits from other accessions with significant phenotypic differences.

sample_organism:
Capsicum annuum
Capsicum chinense
Capsicum annuum var. glabriusculum

overall_design: Pepper ‘Zunla 1’ and other inbred lines were grown in a greenhouse as described in Table S1, with their different developmental stages Plants at full-bloom stage were harvested for roots, stems, and leaves as the same as the samples for phased small RNAs (see text S3.4.2 for details). Mature plants were harvested for unopened flower buds (buds) and fully open flowers (flowers). Additional flowers were allowed to self-pollinate and fruit was harvested at four pre-breaker stages (1-3cm, 3-4cm, 4-5cm fruit length, and mature green), the breaker stage (when the fruit was turning red) and three post-breaker stages (3, 5, and 7 days after breaker). These samples will respectively be referred to as Root, Stem, Leaf, Bud, Flower, F-Dev-1, F-Dev-2, F-Dev-3, F-Dev-4, F-Dev-5, F-Dev-6, F-Dev-7, F-Dev-8, and F-Dev-9. Similar roots, stems, leaves, immature fruit and red fruit were harvested from other inbred lines from domesticated Capsicum species. Meanwhile, chiltepin plants were grown under long days at controlled temperature and RNA was extracted from a mix of leaves from four stages (seedling, early blooming, full bloom, and fruit breaker phases), a mix of flowers from unopened flower buds (buds) and fully open flowers (flowers), and fruit at breaker and breaker plus five days respectively. All tissues were frozen in liquid nitrogen and then stored at -80℃. Total RNA was isolated from different samples by using the Trizol Reagent (Invitrogen) according to manufacturer’s instructions. Strand-specific RNA-Seq library preparations were performed as previously described (39) with 12 independently bar-coded samples sequenced on one lane of an Illumina HiSeq2000 system. The 200 bp paired-end libraries were sequenced using Illumina HiSeq 2000 (90 bp PE).

first: Chen

last: Qin

first: Meng

last: Xu


title: Transcriptional profiling of Drosophila wing pouch following CR32027 RNAi

first: Chris

last: Seidel

summary: The eukaryotic cell cycle, driven by both transcriptional and post-translational mechanisms, is the central molecular oscillator underlying tissue growth throughout animals.  While genome-wide studies have investigated cell cycle-associated transcription in unicellular systems, global patterns of periodic transcription in multicellular tissues remain largely unexplored.  Here we define the cell cycle-associated transcriptome of the developing Drosophila wing epithelium and compare it with that of cultured Drosophila S2 cells, revealing a core set of periodic genes as well as a surprising degree of context-specificity in periodic transcription.  We further employ RNAi-mediated phenotypic profiling to define functional requirements for over 300 periodic genes, with a focus on those required for cell proliferation in vivo.  Finally, we investigate the role of novel genes required for interkinetic nuclear migration. Combined, these findings provide a global perspective on cell cycle control in vivo, and highlight a critical need to understand the context-specific regulation of cell proliferation. Two RNAi lines of CR32027, a non-coding RNA gene identified in this study, are examined for transcriptional changes relative to wt.

overall_design: Transcriptional profiles of two RNAi knockdowns, CR32027-IR1 and CR32027-IR2, are examined  in Drosophila wing pouch relative to OreR wt in triplicate by RNA Seq.

first: Liang

last: Liang

first: Jeff

last: Haug

first: Matthew

last: Gibson


title: Small RNA sequencing analysis of pepper

summary: To facilitate the functional annotation of the pepper genome, analysis of miRNAs was performed for the sequenced data from five small RNA libraries described above, representing five different tissues. Starting with a set of 5,436 plant mature miRNA sequences available in miRBase, we annotated with high confidence 176 pepper miRNAs from 64 families, of which 30 families are computationally predicted to target TFs, suggesting important roles of these miRNA families in post-transcriptional gene regulation and transcription networks consistent with previous findings.

overall_design: To identify genomic regions generating small RNAs, we applied previously described analytical strategies to five small RNA libraries from different tissues. Developing roots, stems and mature leaves were collected from plants grown in soil in a green house at 22 °C with a 16 hr light cycle and harvested from plants at full-bloom stage. Mature plants were harvested for fully open flowers. Additional flowers were allowed to self-pollinate and fruit was harvested in the breaker stage (thirty days after pollination when the fruit was turning red). Total RNA for different tissues was isolated from the frozen root samples by using the Trizol Reagent (Invitrogen) according to manufacturer’s instructions, and libraries were constructed using the Small RNA Sample Prep Kit (Illumina, San Diego, CA) as previously described, then sequenced on an Illumina HiSeq2000 system.

first: Cheng


title: The SWI/SNF Complex Regulates the PRDM Protein Hamlet to Ensure Lineage Directionality in Drosophila Neural Stem Cells

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

summary: Members of the SWI/SNF chromatin-remodeling complex are among the most frequently mutated genes in human cancer. SWI/SNF complex controls self-renewal and differentiation in stem cell lineages but how this function relates to tumorigenesis is currently unclear. Here, we use Drosophila neuroblasts to demonstrate that the SWI/SNF component Osa (ARID1) prevents tumorigenesis in stem cell lineages by ensuring correct unidirectional lineage progression. Our transcriptome anaysis identifies Ham as a key Osa target gene.

overall_design: comparison of transcriptomes of wild type Drosophila melanogaster larval type II NB lineages (excluding neurons) and osa RNAi type II lineages containing mainly NB-like cells and INPs

first: Elif

last: Eroglu

first: Juergen

last: Knoblich


title: miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis

first: Kate

last: Creasey

type: Methylation profiling by high throughput sequencing


title: Pseudo-temporal ordering of individual cells reveals regulators of differentiation

status: Public on Mar 23 2014

city: Cambridge

first: Cole

last: Trapnell

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: Single-cell expression profiling by RNA-Seq promises to exploit cell-to-cell variation in gene expression to reveal regulatory circuitry governing cell differentiation and other biological processes.  Here, we describe Monocle, a novel unsupervised algorithm for ordering cells by progress through differentiation that dramatically increases temporal resolution of expression measurements. This reordering unmasks switch-like changes in expression of key regulatory factors, reveals sequentially organized waves of gene regulation, and exposes regulators of cell differentiation. A functional screen confirms that a number of these regulators dramatically alter the efficiency of myoblast differentiation, demonstrating that single-cell expression analysis with Monocle can uncover new regulators even in well-studied systems.

overall_design:
We selected primary human myoblasts as a model system of cell differentiation to investigate whether ordering cells by progress revealed new regulators of the process. We sequenced RNA-Seq libraries from each of several hundred cells taken over a time-course of serum-induced differentiation.
Please note that this dataset is a single-cell RNA-Seq data set, and each cell comes from a capture plate.  Thus, each well of the plate was scored and flagged with several QC criteria prior to library construction, which are provided as sample characteristics; CONTROL indicates that this library is a off-chip tube control library constructed from RNA of approximately 250 cells and 'DEBRIS' indicates that the well contained visible debris (and may or may not include a cell). Libraries marked DEBRIS thus cannot be confirmed to come from a single cell.

first: Davide

last: Cacchiarelli

first: Jonna

last: Grimbsby

first: Prapti

last: Pokharel

first: Shuqiang

last: Li

first: Michael

last: Morse

first: Tarjei

last: Mikkelsen

first: John

last: Rinn


title: Epigenomic Alterations Define Lethal CIMP positive Ependymomas of Infancy

first: Stephen

middle: Mack

last: Christopher

state: TX

address: 1102 Bates Avenue C1030.02

department: Pediatrics

summary: Ependymomas are common childhood brain tumors that occur throughout the nervous system, but are most common in the pediatric hindbrain.  Current standard therapy comprises surgery and radiation, but not cytotoxic chemotherapy as it does not further increase survival.  Whole-genome and whole-exome sequencing of 47 hindbrain ependymomas reveals an extremely low mutation rate, and zero significant recurrent somatic SNVs.  While devoid of recurrent SNVs and focal copy number aberrations, poor prognosis hindbrain ependymomas exhibit a CpG island methylator phenotype (CIMP). Transcriptional silencing driven by CpG methylation converges exclusively on targets of the polycomb repressor complex 2 (PRC2) that represses expression of differentiation genes through tri-methylation of H3K27. CIMP-positive (CIMP+) hindbrain ependymomas are responsive to clinical drugs that target either DNA or H3K27 methylation both in vitro and in vivo.  We conclude that epigenetic modifiers are the first rational therapeutic candidates for this deadly malignancy, which is epigenetically de-regulated but genetically bland.

overall_design: 10 primary posterior fossa ependymomas have been analyzed

last: Mack

middle: D

last: Taylor


title: The transcription factor GATA3 is critical for the development of all IL-7Ra-expressing innate lymphoid cells (ILCs) and maintenance of type 2 ILCs

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: Innate lymphoid cells (ILCs) play critical roles during innate immune responses to pathogens and lymphoid organ development. IL-7Ra+ ILC subsets, similar to T helper (Th) cell subsets, produce distinctive effector cytokines. The molecular control of IL-7Ra+ ILC development and maintenance has yet to be dissected. Here we report that GATA3 is indispensable for the development of all IL-7Ra+ ILC subsets and T cells. Gata3 conditional deficient mice have no lymph nodes and are susceptible to Citrobactor rodentium infection. Genome-wide gene analyses indicate that GATA3 regulates similar set of cytokines and receptors in ILC2s and Th2 cells and is critical for the maintenance of ILC2s. Thus, GATA3 plays parallel roles in establishing and regulating both adaptive and innate lymphocytes.

overall_design: To identify GATA3 regulated genes in type 2 innate lymphoid cells by tamoxifen-mediated acute deletion of Gata3 gene.

first: Yagi

last: Ryoji

first: Zhong

last: Chao

first: Northrup

last: Daniel

first: Yu

last: Fang

first: Bouladoux

last: Nicolas

first: Spencer

last: Sean

first: Hu

last: Gangqing

first: Barron

last: Luke

first: Sharma

last: Suveena

first: Belkaid

last: Yasmine

first: Zhao

last: Keji

first: Zhu

last: Jinfang


title: Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes

city: Berkeley

first: Jason

middle: T

last: Huff

address: 211 Koshland Hall

department: Plant & Microbial Biology

institute: University of California, Berkeley

summary: Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints.

sample_organism:
Phaeodactylum tricornutum
Emiliania huxleyi
Cryptococcus neoformans
Leishmania major
Thalassiosira pseudonana
Micromonas pusilla
Bathycoccus prasinos
Aureococcus anophagefferens
Cyanidioschyzon merolae
Fragilariopsis cylindrus
Ostreococcus sp. 'lucimarinus'

overall_design: DNA methylation, RNA and nucleosome sequencing data for diverse eukaryotes

first: Daniel

last: Zilberman


title: The histone methyltransferase activity of MLL1 is dispensable for hematopoiesis and leukemogenesis

status: Public on Apr 03 2014

city: Aurora

first: Patricia

last: Ernst

state: CO

institute: University of Colorado

summary: Despite correlations between histone methyltransferase (HMT) activity and gene regulation, direct evidence that HMT activity is responsible for gene activation is sparse. We address the role of the HMT activity for MLL1, a histone H3 lysine 4 (H3K4) methyltransferase critical for maintaining hematopoietic stem cells (HSCs). Here we show that the SET domain and thus HMT activity of MLL1 is dispensable for maintaining HSCs and for supporting leukemogenesis driven by the MLL-AF9 fusion oncoprotein. Upon Mll1 deletion, histone H4 lysine 16 (H4K16) acetylation was selectively depleted at MLL1 target genes in conjunction with reduced transcription. Surprisingly, inhibition of SIRT1 was sufficient to prevent the loss of H4K16 acetylation and the reduction in MLL1 target gene expression. Thus, recruited MOF activity, and not the intrinsic HMT activity of MLL1, is central for the maintenance of HSC target genes. In addition, this work reveals a role for SIRT1 in opposing MLL1 function.

overall_design: 11 Samples, 5 controls and 5 KOs with antibodies H3K4me1, H3K4me3, and H3K27Ac. One input Sample.

first: Bibhu

middle: P

last: Mishra

first: Kristin

last: Zaffuto

first: Erika

middle: L

last: Artinger

first: Tonis

last: Org

first: Hanna

middle: K

last: Mikkola

first: Chao

last: Cheng

first: Malek

last: Djabali


title: Comparative genomics of domesticated peppers and its wild progenitor reveal signature of artificial selection by human

first: CNSA

last: CNGB

platform_organism:
Capsicum annuum
Capsicum chinense
Capsicum annuum var. glabriusculum


title: Characterization of transcriptome dynamics in response to contact with host cells [Phase I In Vitro]

status: Public on Mar 30 2014

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

summary:
Candida albicans is the major invasive fungal pathogen of humans, causing diseases ranging from superficial mucosal infections to disseminated, systemic infections which are often life threatening. Hematogenously disseminated candidiasis (HDC) has a 47% mortality rate despite current antifungal therapy. An increase in prevalence, as well as an increasing resistance to most of the clinically important antifungal therapies, provides a strong impetus to understand the molecular mechanisms of pathogenesis and the acquisition of drug resistance. This information holds promise to identify novel therapeutic targets. A complete and accurate characterization of how the transcriptome of C. albicans responds to its interaction with cells from the host is an absolute necessity to accomplish this goal.
RNA-seq (deep-sequencing of cDNA) provides an unbiased method to define comprehensively and systematically the transcriptome of an organism. We propose a comprehensive characterization of the C. albicans transcriptome in two different human tissue culture models, using RNA-seq. Such a characterization will shed unprecedented light on how fungal pathogens sense and respond to the host environment and how the host tissue responds to fungal invasion.
We performed a comprehensive characterization of the C. albicans transcriptome in two different murine models of candidiasis (HDC and oropharyngeal candidiasis (OPC)), and two different human tissue culture models, using RNA-seq. Because the two murine models accurately recapitulate the pathology that is observed in clinical cases of candidiasis, we are confident that gene expression levels will provide an accurate representation of what occurs during the course of an infection in humans.  Such a characterization of the in vivo transcriptome will shed unprecedented light on how fungal pathogens sense and respond to the host environment and how the host tissue responds to fungal invasion.
PRJNA86065

sample_organism:
Candida albicans
Homo sapiens

platform_organism:
Candida albicans
Homo sapiens

overall_design: Two different strains of C. albicans (SC5314 or WO-1) were used to infect two different types of human tissue culture monolayers (HUVECs or OKF6-TERT2). RNA from the infection mixtures were harvested at 90 minutes, 5 hours and 8 hours post infection. Experiments were performed in biological duplicate.

first: Scott

last: Filler

first: Yaoping

last: Liu


title: Neuropathy of haematopoietic stem cell niche is essential for myeloproliferative neoplasms

status: Public on Mar 12 2014

city: Madrid

first: Simón

last: Méndez-Ferrer

address: Calle Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

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

overall_design: Refer to individual Series


title: mRNA-Seq of head tissue from Doa and fne mutants, Drosophila melanogaster.

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary: Transcriptional profiling of head tissue of Drosophila Darkener of apricot (Doa) and found in neurons (fne) mutants was performed by RNA-SEQ in females and males. The transcriptional and post-transcriptional targets of these genes, which are involved in regulation by several processes including splicing and mRNA stability, are examined and compared to wild-type.

overall_design: Examination of mRNA profiles in heads of wild-type male and female adult flies are compared to mutant

first: David

last: Sturgill

first: John

middle: H

last: Malone

first: Marie-Laure

last: Samson

first: Leonard

last: Rabinow


title: Neuropathy of the haematopoietic stem cell niche is essential for myeloproliferative neoplasms [RNA-seq]

summary: Myeloproliferative neoplasms (MPNs) are diseases caused by mutations in the haematopoietic stem cell (HSC) compartment. Most MPN patients have a common acquired mutation of Janus kinase 2 (JAK2) gene in HSCs that renders this kinase constitutively active, leading to uncontrolled cell expansion. The bone marrow (BM) microenvironment might contribute to the clinical outcomes of this common event. We previously showed that BM nestin+ mesenchymal stem cells (MSCs) innervated by sympathetic nerve fibres regulate normal HSCs. Here we demonstrate that abrogation of this regulatory circuit is essential for MPN pathogenesis. Sympathetic nerve fibres, supporting Schwann cells and nestin+ MSCs are consistently reduced in the BM of MPN patients and mice expressing the human JAK2V617F mutation in HSCs. Unexpectedly, MSC reduction is not due to differentiation but is caused by BM neural damage and Schwann cell death triggered by interleukin-1b produced by mutant HSCs. In turn, in vivo depletion of nestin+ cells or their production of CXCL12 expanded mutant HSCs and accelerated MPN progression. In contrast, administration of neuroprotective or sympathomimetic drugs prevented mutant HSC expansion. Treatment with b3-adrenergic agonists that restored the sympathetic regulation of nestin+ MSCs prevented the loss of these cells and blocked MPN progression by indirectly reducing leukaemic stem cells. Our results demonstrate that mutant HSC-driven niche damage critically contributes to disease manifestation in MPN and identify niche-forming MSCs and their neural regulation as promising therapeutic targets.

overall_design: CD45- CD31- Ter119- GFP+ cells were sorted from the BM of Nes-gfp;Mx1-cre;JAK2-V617F mice and control littermates 6 weeks after pIpC treatment and were subjected to RNA sequencing. Each sample was pooled from 3 animals of the same genotype.

first: Lorena

last: Arranz

first: Simon

last: Mendez-Ferrer


title: Next Generation Sequencing of Wild-Type FVB/NJ Mouse Cardiac Small RNA

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

summary:
Purpose: Next-generation sequencing (NGS) provides for quantitation of RNA abundances and comparison of RNA abundances within tissues and cells in a manner not possible with previous microarray technologies.
We have made widespread use of Illumina sequencing technologies for RNA quantitation in several publications involving mouse hearts, dating from 2010, and wish to share both high-quality raw sequencing data and data processed to quantitate mRNA abundances from wild-type mice, male and female, at a variety of ages.
These data will provide a resource for investigators using microarrays to understand the concentration of transcripts of interest relative to other cardiac RNAs, and will permit deeper interpretation of previous microarray studies.

overall_design: 39 cardiac small RNA (microRNA) profiles of 4- to 16 week-old FVB/NJ wild type (WT) mice were generated on Illumina HiSeq 2000 instruments.

first: Gerald

last: Dorn


title: Next Generation Sequencing of Wild-Type FVB/NJ Mouse Cardiac Polyadenylated RNA

overall_design: 40 cardiac polyA+-RNA profiles of 4- to 16 week-old FVB/NJ wild type (WT) mice were generated on Illumina HiSeq 2000 instruments.


title: Next Generation Sequencing of Wild-Type C57BL/6J Mouse Cardiac Small RNA

overall_design: 6 cardiac small RNA (microRNA) profiles of 18 week-old C57BL/6J wild type (WT) mice were generated on Illumina HiSeq 2000 instruments.


title: Next Generation Sequencing of Wild-Type C57BL/6J Mouse Cardiac Polyadenylated RNA

summary:
Purpose: Next-generation sequencing (NGS) provides for quantitation of RNA abundances and comparison of RNA abundances within tissues and cells in a manner not possible with previous microarray technologies.
We have made widespread use of Illumina sequencing technologies for RNA quantitation in several publications involving mouse hearts, dating from 2010, and wish to share both high-quality raw sequencing data and data processed to quantitate mRNA abundances from wild-type mice, male and female, at a variety of ages (see our FVB/NJ data submission).
These data will provide a resource for investigators using microarrays to understand the concentration of transcripts of interest relative to other cardiac RNAs, and will permit deeper interpretation of previous microarray studies.

overall_design: 4 cardiac polyA+-RNA profiles of 12 week-old C57BL/6J wild type (WT) mice were generated on Illumina HiSeq 2000 instruments.


title: Identification of beta-catenin binding regions in SW480 cells

city: Yokohama

first: Kazuhide

last: Watanabe

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: Riken

summary: Deregulation of canonical Wnt/beta-catenin pathway is one of the earliest events in the pathogenesis of colon cancer. Mutations in APC or CTNNB1 (beta-catenin gene) are highly frequent in colon cancer and cause aberrant stabilization of b-catenin, which activates the transcription of Wnt target genes by binding to chromatin via the TCF/LEF transcription factors. Here we report an integrative analysis of genome-wide chromatin occupancy of b-catenin by chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) and gene expression profiling by microarray analysis upon RNAi-mediated knockdown of beta-catenin in colon cancer cells (GSE53656).

overall_design: Immunoprecipitated samples from human colon cancer SW480 cells with antibodies against beta-catenin and control IgG respectively were used for ChIP-seq experiments.

first: Xing

last: Dai


status: Public on Mar 11 2014

city: Köln

first: Corinna

last: Klein

address: Joseph-Stelzmann-Straße 9b

country: Germany

institute: Max Planck Institute for Biology of Ageing

summary: We performed RNA-seq analysis of WT and blmp-1(tm548) mutant L3 larvae to identify genes regulated by the zing-finger transcription factor BLMP-1.

overall_design: We analyzed three WT and three blmp-1 mutant biological replicates

first: Adam

last: Antebi

first: Moritz

last: Horn


title: Genome-wide high-throughput small RNA sequence analysis of B. cinerea-infected Arabidopsis rosette leaves

city: Riverside

first: Hailing

last: Jin

address: 3447 Boyce Hall

department: Department of Plant Pathology and Microbiology

institute: University of California, Riverside

summary: We profiled small RNAs obtained from B. cinerea-infected Arabidopsis rosette leaves at four different time points after inoculation.

overall_design: Examination of small RNA profiles of B. cinerea-infected Arabidopsis rosette leaves over a time course.

first: Arne

last: Weiberg


title: SOX2 and p63 occupancy in human squamous carcinoma cell lines and embryonic stem cells.

city: Boston

first: Shouyong

last: Peng

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: SOX2 is a transcription factor essential for pluripotent stem cells, and development and maintenance of squamous epithelium. We previously reported SOX2 an oncogene subject to highly recurrent genomic amplification in squamous cell carcinomas (SCCs).  Here we demonstrate in SCCs that SOX2 interacts with another master squamous transcription factor p63, and through ChIP-seq show that genomic occupancy of SOX2 overlaps with that of p63 at a large number of loci and that they cooperatively regulate gene expression including ETV4, which we find essential for SOX2-amplified SCC cell survival. Furthermore, SOX2 binds to distinct genomic loci in SCCs than in embryonic stem cells and the SOX2-p63 coordinate binding is unique to SCC.  In addition, a subset of SOX2 genomic binding sites in SCC that lack p63 co-occupancy are co-occupied by the AP-1 transcriptional complex.  These demonstrate that SOX2’s actions in SCC differ substantially from its role in pluripotency and identify novel SOX2 interactions that will enable deeper characterization of SOX2’s function in SCC.

overall_design: SOX2 and p63 ChIP-seq from three lung and esophageal squamous carcinoma cell lines with amplification of SOX2 as well as SOX2 ChIP-seq from an ES cells.

first: Hideo


title: Genome-wide high-throughput small RNA sequence analysis of B. cinerea

summary: We profiled small RNAs obtained from B. cinerea mycelium and conidiospores.

overall_design: Examination of small RNA profiles of B. cinerea mycelium and conidiospores


title: Integrative Genomic and Transcriptomic Analysis Identified Candidate Genes Implicated in the Pathogenesis of Hepatosplenic T-cell Lymphoma

city: Leuven

first: Julio

last: Finalet

address: Herestraat 49

country: Belgium

institute: KULeuven

summary: Hepatosplenic T-cell lymphoma (HSTL) is an aggressive lymphoma cytogenetically characterized by isochromosome 7q   [i(7)(q10)], of which the molecular consequences remain unknown. We report here results of an integrative genomic and transcriptomic (expression microarray and RNA-sequencing) study of six HSTL cases with i(7)(q10) and three cases with ring 7   [r(7)], a rare variant aberration. Using high resolution array CGH, we prove that HSTL is characterized by the common loss of a 34.88 Mb region at 7p22.1p14.1 (3506316-38406226 bp) and duplication/amplification of a 38.77 Mb region at 7q22.11q31.1 (86259620-124892276 bp). Our data indicate that i(7)(q10)/r(7)-associated loss of 7p22.1p14.1 is a critical event in the development of HSTL, while gain of 7q sequences drives progression of the disease and underlies its intrinsic chemoresistance. Loss of 7p22.1p14.1 does not target a postulated tumor suppressor gene but unexpectedly enhances the expression of CHN2 from the remaining 7p allele, resulting in dysregulation of a pathway involving RAC1 and NFATC2 with a cell proliferation response. Gain of 7q leads to increased expression of critical genes, including RUNDC3B, PPP1R9A and ABCB1, a known multidrug resistance gene. RNA-sequencing did not identify any additional recurrent mutations or fusion, suggesting that i(7)(q10) is the only driver event in this tumor. Our study confirms the previously described gene expression profile of HSTL and identifies a set of 24 genes, including three located on chromosome 7 (CHN2, ABCB1 and PPP1R9A), distinguishing HSTL from other malignancies

overall_design: The fastq files of all samples were mapped to the reference human genome (assembly GRCh37.68). The mapping was performed  allowing detection of insertions and deletions (indels). The mapped reads were used to calculate read counts and FPKM (Fragment Per Kilobase of exon model per Million of mapped read) per gene. The DESeq algorithm was applied to identify differentially expressed genes. The mapped reads were used to predict mutations and gene fusions.

middle: F

last: Ferreiro

first: Leila

last: Rouhigharabaei

first: Helena

first: Jo-Anne

last: van der Krogt1

first: Lucienne

first: Shashirekha

last: Shetty

first: Laszlo

last: Krenacs

first: Thomas

last: Tousseyn

first: Pascale

last: De Paepe

first: Anne

last: Uyttebroeck

first: Gregor

last: Verhoef

first: Tom

last: Taghon

first: Peter

last: Vandenberghe

first: Jan

last: Cools

first: Iwona

last: Wlodarska


title: High-resolution Brachyury DNA-binding Sites Mapping by ChIP-exo

status: Public on Mar 10 2014

city: Ashburn

first: Zhe

last: Liu

state: Virginia

address: 19700 Helix Dr.

department: Janelia Farm Research Campus

institute: Howard Hughes Medical Institute

summary: Mapping ultra high resolution of Brachyury:DNA interaction would provide us with valuable new mechanistic insights into complex molecular transactions at Brachyury-bound enhancers.

overall_design: Embryonic stem cells were differentiated into Brachyury-positive mesoendoderm cells. And, ChIP-exo experiment was then performed to identify detailed Brachyury-DNA binding profiles.

first: Liu

last: Zhe


title: Genome-wide high-throughput small RNA sequence analysis of B. cinerea-infected tomato leaf and fruit

first: Hailing

last: Jin

summary: We profiled small RNAs obtained from B. cinerea-infected tomato leaf and fruit during a time course.

overall_design: Examination of small RNAs from B. cinerea-treated tomato leaf and fruit tissue over a time course.

first: Arne

last: Weiberg


title: Map Brachyury-bound enhancers by ChIP-seq

summary: To gain new mechanistic insights into highly-regulated lineage specification and morphogenetic processes during early embryogenesis, we applied ChIP-seq to identify transcriptional programs mediated by a key developmental regulator - Brachyury.

overall_design: Embryonic stem cells were differentiated into Brachyury-positive mesoendoderm cells. And, ChIP-seq experiments were carried out by two independent Brachyury antibodies.


title: Probing Brachyury Function during ES cell differentiaiton

summary: To probe how Brachyury regulates its target genes, we performed mRNA-seq to analyze gene expression changes after Brachyury depletion by the lentivirus-mediated shRNA

overall_design: WT and Brachytury Knockdown embryoid bodies were collected at EB day 4. Subsequently, mRNA-seq expriments were performed with whole embryoid bodies


title: Human Hepatocytes with Drug Metabolic Function Induced from Fibroblasts by Lineage Reprogramming

city: Beijing

first: Jinlin

last: Wang

state: - If in U.S, Select a State -

address: Yiheyuan Road 5#,Haidian district

institute: Peking University

summary: We generated induced human hepatocyte by transduction of several lineage specific transcription factors and analyzed the gene expression profile of generated hepatocytes and freshly isolated human hepatocytes through RNA sequencing.

overall_design: Global gene expression profile analysis

first: Yuanyuan

last: Du

first: Jun

last: Jia

last: Song

first: Chengang

last: Xiang


title: Probing In vivo Brachyury Function with Tc mouse model

summary: To identify Brachyury target genes in vivo and elucidate how Brachyury-mediated regulation contributes to early mouse developmental homeostasis and coordination, we performed mRNA-seq to compare gene expression profiles of WT and Tc/Tc embryos at both E7.5 ~ 8.0 and E10.0 ~ 10.5

overall_design: WT and Tc/Tc embryos were isolated at both E7.5 ~ 8.0 and E10.0 ~ 10.5. Subsequently, directional mRNA-seq expriments were performed with wild-type and Tc/Tc whole embryos


title: Charting Brachyury-mediated Developmental Pathways During Early Mouse Embryogenesis

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

overall_design: Refer to individual Series


title: Dynamics of SREBP1 binding to DNA in mouse liver

city: Lausanne

first: Beatrice

last: Desvergne

state: Vaud

address: Dorigny

department: CIG

country: Switzerland

institute: UNIL

summary: To systematically understand how the circadian clock and the nutrient-driven rhythm integrate to regulate SREBP1 activity, we evaluated genome-wide the binding of SREBP1 to its targets along the day in wild-type (WT) C57BL/6mice. The recruitment of SREBP1 to the DNA showed a highly circadian behaviour, with a maximum during the fed status. However, the temporal expression of SREBP1 targets was not always synchronized with its binding. In particular, a different phase of expression was observed for SREBP1 target genes depending on their function, suggesting the involvement of other transcription factors in their regulation. The proper temporal expression pattern of these genes was dramatically changed in Bmal1KO mice upon time-restricted feeding, in spite of the rhythmic, although slightly delayed, binding of SREBP1. Our results show that besides the nutrient-driven regulation of SREBP1 nuclear translocation, a second layer of modulation of SREBP1 transcriptional activity exists and is strongly dependent from the circadian core clock. This system allows to fine tune the expression timing of SREBP1 target genes, thus helping to temporally separate the different physiological processes in which these genes are involved.

overall_design:
6 samples examined, 6 SREBP1 samples, as well  as 6 Polr2b and 6 input samples from GEO series GSE35788
CycliX Consortium was a contributor to this submission.

first: Federica

last: Gilardi

first: Eugenia

last: Migliavacca

first: Naldi

last: Aurelien

first: Baruchet

last: Michael

first: Donatella

last: Canella

first: Gwendal

last: Le Martelot

first: Nicolas

last: Guex

first: Béatrice


title: Fed State Prior to Hemorrhagic Shock and Polytrauma in a Porcine Model Results in Altered Liver Transcriptomic Response

status: Public on Mar 07 2014

city: Minneapolis

first: Charles

middle: Edward

last: Determan Jr

state: MN

address: PWB B150 516 Delware St.

department: Department of Surgery

institute: University of Minnesota

summary: We sequenced liver mRNA from 23 individual pigs (5 prefed and 18 fasted) taken at 4 separate time points to evaluate the change in gene expression over the course of hemorrhagic shock and resuscitation in response to a carbohydrate prefed state.

overall_design: Examination of mRNA levels in liver biopsies from pigs at 4 timepoints throughout hemorrhagic shock and resuscitation

middle: E


title: Small RNA content in mouse serum upon S.mansoni infection

status: Public on Mar 08 2014

city: Edinburgh

first: Amy

last: Buck

address: West Mains Road

country: United Kingdom

institute: The University of Edinburgh

summary:
MicroRNAs (miRNAs) are a class of short non-coding RNA that play important roles in disease processes in animals and are present in a highly stable cell-free form in body fluids. Here we examine the capacity of host and parasite miRNAs to serve as tissue or serum biomarkers of Schistosoma mansoni infection.
Sequencing of small RNAs from serum confirmed the presence of  miRNAs and revealed 11 parasite-derived miRNAs that were detectable by 8 weeks post S.mansoni infection.

overall_design: Small RNA content in serum of naïve and Schistosoma mansoni infected mice were examined in two different librarys. 1- prepared according to the  290 Illumina small RNA Sample Preparation Kit version 1.5 and sequenced on the GAIIX  and 2- prepared according to the TruSeq Small RNA protocol (without size-selecting small  295 RNA) and sequenced on the HiSeq2

first: Anna

middle: M

last: Hoy

first: Juan

last: Quintana

first: Alasdair

last: Ivens


title: Methylome of soil bacterium Gemmatirosa kalamazoonensis KBS708, a member of the rarely cultivated Gemmatimonadetes phylum

city: Menlo Park

first: Tyson

middle: A

last: Clark

address: 1380 Willow Rd.

institute: Pacific Biosciences

summary: Bacteria belonging to phylum Gemmatimonadetes are found in a wide variety of environments and are particularly abundant in soils.  To date, only two Gemmatimonadetes strains have been characterized.  Here we report the complete genome sequence and methylation pattern of Gemmatirosa kalamazoonensis KBS708 (ATCC BAA-2150; NCCB 100411), the first characterized Gemmatimondetes strain isolated from soil.

overall_design: Examination of the methylome of Gemmatirosa kalamazoonenis KBS708 using kinetic data from single-molecule, real-time (SMRT) sequencing on the PacBio RS

first: Jennifer

last: DeBruyn

first: Mark

last: Radosevich

first: K

last: Wommack

first: Shawn

middle: W

last: Polson

first: Loren

last: Hauser

first: Mariam

middle: N

last: Fawaz

first: Jonas

last: Korlach

first: Yu-Chih

last: Tsai


title: H3K4 tri-methylation provides an epigenetic signature of active enhancers

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

country: France

institute: TAGC INSERM U1090

summary: Combinations of post-translational histone modifications shape the chromatin landscape during cell development in eukaryotes. However, little is known about the modifications exactly delineating functionally engaged regulatory elements. For example, although histone H3 lysine 4 mono-methylation (H3K4me1) indicates the presence of transcriptional gene enhancers, it does not provide clear-cut information about their actual position and stage-specific activity. Histone marks were, therefore, studied here at genomic loci differentially expressed in early stages of T-lymphocyte development. The concomitant presence of the three H3K4 methylation states (H3K4me1/2/3) was found to clearly reflect the activity of bona fide T-cell gene enhancers. Globally, gain or loss of H3K4me2/3 at distal genomic regions correlated with, respectively, the induction or the repression of associated genes during T-cell development. In the Tcrb gene enhancer, the H3K4me3-to-H3K4me1 ratio decreases with the enhancer’s strength. Lastly, enhancer association of RNA-polymerase II (Pol II) correlated with the presence of H3K4me3 and Pol II accumulation resulted in local increase of H3K4me3. Our results suggest the existence of functional links between Pol II occupancy, H3K4me3 enrichment and enhancer activity.

overall_design: ChIP-seq for H3K4me1, H3K4me3 and Pol II was performed from DRag thymocytes or DRag thymocytes from CD3 stimulated mice

first: Aleksandra

last: Pekowska

first: Touati

last: Benoukraf

first: Joaquin

last: Zacarias-Cabeza

first: Mohamed

last: Belhocine

first: Frederic

last: Koch

first: Helene

last: Holota

first: Jean

last: Imbert

first: Jean-Christophe

last: Andrau

first: Pierre

last: Ferrier

first: Salvatore

last: Spicuglia


title: Gene expression profile of metastasis-associated neutrophils

city: Amsterdam

first: Karin

last: de Visser

address: Plesmanlaan 121

department: Immunology

institute: Netherlands Cancer Institute

summary: The goal of this experiment was to determine gene expresssion differences between neutrophils from either K14cre;CdhF/F;Trp53F/F mammary tumor-bearing mice or wild-type mice.

overall_design: Neturophil expression profiles were compared between four wild-type mice and five K14cre;CdhF/F;Trp53F/F mice.

first: Seth

middle: B

last: Coffelt


title: Transcriptome analysis of a Sordaria macrospora nox1 mutant

city: Bochum

first: Minou

last: Nowrousian

address: Universitaetsstr. 150

department: Molecular and Cellular Botany

institute: Ruhr-University Bochum

summary: The Sordaria macrospora nox1 mutant has a block in sexual development at the stage of protoperithecia formation, and therefore is sterile. The aim of this study was to determine the transcriptome of microdissected protoperithecia from the mutant, as well as the transcriptomes of total RNA from the mutant and the wild type for comparison. The data were then compared with transcriptome data from protoperithecia of the wild type and the developemental mutant pro1; the corresponding data were generated in a previous study (Teichert et al. 2012, BMC Genomics 13: 511, GEO accession GSE33668).

overall_design: The samples (amplified RNA from nox1 microdissected protoperithecia and total RNA from nox1 and wild type mycelia undergoing sexual development) were sequenced as paired-end reads on an Illumina HiSeq 2000, two independent biological replicates for each nox1 sample and one replicate for the wild type.

first: Daniela

last: Dirschnabel

first: Nallely

last: Cano-Dominguez

first: Jesus

last: Aguirre

first: Ines

last: Teichert

first: Ulrich

last: Kück


title: Genomic profiling of human Leishmania braziliensis lesions identifies transcriptional modules associated with cutaneous immunopathology

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

summary: The host immune response plays a critical role not only in protection from human leishmaniasis, but also in promoting disease severity. Although candidate gene approaches in mouse models of leishmaniasis have been extremely informative, a global understanding of the immune pathways active in lesions from human patients is lacking. To address this issue, genome-wide transcriptional profiling of Leishmania braziliensis-infected cutaneous lesions and normal skin controls was carried out. A signature of the L. braziliensis skin lesion was defined that includes over 2,000 differentially regulated genes. Pathway-level analysis of this transcriptional response revealed key biological pathways, as well as specific genes, associated with cutaneous pathology, generating a testable 'metapathway' model of immune-driven lesion pathology, and providing new insights for treatment of human leishmaniasis.

overall_design: Thirty-five skin biopsies were analyzed, including 10 normal skin biopsies (2 from North America and 8 from non-endemic area in Brazil), and 25 skin lesion biopsies (8 early cutaneous lesions, 17 late cutaneous lesions) obtained from Leishmania brazilensis-infected patients presenting at the Corte de Pedra Health Post in Corte de Pedra, Bahia, Brazil.

first: Daniel

last: Beiting

first: Phillip

last: Scott

first: Fernanda

last: Novais

first: Edgar

last: Carvalho

first: Lucas


title: RNA-seq of C.elegans and M.musculus in the presence and absence of D-Glucosamine (GlcN)

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

summary:
D-Glucosamine (2-amino-2-deoxy-D-glucose, C.A.S.# 3416-24-8) (GlcN) is a freely available and commonly used dietary supplement possibly promoting cartilage health in humans which also acts as an inhibitor of glycolysis.
We here find that GlcN extends C. elegans lifespan by impairing glucose metabolism to activate AMP-activated protein kinase (AMPK/AAK2) leading to increased mitochondrial biogenesis.
Consistent with the concept of mitohormesis, this promotes increased formation of mitochondrial reactive oxygen species (ROS) and p38/PMK-1-mediated stress signaling culminating in increased expression of the nematodal amino acid-transporter 1 (aat-1) gene.
Ameliorating mitochondrial ROS formation as well as impairment of aat-1-expression abolishes GlcN-mediated lifespan extension in a NRF2/SKN-1-dependent fashion.
Notably and unlike other calorie restriction mimetics (CRM) like 2-deoxy-D-glucose (2DG, DOG), GlcN extends lifespan of aging C57BL/6 mice (log-rank: p=0.002; cox regression: p=0.01) similarly paralleled by an induction of mitochondrial biogenesis, increased expression of several murine amino acid transporters, as well as increased amino-acid catabolism.
Taken together, GlcN mimics a ketogenic diet to extend healthspan in evolutionary distinct species.

sample_organism:
Caenorhabditis elegans
Mus musculus

platform_organism:
Caenorhabditis elegans
Mus musculus

overall_design: 24 samples: 12 mRNA profiles of C.elegans: 6 without GlcN and 6 with GlcN supplementaion; 12 mRNA profiles of M.musculus: 6 without GlcN and 6 with GlcN supplementaion

first: Sandra

last: Weimer

first: Josephine

last: Priebs

first: Doreen

last: Kuhlow

first: Steffen

last: Priebe

first: Johannes

last: Mansfeld

first: Troy

last: Merry

first: Sébastien

last: Dubuis

first: Andreas

last: Pfeiffer

first: Tim

middle: J

last: Schulz

first: Reinhard

last: Guthke

first: Matthias

last: Platzer

first: Nicola

last: Zamboni

first: Kim

last: Zarse

first: Michael

last: Ristow


title: ChIP-seq analysis of Rpb1 from 12hr conjugating Oxytricha trifallax cells

city: New York

first: Jaspreet

last: Khurana

state: NY

address: 701 West 168th St.

institute: Columbia University

summary: To study the biogenesis of long non-coding RNAs transcribed during genome rearrangements in Oxytricha development, genome-wide localization pattern of Rpb1 (RNA Pol-II largest subunit) was studied from Oxytricha cells undergoing conjugation.

overall_design: Chromatin from 12hr conjugating O.trifallax cells was subjected to chromatin immunoprecipitation (ChIP) followed by sequencing of Input and ChIP samples via Illumina paired-end sequencing.

middle: S

first: Laura

last: Landweber


title: Analysis of the humoral immune response against aberrant self by RNA sequencing of the fat body in Drosophila melanogaster

city: Stockholm

first: Ulrich

last: Theopold

address: Svante Arrhenius Laboratories 20c

department: Molecular Biology and Functional Genomics

country: Sweden

institute: Stockholm University

summary: The early stages of the immune response against aberrant tissues such a tumors are technically difficult to study and therefore little understood. To analyze the innate immune response towards modified self-tissue we expressed a dominant-active version of the Ras oncogene in Drosophila imaginal discs and salivary glands. Signs of an immune response are observed on wings of adult flies, which show spots of melanization and in larvae, where the salivary glands attract blood cells. In line with the strong response mounted against salivary glands, they are found to express metalloproteases and apoptotic markers making them both accessible and recognizable for the immune system. The response against the glands bears several hallmarks of an encapsulation response including flattening of plasmatocytes, differentiation of lamellocytes, attachment of crystal cells and melanization at the final stage. RNA sequencing of the fat body, the primary producer of immune effectors, reveals a pattern of induced genes, which overlaps the one previously found upon wasp infestation but shows also several specific features. Evidence for the functional importance of one of the induced genes is presented proving the power of our approach to identify regulators of the response against modified self.

overall_design:
Transcriptome analysis of the immune response in the fat body after expression of  dominant-active RAS in the wing imaginal discs and salivary glands.
Comparison of fat bodies from 3 control and 3 RAS-expressing larvae. For each sample fat bodies from 40 individuals were dissected.

Differential gene expression files [output of Cuffdiff] are linked below:
ResultsContr123vsRas123Individual.xls: Output file of Cuffdiff. Differential gene expression analysis, three control compared to individual Ras induced; replicate analysis using Cuffdiff.
ResultsContr123vsRas123Multiple.xls: Output file of Cuffdiff. Differential gene expression analysis, three control compared to three Ras induced; replicate analysis using Cuffdiff.
ResultsContr123vsRas12Multiple.xls: Output file of Cuffdiff. Differential gene expression analysis, three control compared to two Ras induced;  replicate analysis using Cuffdiff.

first: Robert

last: Markus


title: Differential gene expression in nephron progenitors lacking miR-17~92

city: Pittsburgh

first: Jacqueline

last: Ho

address: 4401 Penn Avenue

institute: Children's Hospital of Pittsburgh

summary: Purpose: The goal of this study is to compare the differential expression of transcripts in control kidneys compared to kidneys lacking the miR-17~92 cluster in nephron progenitors and their derivatives by RNA-seq to identify potential miRNA targets in the mutant kidneys.

overall_design: mRNA profiles of control and mutant (=Six2-TGC; miR-17~92 flx/flx) embryonic day 16 kidneys were generated by deep sequencing, in triplicate, using Illumina HiSeq2000

first: April

last: Marrone

first: Dennis

last: Kostka


title: Cell type-specific epigenomic analysis in the developing heart

status: Public on Mar 06 2014

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

institute: Amsterdam UMC

summary: The molecular mechanisms governing heart development provide an important framework to understand congenital heart disease. The embryonic vertebrate heart tube develops an atrioventricular canal that divides the atrial and ventricular chambers, forms atrioventricular conduction tissue and organizes valve development. To better understand the molecular mechanism underlying atrioventricular canal versus chamber myocardium expression, a double-reporter transgenic mouse line was generated in which the expression of EGFP (green fluorescent protein) and Katushka (red fluorescent protein) are selectively expressed in the atrioventricular canal and in the chamber myocardium, respectively. We assessed the genome-wide H3K27ac pattern in isolated embryonic AV canal and in chamber cardiomyocytes, respectively.

overall_design: EGFP and Katushka-positive cells were purified by FACS and fixed. ChIP was performed with the truemicro ChIP (Diagenode) according to the manufacturer’s protocol using the H3K27ac antibody (abcam ab4729). Chipped DNA were subjected to library preparation using the 5500 Series SOLiD™ Systems ample preparation kit (Applied Biosystems) according to manufactures recommendations and sequenced using the 5500 wildfire system (SOLiD).

first: Sonia

last: Stefanovic

first: Karel

last: van Duijvenboden

first: Phil

last: Barnett


title: miRNA high-throughput sequencing of follicular thyroid tumors

city: Warsaw

first: Michal

last: Swierniak

address: Banacha 2C

department: Centre of New Technologies

country: Poland

institute: University of Warsaw

summary: We report data obtaibed from high-throughput sequencing of small RNAs in 20 samples of follicular thyroid tumors. We analyzed a total of 4.7±1.5million reads per sample with 3 different pipelines. The main goal was to evaluate the usefulness of next generation sequencing in small RNA profiling and the concordance of its results with microarrays and qPCR. Additionally we verified published follicular thyroid tumor biomarkers in the set of our samples.

overall_design: Small RNA expression profiling  with High Throughput Sequencing of 20 thyroid tumor samples, performed on an Illumina HiScan-SQ.

first: Tomasz

last: Stokowy

first: Knut

last: Krohn


title: Next Generation Sequencing of Wild-Type C57BL/6J and FVB/NJ Mouse Cardiac Polyadenylated RNA and Small RNA

city: Indianapolis

first: Scot

last: Matkovich

address: Lilly Corporate Center

institute: Eli Lilly and Company


title: Differential gene expression profilings between diploid and triploid Fujian Oyster

city: xiamen

first: zeng

last: zhen

address: daxue road

institute: xiamen university

summary: The systematic deep sequencing analysis provided a comprehensive understanding of the transcriptome complexity of 2n and 3n Fujian oyster. This information broadens our understanding of the mechanisms of C.angulata polyploidization and contributes to molecular and genetic research by enriching the oyster database. This is the first report on genome-wide transcriptional analysis of adductor muscle of diploid and triploid Fujian oyster and has demonstrated triploid oysters are morphologically almost identical to their diploid counterparts, but have faster growth, due to the reorientation of energetic allocation from gametogenesis to somatic investment. This study provides a foundation for further analysis of the gene expression patterns and signaling pathways which regulate the molecular mechanisms of diploid and triploid oyster.

overall_design: Examination of 3 different samples, including diploid (DF and DM) and triplod(T) oyster.

first: Zhen

last: Zeng

first: Caihuan

last: Ke


title: Single-molecule Dynamics of Enhanceosome Assembly In Embryonic Stem Cells

city: Ashburn

first: Zhe

last: Liu

address: 19700 Helix Dr.

institute: Howard Hughes Medical Institute

summary: These ChIP-exo data were used to validate the predictions from our live-cell single-molecule imaging experiment

overall_design: The ChIP-exo mapping of ultra-fine localization of endogenous Sox2, halo-Sox2, and two halo-Sox2 mutants (halo-Sox2M and halo-Sox2D) in embryonic stem cells.

first: Li

last: Li

first: Liu

last: Zhe


title: Retinoic acid induced changes in gene expression in TAF4 knock out fibroblasts

city: Illkirch

first: Igor

last: Martianov

address: 1 rue Laurent Fries

institute: IGBMC

summary: Collagen 6A3 (Col6a3), a component of extracellular matrix, is often up-regulated in tumours and is believed to play a pro-oncogenic role. However the mechanisms of its tumorigenic activity are poorly understood. We show here that Col6a3 is highly expressed in densely growing mouse embryonic fibroblasts (MEFs). In MEFs where the TAF4 subunit of general transcription factor IID (TFIID) has been inactivated, elevated Col6a3 expression prevents contact inhibition promoting their 3 dimensional growth as foci and fibrospheres. Analyses of gene expression in densely growing Taf4-/- MEFs revealed repression of the Hippo pathway and activation of Wnt signalling. The Hippo activator Kibra/Wwc1 is repressed under dense conditions in Taf4-/- MEFs, leading to nuclear accumulation of the proliferation factor YAP1 in the cells forming 3D foci. At the same time, Wnt9a is activated and the Sfrp2 antagonist of Wnt signalling is repressed. Surprisingly, treatment of Taf4-/- MEFs with all-trans retinoic acid (ATRA) restores contact inhibition suppressing 3D growth. ATRA represses Col6a3 expression independently of TAF4 expression and Col6a3 silencing is sufficient to restore contact inhibition in Taf4-/- MEFs and to suppress 3D growth by reactivating Kibra expression to induce Hippo signalling and by inducing Sfrp2 expression to antagonize Wnt signalling. All together, these results reveal a critical role for Col6a3 in regulating both Hippo and Wnt signalling to promote 3D growth, and show that the TFIID subunit TAF4 is essential to restrain the growth promoting properties of Col6a3. Our data provide new insight into the role of extra cellular matrix components in regulating cell growth.

overall_design: 7 samples corresponding to non-treated cells, 12 hours RA treated cells and72 hours RA treated cells  were analyzed. First two conditions were done in triplicate. 72 hs point was done in duplicate.

first: Emilie

last: Cler

first: Irwin

last: Davidson


title: Genome-wide maps of H3K27ac, PPARβ/δ and Pol II localization in HUVECs

city: 4-6-1, Komaba, Meguroku

first: Takahide

last: Kohro

state: Tokyo

institute: LSBM, RCAST

summary: H3K27Ac is one of the expressed enhancer markers, PPARβ/δ is a transcription factor and Pol II (RNA polymerase II) is an enzyme which catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA. These genomic localization in endothelial cells is unknown in endothelial cells. This time, we established a new antibody for H3K27ac, PPARβ/δ and Pol II and performed ChIP-seq to identify H3K27ac, PPARβ/δ and Pol II binding site in whole genome manner under PPARβ/δ agonist and/or hypoxia.

overall_design: We used chromatin immunoprecipitation with deep sequencing (ChIP-seq) of HUVECs treated with PPARβ/δ agonist (GW501516 100nM) and/or hypoxia (1%O2) for 24hours, then H3K27ac, PPARβ/δ and Pol II binding regions were identified.  Normoxia and DMSO was used as a control condition.  HUVECs were used within the first 6 passages.

first: Tsuyoshi

last: Inoue

first: Youichiro

last: Wada

first: Kiyomi

last: Kaneki

first: Shogo

last: Yamamoto

first: Tatsuhiko

last: Kodama


title: H3K9ac.14-16 hr OR embryo.Solexa

status: Public on Mar 05 2014

city: Boston

first: Peter

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

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

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type; EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody H3K9ac (target is H3K9ac); Developmental Stage Embryo 14-16hr OR

first: G

last: Karpen

first: S

last: Elgin

first: A

last: Gortchakov

last: Shanower

first: M

last: Tolstorukov

first: P

last: Kharchenko

last: Kuroda

first: V

last: Pirrotta

last: Minoda

first: N

last: Riddle

first: Y

last: Schwartz

last: Alekseyenko

first: C

last: Kennedy


title: Gene expression changes associated with 3D growth of TAF4 knock out fibroblasts

first: Igor

last: Martianov

overall_design: 6 samples corresponding to non-confluent cells, confluent cells and cells growing as fibrospheres were analyzed. Each growing condition was done in duplicate.

first: Irwin

last: Davidson


title: Genome wide localization of chromatin bound NUP98-PHF23 (NP23)

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

summary: We analyzed the genome wide localization of H3K4me3, H3K27me3 and the NUP98-PHF23 (with V5 tag) fusion protein which binds H3K4me3 via its PHD finger, using ChIP-seq. Results correlated with gene expression profiles. NUP98-PHF23 bound only 1.6% of H3K4me3 marks including Hoxa/b + Meis1.

overall_design: Assess H3K4me3 and H3K27me3 histone marks, and correlate these marks with chromatin binding of the NP23 fusion protein using lymphoblast and myeloblast cell lines derived from NP23 leukemias.

first: Sheryl

last: Gough

first: Fan

last: Yang

first: Robert

last: Walker

first: Marbin

last: Pineda

first: Sven

last: Bilke

first: Paul

last: Meltzer

middle: D

last: Aplan


title: Prep1 and Meis1 competition for Pbx1 binding regulates protein stability and tumorigenesis [hM, hMP]

city: Milan

first: Francesco

last: Blasi

address: Via Adamello 16

country: Italy

institute: IFOM

summary: Prep1 is a tumor-suppressor, whereas Meis1 is an oncogene. We show that to perform these activities in MEFs both proteins competitively hetero-dimerize with Pbx1. Meis1 alone transforms Prep1-deficient fibroblasts while Prep1 overexpression inhibits Meis1 tumorigenicity. Pbx1 can therefore alternatively act as oncogene or tumor-suppressor. Prep1 post-translationally controls the level of Meis1 decreasing its stability by sequestering Pbx1. The different levels of Meis1 and the presence of Prep1 are followed at the transcriptional level by the induction of specific transcriptional signatures. The decrease of Meis1 prevents Meis1 interaction with Ddx3x and Ddx5, which are essential for Meis1 tumorigenesis, and modifies the growth promoting DNA binding landscape of Meis1 to the growth controlling landscape of Prep1. Hence the key feature of Prep1 tumor inhibiting activity is the control of Meis1 stability.

overall_design: Examination of Prep1 and Meis1 in three cell type

first: Leila

last: Dardaei


title: Genome-wide maps of Tcf1 binding locations in splenic CD8 T cells.

city: Nutley

first: Hai-Hui

last: Xue

state: NJ

address: 111 Ideation Way

department: Center for Discovery and Innovation

institute: Hackensack University Medical Center

summary: We mapped genome-wide Tcf1 binding locations in mature CD8 T cells to identify its direct target genes.

overall_design: This experiment aims to identify genome-wide binding locations for Tcf1 transcription factor in mature CD8 T cells. The CD8 T cells were isolated from wild-type C57BL/6 mice by negative selection. The chromatin fragments were immunoprecipitated by an anti-Tcf1 antiserum or control rabbit serum (without immunization). The immunoprecipitated fragments were then used in high throughput sequencing. Data processing then revealed >3000 high-confidence Tcf1 binding peaks across the CD8 T cell genome. One important finding is that Tcf1 binds directly to Cd4 gene silencer, and thus explain its important role in suppressing the CD4 coreceptor in mature CD8 T cells.

first: Xue

last: Hai-Hui

first: Tan

last: Kai


title: H3K4me2-Abcam.14-16 hr OR embryo.Solexa

first: Peter

last: Park

state: MA

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type; EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody H3K4me2-Abcam (target is H3K4me2); Developmental Stage Embryo 14-16hr OR

first: G

last: Karpen

first: S

last: Elgin

first: A

last: Gortchakov

last: Shanower

first: M

last: Tolstorukov

first: P

last: Kharchenko

last: Kuroda

first: V

last: Pirrotta

last: Minoda

first: N

last: Riddle

last: Schwartz

last: Alekseyenko


title: Identification of direct targets of Arabidopsis JAGGED in floral buds

city: NORWICH

first: Robert

last: Sablowski

state: Norfolk

address: The John Innes Centre

department: CDB

institute: JIC

summary: JAGGED (JAG) is a regulatory gene that controls shoot organ growth in Arabidopsis. To reveal the molecular links between JAG and the cellular activities required for tissue growth, we used chromatin immunoprecipitation-high-throughput sequencing (ChIP-Seq).

overall_design: To reveal the genome-wide JAG binding sites, we used anti-GFP antibodies to pull down JAG-bound DNA from jag-2 inflorescences complemented with a genomic JAG-GFP fusion (JAG:JAG-GFP) [14]. ChIP-Seq was performed and analyzed in triplicate, with wild-type inflorescences used as epitope-negative controls.

first: Katharina

last: Schiessl

first: Jose

last: Muino


title: The Path to Triacylglyceride Obesity in the sta6 Strain of Chlamydomonas reinhardtii

status: Public on Mar 09 2014

city: Los Angeles

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

summary: When the sta6 (starch-null) strain of the green microalga Chlamydomonas reinhardtii is nitrogen-starved in acetate and then "boosted" after two days with additional acetate, the cells become "obese" after eight days, with triacylglyceride-filled lipid bodies filling their cytoplasm and chloroplasts. To assess the transcriptional correlates of this response, sta6 and the starch-forming cw15 strain were subjected to RNA-Seq analysis during the two days prior and two days post boost, and the data were compared with published reports using other strains and growth conditions. During the two hours post boost, ~425 genes are up-regulated ≥2-fold and ~875 genes are down-regulated ≥2-fold in each strain. Expression of a small subset of "sensitive" genes, encoding enzymes in the glyoxylate and Calvin Benson cycles, gluconeogenesis, and the pentose phosphate pathway, is responsive to culture conditions and genetic background as well as to boost. Four genes--encoding a diacylglycerol acyltransferase (DGTT2), a glycerol-3-P dehydrogenase (GPD3), and two candidate lipases (Cre03.g155250 and Cre17.g735600)--are selectively up-regulated in sta6. Although the bulk rate of acetate depletion from the medium is not boost-enhanced, three candidate acetate permease-encoding genes in the GPR1_FUN34_YaaH superfamily are boost-up-regulated, and 13 of the "sensitive" genes are strongly responsive to the cell's acetate status. A cohort of 64 autophagy-related genes is down-regulated by boost. Our results indicate that the boost serves both to avert an autophagy program and to prolong the operation of key pathways that shuttle carbon from acetate into storage lipid, the combined outcome being enhanced TAG accumulation, notably in sta6.

overall_design: Here we report studies on gene-expression patterns during the path to obesity. The Merchant/Pellegrini and Los Alamos laboratories recently generated and analyzed RNA-Seq transcriptomes of cw15, sta6, and several complemented sta6 strains during two days of N-starvation (0→48 h). In collaboration with these groups, the Goodenough lab generated a second pair of transcriptomes using cw15 and sta6, tracing 0→48 h gene expression patterns under a different set of culture conditions and taking the time course out to 96 h, with an intervening acetate boost. Analysis of these data was deeply informed by cross-comparisons with the Blaby et al. data. Three additional RNA-Seq studies of wild-type strains were also considered.

first: Ursula

last: Goodenough

first: Ian

last: Blaby

first: David

last: Casero

first: Sean

last: Gallaher

first: Carrie

last: Goodson

first: Shannon

last: Johnson

first: Jae

last: Lee

first: Matteo

last: Pellegrini

first: Robyn

last: Roth

first: Jannette

last: Rusch

first: Manmilan

last: Singh

first: James

middle: G

last: Umen

first: Taylor

middle: L

last: Weiss

first: Tuya

last: Wulan


title: A basic helix-loop-helix transcription factors network mediates the brassinosteroid signal

city: Columbus

first: Kengo

last: Morohashi

state: OH

address: 1060 Carmack Rd

department: Molecular Genetics

institute: The Ohio State University

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

overall_design: Refer to individual Series

first: Miroslava

middle: K

last: Zhiponova

first: Erich

last: Grotewold

first: Eugenia

last: Russinova


title: A basic helix-loop-helix transcription factors network mediates the brassinosteroid signal [ChIP-seq]

summary: To investigate the genome-wide occupancies of  INCREASED LEAF INCLINATION1 (ILI1)-BINDING bHLH-1 (IBH1) (At2g43060), IBH1 ChIP analysis followed by direct sequencing (ChIP-Seq) on the p35S::IBH1-GFP (IBH1OE) line and a control line p35S::GFP (GFP OE) were conducted. Antibodies against GFP in the GFP-tagged IBH1 were utilized for immunoprecipitation of the endogenous protein-DNA complex, and the obtained DNA was subjected to next generation sequencing.

overall_design: Observation of genome-wide occupancies of atypical bHLH, INCREASED LEAF INCLINATION1 (ILI1)-BINDING bHLH-1 (IBH1) (At2g43060)


title: A basic helix-loop-helix transcription factors network mediates the brassinosteroid signal [RNA-seq]

summary: To understand how atypical bHLH, INCREASED LEAF INCLINATION1 (ILI1)-BINDING bHLH-1 (IBH1) (At2g43060), and close homologue, IBH1-like1 (IBL1) (At4g30410), interact to regulate cell elongation, genome-wide RNA-Seq expression analyses of IBH1 and IBL1 gain-(IBH1OE, IBL1OE) and loss-of-function (ibh1 (SALK 049177), ibl1(SALK 119457)) mutants were conducted.

overall_design: For loss-of-function mutant, homozygous ibh1(SALK 049177) and ibl1(SALK 119457) were compared to wild type (Col). For gain-of-function mutant, homozygous 35Spro:IBH1-GFP and 35Spro:IBL1-GFP were compared to wild type (Col). Total RNAs were extactced from seedling of each genotypes. For each genotype two biological replicates were sequenced.


title: Identification of Myc and Max genomic targets in mouse embryonic stem cells.

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

institute: University of Torino

summary: Myc is a master transcription factor that has been demonstrated to be required for embryonic stem cell (ESC) pluripotency, self-renewal, and inhibition of differentiation. Although recent works identified several Myc-targets in ESC the list of Myc binding sites is largely incomplete due to the low sensitivity and specificity of the antibodies available so far. To systematically identify Myc binding sites in mouse ESCs here we used a stringent streptavidin based genome-wide chromatin immunoprecipitation (ChIP-Seq) of a biotin-tagged Myc (Bio-Myc) as well as a ChIP-Seq of the Myc partner Max. This analysis identified 4273 Myc binding sites of which more than 85%  co-occupied by Max, overlap with H3K4me3 positive promoters and active enhancers of transcriptional regulators, chromatin modifiers, and genes involved in stem cell self-renewing. The new sites identified were validated experimentally. This study provides a new Myc and Max binding reference in mouse ESCs.

overall_design: ChIP-seq of bio-Myc and Max in E14 and respective controls; Bio-Myc ChIP-seq was performed in a stable clone of E14 mouse embryonic stem cell expressing Biotin-tagged Myc; Mock, Max and IgG were performed in parental wt E14 mESC.

first: Salvatore

last: Oliviero


title: Comparative gene expression profiling of human PGP1 iPS, lymphocyte, donor fibroblasts

status: Public on Mar 04 2014

first: Je

middle: Hyuk

address: 3 Blackfan Circle, CLSB 528

department: Wyss Institute

summary: Human iPS cell line, immortalized B-cells, and primary fibroblasts frome Personal Genome Project voluteer 1

overall_design: Each sample per cell type.

middle: H

first: Kim

last: Robasky

first: Evan

last: Daugharthy

first: George

last: Church


title: Genome-wide activity of unliganded Estrogen Receptor alpha in breast cancer cells [ChIP-Seq]

status: Public on Mar 03 2014

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

institute: University of Turin

summary: Estrogen Receptor α (ERα) has central role in hormone-dependent breast cancer and its ligand-induced functions have been extensively characterized. However, evidence exists that ERα has functions which are independent of ligands. In the present work, we investigated the binding of ERα to chromatin in absence of ligands, and its function(s) on gene regulation. We demonstrated that in MCF7 breast cancer cells unliganded ERα binds to more than four thousands chromatin sites. Unexpectedly, although almost entirely comprised in the larger group of estrogen-induced binding sites, we found that unliganded-ERα binding is specifically linked to genes with developmental functions, as compared to estrogen-induced binding. Moreover, we found that siRNA-mediated downregulation of ERα in absence of estrogen is accompanied by changes in the expression levels of hundreds of coding and noncoding RNAs. Downregulated mRNAs showed enrichment in genes related to epithelial cell growth and development. Stable ERα downregulation using shRNA, which caused cell-growth arrest, was accompanied by increased H3K27me3 at ERα binding sites. Finally, we found that FOXA1 and AP2γ binding to several sites is decreased upon ERα silencing, suggesting that unliganded ERα participates, together with other factors, to the maintenance of the luminal-specific cistrome in breast cancer cells.

overall_design: Examination of unliganded estrogen receptor alpha (ERα) DNA interactions in control and ERα siRNA treated MCF7 cells.

first: Livia

last: Caizzi

first: Santina

last: Cutrupi

first: Francesca

last: Cordero

first: Cecilia

last: Ballarè

first: Valentina

last: Miano

first: Stefania

last: Reineri

first: Laura

last: Ricci

first: Olivier

last: Friard

first: Alessandro

last: Testori

first: Davide

last: Corà

first: Michele

last: Caselle

first: Luciano

last: Di Croce

last: De Bortoli


city: Tel-Aviv

first: Irit

last: Gat-Viks

address: Tel-Aviv

department: Department of Cell Research and Immunology

country: Israel

institute: Tel-Aviv University

summary: Hundreds of immune cell types work in coordination to maintain tissue homeostasis. Upon infection, dramatic changes occur with the localization, migration and proliferation of the immune cells to first alert the body of the danger, confine it to limit spreading, and finally extinguish the threat and bring the tissue back to homeostasis. Since current technologies can follow the dynamics of only a limited number of cell types, we have yet to grasp the full complexity of global in vivo cell dynamics in normal developmental processes and disease. Here we devise a computational method, digital cell quantification (DCQ), which combines genomewide gene expression data with an immune cell compendium to infer in vivo dynamical changes in the quantities of 213 immune cell subpopulations. DCQ was applied to study global immune cell dynamics in mice lungs at ten time points during a 7-day time course of flu infection. We find dramatic changes in quantities of 70 immune cell types, including various innate, adaptive and progenitor immune cells. We focus on the previously unreported dynamics of four immune dendritic cell subtypes, and suggest a specific role for CD103+CD11b- cDCs in early stages of disease and CD8+ pDC in late stages of flu infection.

overall_design: To study pathogenesis of Influenza infection, C57BL/6 mice (5 weeks) were infected intranasally with 4x103 PFU of influenza PR8 virus. We measured using RNA-Seq global gene expression in lung tissue at ten time points during a 7-day time course of infection, two infected individuals in each time point and four un-infected individuals as control. The lung organ was removed and transferred immediately into RNA Latter solution (Invitrogen).

first: Mandelboim

last: Michal

first: Gat-Viks

last: Irit

first: Amit

last: Ido


title: Mutant Huntingtin promotes neuronal death through cell autonomous microglial activation via myeloid lineage- determining factors

status: Public on Mar 02 2014

city: La Jolla

first: Christopher

last: Benner

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: Huntington's Disease (HD) is a fatal neurodegenerative disorder caused by an extended polyglutamine repeat in the N-terminus of the huntingtin (Htt) protein. Reactive microglia and elevated cytokine levels are observed in the brains of HD patients, but the extent to which neuroinflammation results from extrinsic or cell-autonomous mechanisms is unknown. Furthermore, the impact of microglia activation on the pathogenesis of HD remains to be established. Using genome-wide approaches, we show that expression of mutant Htt in microglia promotes cell-autonomous pro-inflammatory transcriptional activation within microglia by increasing the expression and transcriptional activities of the myeloid lineage-determining factors PU.1 and C/EBPs. Elevated levels of PU.1 and its target genes are observed in the brains of mouse models and HD individuals. Moreover, mutant Htt expressing microglia exhibit an increased capacity to induce neuronal death ex vivo and in vivo in the presence of sterile inflammation. These findings suggest that expression of mutant Htt in microglia may contribute to neuronal pathology in Huntingtin disease.

overall_design: RNA-Seq and ChIP-Seq for PU.1, C/EBP, and H3K4me2 in BV2 cells and RNA-Seq in primary microglia and macrophages

first: Andrea

last: Crotti

last: Glass


title: Maternal Nutrition Induces Pervasive Gene Expression Changes but no Detectable DNA Methylation Differences in the Liver of Adult Offspring

first: Matt

last: Cannon

address: 700 Children's Dr.

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

first: Matthew

middle: V

first: David

last: Buchner

first: James

last: Hester

first: Hadley

last: Miller

first: Ephraim

last: Sehayek

first: Joseph

last: Nadeau

last: Serre


title: ChIP-Seq analysis of BATF, IRF4, the Jun proteins, and histone modifications in effector CD8+ T cells

first: R. Anthony

last: Barnitz

address: 450 Brookline Ave.

department: Department of Pediatric Oncology

institute: Dana-Farbert Cancer Institute, Harvard Medical School

summary: The transcription factor BATF is required for Th17 and TFH differentiation. Here, we show that BATF also has a fundamental role in regulating effector CD8+ T cell differentiation.  BATF-deficient CD8+ T cells show profound defects in effector expansion and undergo proliferative and metabolic catastrophe early after antigen encounter.  BATF, together with IRF4 and Jun proteins, binds to and promotes early expression of genes encoding lineage-specific transcription-factors (T-bet and Blimp-1) and cytokine receptors, while paradoxically repressing genes encoding effector molecules (IFNg and granzyme B). Thus, BATF amplifies TCR-dependent transcription factor expression and augments inflammatory signal propagation but restrains effector gene expression.  This checkpoint prevents irreversible commitment to an effector fate until a critical threshold of downstream transcriptional activity has been achieved.

overall_design: This is an examination of 5 different transcription factors (TFs) with 5 different histone modifications in effector CD8+ T cells.  Two of the TFs (BATF and IRF4) and the histone modifications were replicated.  Appropriate control sequence files for ChIP input, IgG ChIP, and Total H3 are also included.

first: R

first: W

last: Haining

first: E

last: Wherry


title: Maternal Nutrition Induces Pervasive Gene Expression Changes but no Detectable DNA Methylation Differences in the Liver of Adult Offspring [selected loci]

summary:
Aims: Epidemiological and animal studies have shown that maternal diet can influence metabolism in adult offspring. However, the molecular mechanisms underlying these changes remain poorly understood. Here, we aim to explore phenotypes induced by maternal obesity in a mouse model and examine gene expression and epigenetic alterations in adulthood induced by maternal diet.
Methods: We analyzed genetically identical male mice born from dams fed a high- or low-fat diet throughout pregnancy and until day 21 postpartum. After weaning, half of the males of each group were fed a high-fat diet, the other half a low-fat diet. We first characterized the genome-wide gene expression patterns of six tissues of adult offspring - liver, pancreas, white adipose, brain, muscle and heart [GSE40903] . We then measured DNA methylation patterns in liver at selected loci and throughout the genome.
Results: Maternal diet had a significant effect on the body weight of the offspring when they are fed an obesogenic diet after weaning. Our analyses showed that maternal diet had a pervasive effect on gene expression, with a pronounced effect in liver where it affected many genes involved in inflammation, cholesterol synthesis and RXR activation. Maternal diet had no detectable effect on DNA methylation in the liver.
Conclusions: Overall, our findings highlighted the persistent influence of maternal diet on adult tissue regulation and suggested that the transcriptional changes were unlikely to be caused by DNA methylation differences in adult liver.

overall_design:
Methylation is compared between nine week old animals fed a common diet as adults, but derived from mothers fed different diets.
Sequence of PCR amplification of bisulfite converted genomic DNA of numerous loci


title: Flu infection

first: Irit

last: Gat-Viks


title: Transcriptomes for hybrids (F1s) between 18 Arabidopsis thaliana parents of the Multiparent Advanced Generation Inter-Cross (MAGIC) genetic mapping resource

status: Public on Mar 01 2014

city: Salt Lake City

first: Richard

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

summary: We produced RNA-Seq reads from messenger RNA isolated from aerial seedling tissue for 9 hybrids (F1s) generated by crossing in a pairwise manner 18 of the founding accessions (inbred strains) of the Multiparent Advanced Generation Inter-Cross (MAGIC) genetic mapping resource for Arabidopsis thaliana (see Gan et al. 2011. Nature, 477:419-23 for a description of the MAGIC genetic mapping resource). The resulting RNA-Seq data provides a resource to assess allele-specific gene expression between A. thaliana accessions.

overall_design: With 18 of the MAGIC parental inbred accessions (Bur-0, Can-0, Col-0, Ct-1, Edi-0, Hi-0, Kn-0, Ler-0, Mt-0, No-0, Oy-0, Rsch-4, Sf-2, Tsu-0, Wil-2, Ws-0, Wu-0, and Zu-0) crosses were performed to generate 9 sets of F1 progeny from which RNA was extracted with biological replication (three replicates) and for which mRNA-seq was performed to generate strand-specific reads. Library construction and sequencing was performed such that each set of biological replicates were sequenced as a pool (with 9-plex barcoding; each 9-plex was run on two HiSeq lanes).

first: Joshua

last: Steffen

first: Robert

middle: T

last: Greenhalgh

first: Edward

last: Osborne

first: Andre

last: Kurlovs

first: Li

last: Lei

last: Toomajian


title: Maternal Nutrition Induces Pervasive Gene Expression Changes but no Detectable DNA Methylation Differences in the Liver of Adult Offspring [RRBS]

first: Matt

last: Cannon

overall_design: Methylation is compared between nine week old animals fed a common diet as adults, but derived from mothers fed different diets.

first: Matthew

last: Buchner