title: Transcriptome sequencing for cancer stem cell properties in MCF-7 cells with knocked down CD24

status: Public on Oct 15 2014

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

institute: NAR Center, Inc. & Genoplan, Inc.

summary: CD24 is the one of cell surface protein that anchored via glycosyl phosphatidylinositol that links to cell surface and modulates growth and differentiation signal many of cell types. A small population of cells, namely ‘Cancer Stem Cells (CSCs)’, charges highly aggressive and metastatic character of cancer cells and shows conformational change of ‘epithelial to mesenchymal transition (EMT). To understand the role of CD24 in CSC and EMT, CD24 was knocked down using siRNA in the MCF7 cell line (MCF-7 hCD24 KD) and analyzed transcriptome profiles by mRNA-sequencing. Corresponding author: Chul Geun Kim, Department of Life Science, Hanyang University, Seoul 133-791, Korea (e-mail, cgkim@hanyang.ac.kr).

overall_design: mRNA profiles of MCF-7 hCD24 KD cells [‘monolayer (m) cultured MCF7 wild type (WT) and mMCF7 CD24KD’ and ‘sphere-forming (s) MCF7 WT and sMCF7 CD24KD’] were generated by deep sequencing using Illumina GAIIx.

first: Dae

middle: H

last: Ha

first: Chang

last: Lim

first: Ji

first: Tae-Young

last: Roh

first: Cheong

middle: K

last: Auh

first: Su-Jae

last: Lee

first: Incheol

last: Shin

first: Jung

middle: M

first: Chul

middle: G


title: The Global Landscape of Transcription Initiation During the Caulobacter Cell Cycle

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

country: USA

institute: Indiana University

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Specific phosphorylation of histone demethylase KDM3A determines target gene expression in response to heat shock

city: Beijing

first: Ye

last: Zhang

state: Not applicable

address: 5 Dongdan Santiao

country: China

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Histone lysine (K) residues, which are modified by methyl- and acetyl-transferases, diversely regulate RNA synthesis. Unlike the ubiquitously activating effect of histone K acetylation, the effects of histone K methylation vary with the number of methyl groups added and with the position of these groups in the histone tails. Histone K demethylases (KDMs) counteract the activity of methyl-transferases and remove methyl group(s) from specific K residues in histones.KDM3A (also known as JHDM2A or JMJD1A) is an H3K9me2/1 demethylase. KDM3Aperforms diverse functions via the regulation of its associated genes, which are involved in spermatogenesis, metabolism, and cell differentiation. However, the mechanism by which the activity of KDM3A is regulated is largely unknown. First, we demonstrated that mitogen- and stress-activated protein kinase 1 (MSK1) specifically phosphorylates KDM3A at Ser264 (pKDM3A), which is enriched in the regulatory regions of gene loci in the human genome under heat shock conditions. p-KDM3A directly interacts with and is recruited by the transcription factor Stat1 to activate KDM3A target genes. The demethylation of H3K9me2 at the Stat1 binding site specifically depends on the co-expression of p-KDM3A under heat shock conditions. In contrast to heat shock treatment, IFN-γ  treatment does not phosphorylate KDM3A via MSK1, thereby abrogating its downstream effects. To our knowledge, this is the first evidence that a KDM can be modified via phosphorylation to determine its specific binding to target genes in response to cellular stress.

overall_design: 3 ChIP samples and two input as controls

first: Mo-bin

last: Cheng

first: Yan

first: Chun-yu

last: Cao

first: Wei-long

first: Yu-fei

last: Shen


title: Transcriptome Analysis of KSHV during de novo primary infection of human CD14+ cells

status: Public on Oct 16 2014

city: Reno

first: Subhash

middle: C

last: Verma

state: NV

address: 1664 N Virginia Street, MS 320

department: Microbiology and Immunology

institute: University of Nevada, Reno

summary: The objective of this study was to identify the viral transcripts packaged into the virion particles and the transcription profiles of the viral genome during early infection, till the virus establishes latent infection in B-cells as well as in endothelial cells

overall_design: Samples from each time points were analyzed and the experiments were done in duplicate.

first: Pravinkumar

last: Purushothaman


title: The neural crest is a source of mesenchymal stem cells with specialized hematopoietic stem-cell-niche function

city: Madrid

first: Carlos

last: Torroja

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Bioinformatics Unit

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

summary: Mesenchymal stem cells (MSCs) And osteolineage cells contribute to the hematopoietic stem cell (HSC) Niche in the bone marrow of long bones. However, Their developmental relationships remain unclear. Here we demonstrate that different MSC populations in the developing marrow of long bones have distinct functions. Proliferative mesoderm-derived nestin- MSCs participate in fetal skeletogenesis, And lose MSC activity soon after birth. In contrast, Quiescent neural-crest-derived nestin+ Cells in the same bones preserve MSC activity, But do not generate fetal chondrocytes. Instead, They differentiate into HSC-niche-forming MSCs, Helping to establish the HSC niche by secreting Cxcl12. Perineural migration of these cells to the bone marrow requires the ErbB3 receptor. The neonatal Nestin-GFP+ PDGFR- Cell population also contains Schwann-cell precursors, But does not comprise mature Schwann cells. Thus, In the developing bone marrow HSC-niche-forming MSCs share a common origin with sympathetic peripheral neurons and glial cells, And ontogenically distinct MSCs have non-overlapping functions in endochondrogenesis and HSC niche formation.

overall_design: Total RNA was isolated from small numbers of FACS sorted stromal cells, obtained from neonatal Nes-Gfp bone marrow preparations (2  biological replicates). Each independent set of samples was obtained from pooled skeletal elements (long bones and sterna) form multiple littermates.

first: Joan

last: Isern

first: Fatima

last: Sanchez-Cabo

first: Simón

last: Méndez-Ferrer


title: Role of MacroH2A core histone variants in liver

city: Philadelphia

first: John

last: Pehrson

state: PA

address: 3800 Spruce Street

institute: University of Pennsylvania


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and opaque2 mutant Transcriptomes

city: Shanghai

first: Weiwei

last: Qi

address: 333 Nanchen Road

institute: Shanghai University

summary: Analysis of  gene expression level. The hypothesis tested in the present study was that opaque2 mutant influence the expression of storage proteins. Results provide important information of the gene expression level regulation of storage proteins and other biological processes.

overall_design: Endosperm mRNA profiles of 15DAP wild type (WT) and opaque2 mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 (Zea mays).

first: Zhenyi

last: Qiao


title: Identification of genes differentially expressed in MZeomesa embryos compared with wild-type

city: Coventry

first: Andrew

middle: Christopher

last: Nelson

address: Gibbet Hill Campus

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

summary: Study of Smad2 and Eomesa genomic binding in zebrafish blastulas, their relationship to eachother and the relaptionship between genomic binding and Ndr1 and Eomesa responsive genes as identified by microarray and RNA-seq.

overall_design: Replicate RNA samples from wild-type and MZeomesa sphere stage embryos

first: Stephen

middle: J

last: Cutty

first: Derek

middle: L

last: Stemple

first: Paul

last: Flicek

first: Ashley

middle: E

last: Bruce

first: Fiona

last: Wardle


title: A Novel Population of Human Cardiac Resident Mesenchymal Stem Cells

city: East Melbourne

first: Alex

last: Hewitt

address: 32 Gisborne St

country: Australia

institute: University of Melbourne

summary: We describe a novel population of human adult cardiac resident stem cells (CRSCs), which are positive for W8B2 antigen, originating from human adult atrial appendages. W8B2+ CRSCs exhibit a spindle-shaped morphology, are clonogenic and able to self-renew. W8B2+ CRSCs show high expression of mesenchymal but not hematopoietic nor endothelial markers. W8B2+ CRSCs expressed GATA4, HAND2, and TBX5, but not C-KIT, SCA-1, NKX2.5, PDGFRα, ISL1 or Wilm’s tumor gene-1 (WT1). W8B2+ CRSCs can differentiate into the cardiovascular lineages and secrete various cytokines.

overall_design: Comparative RNA sequencing was performed using W8B2+ cell from human atrial appendages (passage 2 from 3 different patients), c-Kit+ cell from human atrial appendages (passage 2 from 3 different patients) and W8B2+ cell from bone marrow (passage 3 from 2 different patients, from PromoCell, Heidelberg, Germany).

first: Shiang

middle: Y

last: Lim

middle: W


title: Generation of Naïve Induced Pluripotent Stem Cells from Rhesus Monkey Fibroblasts

status: Public on Oct 14 2014

first: Kang

last: Liu

address: Yiheyuan Road 5

institute: PKU

summary: Conventional embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs) derived from primates resemble mouse epiblast stem cells, raising an intriguing question regarding whether the naïve pluripotent state resembling mouse embryonic stem cells (mESCs) exists in primates and how to capture it in vitro. Here we identified several specific signaling modulators that are sufficient to generate rhesus monkey fibroblast-derived iPSCs with the features of naïve pluripotency in terms of growth properties, gene expression profiles, self-renewal signaling, X-reactivation and the potential to generate cross-species chimeric embryos. Interestingly, together with recent reports of naïve human pluripotent stem cells, our findings suggest several conserved signaling pathways shared with rodents and specific to primates, providing significant insights for acquiring naïve pluripotency from other mammal species. In addition, the derivation of rhesus monkey naïve iPSCs also provides a valuable cell source for use in preclinical research and disease modeling.

overall_design: mRNA expression analysis of  4 rhesus monkey naive iPSC lines and 2 primed iPSC lines were examed.

first: Riguo

last: Fang

first: Yang

last: Zhao

first: Jun

last: Xu

first: Hongkui

last: Deng


title: The Global Landscape of Transcription Initiation During the Caulobacter Cell Cycle [mapping]

first: Jared

last: Schrader

summary: The Caulobacter cell cycle includes in an asymmetric cell division that is driven by a core regulatory circuit comprised of 4 transcription factors (DnaA, GcrA, CtrA, and SciP) and a DNA methyltransferase (CcrM).  Using a modified global 5’ RACE protocol we mapped 2,726 transcriptional start sites (TSS) in the 4mb Caulobacter genome and identified 586 cell cycle-regulated TSS.  The core cell cycle circuit directly controls about 55% of cell cycle-regulated TSS by integrating multiple regulatory inputs within at least 322 promoters, providing a large number of transcription profiles from a small number of regulatory factors.  Here, we identified  previously unknown features of the core cell cycle circuit, including antisense TSS within dnaA and ctrA, plus newly identified TSS for ctrA and ccrM.  Altogether, we identified 615 antisense TSS plus 241 genes that are transcribed from multiple TSS. The multiple TSS in the same promoter region often exhibit different cell cycle activation timing, These novel features of the global transcript profile add significant insight to the system architecture of the Caulobacter cell cycle regulatory circuit.

overall_design: Global 5' RACE was performed to map Transcription Start Sites in the Caulobacter NA1000 genome

first: Bo

last: Zhou

first: Harley

last: McAdams

first: Lucy

last: Shapiro


title: Genome-wide profiling of Smad2 and Eomesa binding in zebrafish blastulas

first: Andrew

last: Nelson

overall_design: Replicate ChIP samples with associated input for Smad2 and Eomesa - 4x ChIP samples (2 per factor); 2x input samples


title: Genome-wide maps of SNAI2 binding in undifferentiated and differentiated keratinocytes

city: La Jolla

first: George

last: Sen

state: CA

address: 9500 GIlman Drive

department: Dermatology/CMM

institute: UCSD

summary: We report the ChIP-Seq results of SNAI2 in several different conditions which include: SNAI2 binding in both control and SNAI2 knockdown cells to demonstrate specificity of the binding. SNAI2 ChIP-Seq was also performed in SNAI2 or control LACZ overexpressing cells cultured in growth medium as well as LACZ or SNAI2 overexpressing cells in differentiation medium.

overall_design: Examination of SNAI2 binding sites across the genome using the 6 different conditions

first: Devendra

last: Mistry


title: Smad2 and Eomesa


title: Purification of macroH2A.1 and macroH2A.2 Nucleosomes from Fetal Mouse Liver

first: John

last: Pehrson

summary: MacroH2As core histone variants have a unique structure that includes C-terminal nonhistone domain. MacroH2As are highly conserved in vertebrates, and are thought to regulate gene expression. However the nature of genes regulated by macroH2As and the biological significance of macroH2As for the organism remain unclear. Our gene expression studies indicate that macroH2A.1 and macroH2A.2 work together to regulate specific genes. In these studies we examine the distributions of macroH2A.1 and macroH2A.2 nucleosomes to determine if they are localized to the genes that show altered expression in macroH2A knockout mouse liver.

overall_design: MacroH2A.1 and macroH2A.2 nucleosomes prepared from ~ 50 fetal mouse livers were purified by thio-affinity chromatography. Five samples were sequenced: Thiopropyl Sepharose, Normal Liver - contains mononucleosomal DNA from macroH2A.1-containing nucleosomes; Activate Thiol Sepharose, Normal Liver - contains mononucleosomal DNA primarily from macroH2A.2-containing nucleosomes. Starting Material, Normal Liver - this is a reference samplefor the first two samples. It contains mononucleosomal DNA from bulk fetal liver chromatin. Activated Thiol Sepharose, Knockout Livers - this is a control sample that contains mononucleosomal DNA from non-macroH2A nucleosomes that contaminate the macroH2A.2 nucleosomes. This fraction was prepared from macroH2A1/2 double knockout fetal livers; Starting Material, Knockout Liver - this is a reference sample for the fourth sample. It contains mononucleosomal DNA from bulk chromatin prepared from macroH2A1/2 double knockout fetal livers.

middle: R


title: RNA sequencing identifies specific PIWI-interacting small non-coding RNA expression patterns in breast cancer

city: Oslo

first: Adnan

last: Hashim

state: Oslo

address: NCMM - Forskningsparken, House 1, 3rd Floor - Gaustadalléen 21

department: NCMM (Centre for Molecular Medicine Norway)

country: Norway

institute: UiO (University of Oslo)

type: Non-coding RNA profiling by high throughput sequencing

summary: PIWI-interacting RNAs (piRNAs) are a novel class of small ncRNAs initially isolated from germ line cells; although recent studies report that they are expressed also in somatic cells. To elucidate the role of piRNAs in somatic cells, in particular from breast cancer, we performed the first extensive next generation sequencing expression analysis of small RNA transcriptomes of hormone responsive breast cancer cell lines in different culture conditions. In addition, to understand the behavior of piRNAs with respect to miRNAs in breast tumor tissues, small RNA sequence data set available in Gene Expression Omnibus (GSE39162)  database was used. Results led to the identification of ~100 and ~150 human piRNAs in the breast cancerous cell lines and tumors respectively, several of which differentially expressed in cell lines under different experimental conditions tested or in response to ERβ and in tumor tissues. Western blotting and Q-PCR analysis also revealed the presence in breast cell lines of PIWIL (PIWI Like) subfamily members proteins encoded in the human genome (PIWIL2/HILI and PIWIL4/HIWI2) and of other components of the piRNA biogenesis pathways, suggesting that this might indeed be functional in somatic cells. These results show that piRNAs are expressed in human somatic cells, in particular in cancer, where their expression is influenced by neoplastic transformation, growth conditions and estrogen receptor beta. More important, we demonstrate for the first time a distinct pattern of piRNAs expression in cancerous vs normal breast tissues, which suggests a potential role of these epigenetic modulators in mammary carcinogenesis and maintenance of the cancer cell phenotype.

overall_design: In addition, to understand the behavior of piRNAs with respect to miRNAs in breast tumor tissues, small RNA sequence data set available in Gene Expression Omnibus (GEO; GSM957192 TAX577740T ,GSM957194 TAX577740N, GSM957195 TAX577453T, GSM957197 TAX577453N, GSM957198 TAX577745T, GSM957200 TAX577745N, GSM957201 TAX577579T, GSM957203 TAX577579N) was used.

first: Alessandro

last: Weisz

first: Francesca

last: Rizzo


title: Detection of circRNA in Drosophila Fly heads and S2 cells using RNA-seq with or without RNaseR tretment

city: Waltham

first: Sebastian

last: Kadener

state: MA

address: 415 South Street

institute: Brandeis University

summary:
We determined circRNA abundance in fly Heads and S2 cells by generating and analyzing high-throughput RNA-sequencing libraries prepared from rRNA-depleted RNA.
In order to determine whether the observed sequencing reads are due to bona fide circRNAs, we pre-treated the RNA with RNAse-R before the rRNA-depletion procedure. Indeed, most of the identified circRNAs  were more enriched in comparison to the canonical mRNA isoforms following the RNAse-R treatment.
We compare circRNA levels in wt (Canton S) flies with flies  carrying the C4  ("slow polymerase") mutation.

overall_design: 4 samples of Drosophila Canton S and 4 samples of flies carrying the C4  ("slow polymerase") mutation. For each sample, one library was prepared from RNA after RNaseR treatment and the second from RNA with without treatment (mock). RNA library from one Canton Sample was used for stranded libray preprepation.

first: Nikolaus

last: Rajewsky


title: Quantitative Analysis of Wild Type(wt) and Setd2 knockout(ko) mESCs Transcriptomes [RNA-Seq]

first: Qiuhua

last: Huang

address: 197 ruijin road II

institute: Shanghai Institute of Hematology

summary:
Purpose: This study aimed at exploring the deregulated genes in setd2 knockout mESCs compared with wt, more particularly to find the mechanism controlled by setd2,which was required for endoderm differentiation.
Methods: Setd2 wt and ko mESCs were generated by deep sequencing, using Illumina GAIIx. Using Avadis NGS (version:1.3) software to analyze the sequence reads that passed quality filter to acquire the expression level of all genes. qRT–PCR validation was performed usingSYBR Green assays.
Results: Using an optimized data analysis workflow, we mapped about 80 million sequence reads per sample to the mouse genome (build mm9) and identified 17,827 transcripts in the sted2 wt and ko mESCs. About 2,516 genes were deregulated in setd2 ko mESCs, more than 10 genes were validated using qRT-PCR.
Conclusions: Through RNA-seq,we noticed that a subset of genes that related to MAPK signaling pathways were down-regulated in ko mESCs. This provided a bridge to connect setd2 and mESCs endoderm differentiation.

overall_design: One wt and one ko mESCs were generated by deep sequencing, using Illumina GAIIx.

first: Yuanliang

last: Zhang

first: Zhu

last: Chen

first: Qiuhuang

first: Saijuan


title: TOP1α functions on nucleosome density

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

institute: shenzhen university

summary: DNA topoisomerases release supercoils in DNA introduced during replication or transcription. How DNA topoisomerases impact transcription in the context of eukaryotic chromatin is poorly understood. In this study, using a floral stem cell model in Arabidopsis, we uncovered a role of TOP1α in Polycomb Group (PcG) protein-mediated histone lysine 27 trimethylation at, and transcriptional repression of, the stem cell maintenance gene WUSCHEL (WUS). The strong genetic interactions between a top1α mutant and mutations in PcG genes and the overwhelming enrichment of PcG targets among genes affected in expression in the top1a mutant revealed a role of TOP1α in PcG-mediated regulation. Intriguingly, not only the repression of some PcG target genes but also the expression of others requires TOP1α. The mechanism that unifies the opposing effects of TOP1α on PcG target genes appears to lie in its role in decreasing nucleosome density. Genome-wide nucleosome mapping shows that TOP1α is required for the depletion of nucleosomes at regulatory regions of genes, which probably allows the binding of factors that either recruit PcG, as we show for AGAMOUS at the WUS locus, or counteract PcG-mediated regulation. This study uncovers a strong and previously unknown connection between TOP1α and PcG.

overall_design: 4 samples in total, two replicates from Ler and top1a-2 plants

first: Xigang

last: Liu

first: Xuemei


title: Gene expression pattern between Wild-type and Setd2 knockout mESCs


title: Large-Scale Identification of Coregulated Enhancer Networks in the Adult Human Brain

city: Rotterdam

first: Menno

middle: P

last: Creyghton

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus MC

summary: The complexity of the brain and the links entailed to its functional diversity remain a major challenge of biology to understand. Distinct anatomical areas regulate a vast array of processes including organismal homeostasis, cognitive functions and susceptibility to neurological pathologies, many of which define our species. Distal enhancers have emerged as key regulatory elements that acquire epigenetic modifications in a cell-type specific manner, thus enforcing cell- and species-specific gene expression programs. Here, we survey the epigenetic landscape of promoters and cis-regulatory elements in 87 anatomically distinct regions of the human brain, spanning over a hundred different anatomical structures.

overall_design:
ChIP-Seq of various regions of the human brain. Also includes mouse and rat samples.

Contributor: The Netherlands Brain Bank

first: Marit

last: Vermunt

first: Peter

last: Reinink

first: Jeroen

last: Korving

first: Ewart

last: de Bruijn

first: Paul

last: Creygthon

first: Onur

last: Basak

first: Geert

last: Geeven

first: Pim

last: Toonen

first: Nico

last: Lansu

first: Charles

last: Meunier

first: Sebastiaan

last: van Heesch

first: Hans

last: Clevers

first: Wouter

last: de Laat

first: Edwin

last: Cuppen


title: Comparative transcriptome of S. aureus strains

status: Public on Oct 13 2014

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

summary: We report the transcriptome profiles (RNA seq) of three different co-isolates of S.aureus that have been identified and isolated in both laboratory and infective scenarios. The transcriptome profiles were generated by deep sequencing and transcript levels assessed. For this the raw reads underwent quality-trimming (using the FastX suite), polyA-clipping, size filtering, mapping to the reference genome, coverage calculation, gene wise expression quantification followed by differential gene expression analysis (all done by the tool "READemption" (Förstner et al., unpublished) using "segemehl" (Hoffmann et al., 2009) and "DESeq" (Anders et al., 2010). RT-PCR as well as phenotypical assays were further used to validate the data. Differential gene expression between the isolates was observed in 4% (116 of 2774 genes). This had a significant impact on the physiology of each strain.

sample_organism: Staphylococcus aureus subsp. aureus USA300

overall_design: RNA profiles of 3 different subpopulations of S.aureus generated by deep sequencing

first: Gudrun

last: Koch

middle: U

first: Ana

last: Yepes

first: Charlotte

last: Wermser

first: Jennifer

last: Modamio

first: Kevin

last: Foster

first: Daniel

last: Lopez


title: miR-155 promotes Th17 development by targeting Jarid2

status: Public on Oct 12 2014

city: Dallas

first: Gokhul

middle: Krishna

last: Kilaru

state: TEXAS

address: 6000 Harry Hines Boulevard

department: Department of Neuroscience

institute: University of Texas Southwestern Medical Center

summary: Genome-wide analysis was performed on microRNA 155+/+ and -/- Th17 cells to determine the differentially expressed transcripts that are regulated by miR-155. We found that Jarid2 was differentially expressed in absence of miR-155 and highlight the mechanism for the silencing of IL-22 by Jarid2 and PRC2 in miR-155-/- Th17 cells.

overall_design: Comparison of transcriptome of Th17 cells in presence or absence of microRNA 155

first: Thelma

last: Escobar

first: Patrick

last: Burr

first: Cuong

last: Nguyen

first: Stefan

middle: A

last: Muljo


title: Exploring the mechanism of C4 photosynthetic differentiation through a unified comparative analysis of maize and rice leaf transcriptomes

city: New Haven

first: Timothy

last: Nelson

state: CT

department: Department of Molecular, Cellular and Developmental Biology

institute: Yale University

summary: Maize and rice are the two most economically important grass crops and utilize distinct forms of photosynthesis to fix carbon: C4 and C3 respectively. Relative to C3 photosynthesis, C4 photosynthesis reduces photorespiration and affords higher water and nitrogen use efficiencies under hot arid conditions. To define key innovations in C4 photosynthesis, we profiled metabolites and gene expression along a developing leaf gradient. A novel statistical method was implemented to compare transcriptomes from these two species along a unified leaf developmental gradient and define candidate cis-regulatory elements and transcription factors driving photosynthetic gene expression. We also present comparative primary and secondary metabolic profiles along the gradients that provide new insight into nitrogen and carbon metabolism in C3 and C4 grasses. These resources, including community viewers to access and mine these datasets, will enable the elucidation and engineering of C4 photosynthetic networks to improve the photosynthetic capacity of C3 and C4 grasses.

sample_organism:
Oryza sativa
Zea mays

platform_organism:
Oryza sativa
Zea mays

overall_design:
[Maize]  Nine day old third leaves of maize were cut into fifteen 1 cm segments; samples were pooled from an average of seven plants per biological replicate and six biological replicates in total were collected on different dates.
[Rice]  14 day old third leaves of rice were cut into eleven 2 cm segments, samples were pooled from an average of 15 plants per biological replicate and four replicates in total were collected.

first: Thomas

last: Brutnell

first: Lin

last: Wang


title: Deep sequencing analyses of Pine wood nematode Bursaphelenchus xylophilus microRNAs reveal distinct miRNA expression patterns during the pathological process of pine wilt disease

status: Public on Oct 11 2014

city: Nanjing

first: Xiaolei

last: Ding

address: No.159 Longpan Road

institute: Nanjing Forestry University

summary: Bursaphelenchus xylophilus is known as the causative agent of pine wilt disease with complex life cycles. In this research, newly published Bursaphelenchus xylophilus genome data were employed to annotate its miRNAs based on deep sequencing technologies.  Four small RNA libraries derived from different infection stages of pine wilt disease were constructed and sequenced. Consequently, we obtained hundreds of evolutionarily conserved miRNAs as well as novel miRNA candidates. The analysis of miRNA expression patterns showed that most miRNAs were expressed at extraordinarily high levels during the middle stage of pine wilt disease. Subsequent stem-loop RT-PCR experiments were carried out to validate our results. Functional analysis proved that expression levels of miR-73 and miR-239 were mutually exclusive with their target GH45 cellulase genes., genes known to be responsible for the degradation of the pine cell walls.  In addition, another set of atypical miRNAs, termed mirtrons, were identified from B. xylophilus introns. This discovery has expanded the current knowledgebase of such splicing-derived miRNAs into B. xylophilus. Thus, our research has provided detailed characterization of B. xylophilus miRNAs expression patterns during the pathological process of pine wilt disease. The findings will contribute to more in-depth understanding of this devastating plant disease.

overall_design: For the purposes of this study, we classified the pathogenic process associated with PWD into three stages in order to best characterize the expression patterns of microRNAs during the development of this devastating disease. The following describes the first stage (F): about seven days after pine trees are infected with PWNs, the tips of the pine needles begin to turn brown. Next, the middle stage (M) ensues approximately seven days later, when half of the needles on pine trees turn brown. The last stage (L) occurs another 10 days later and pine needles are complete browning. PWNs cultured on Botrytis cinerea grown on PDA medium served as the control stage (C).

first: Jianren

last: Ye


title: Identifying genes regulated by Kruppel-like factor-9 by RNA-seq in human glioblastoma stem cells.

status: Public on Oct 10 2014

city: Baltimore

first: Mingya

last: Ying

state: MD

address: 707 N Broadway

department: Neurology

institute: Kennedy Krieger Institute

summary: Kruppel-like factor-9 (KLF9), a member of the large KLF transcription factor family, has emerged as a regulator of oncogenesis, cell differentiation and neural development; however, the molecular basis for KLF9’s diverse contextual functions remains unclear. This study focuses on the functions of KLF9 in human glioblastoma stem-like cells. We establish for the first time a genome-wide map of KLF9-regulated targets in human glioblastoma stem-like cells, and show that KLF9 functions as a transcriptional repressor and thereby regulates multiple signaling pathways involved in oncogenesis and stem cell regulation. A detailed analysis of one such pathway, integrin signaling, shows that the capacity of KLF9 to inhibit glioblastoma cell stemness and tumorigenicity requires ITGA6 repression. These findings enhance our understanding of the transcriptional networks underlying cancer cell stemness and differentiation, and identify KLF9-regulated molecular targets applicable to cancer therapeutics.

overall_design: Two cell lines were used as biological replicates. Each cell line has one KLF9 induction sample and one control sample.

first: John

last: Laterra

first: Mingyao

first: Hongkai

last: Ji

first: Yingying

last: Wei

first: Jessica

last: Tilghman


title: Su(H) early embryonic ChIP-seq

city: Pasadena

first: Angelike

last: Stathopoulos

address: 1200 E. California Blvd - MC114-96

department: Biology and Biological Engineering

institute: California Institute of Technology

summary: This submission data was generated in Angela Stathopoulos's lab.  Project goal was to map Su(H) associated regions on Drosophila melanogaster genome.  In Drosophila embryos, a nuclear gradient of Dorsal (Dl) directs differential gene expression along the dorsoventral (DV) axis, translating it into distinct domains separated by sharp boundaries between future mesodermal, neural and ectodermal territories. However, the mechanisms used to differentially position gene expression boundaries along this axis are not fully understood. Here, we show that the transcription factor Suppressor of Hairless [Su(H)] influences the positioning of dorsal boundaries for many genes expressed along the DV axis. Synthetic reporter constructs provide molecular evidence that Su(H) binding sites support repression and act to counterbalance activation through Dl and the ubiquitous activator Zelda.  Overall, our study highlights a role for broadly expressed repressors, like Su(H), and organization of transcription factor binding sites within cis-regulatory modules as important elements controlling spatial domains of gene expression, to facilitate flexible positioning of boundaries across the entire DV axis.

overall_design: 1 g of 2-4 hour yw embryos were used.  Two replicate ChIP-seq samples were analyzed using goat (Santa cruz goat polyclonal #sc-15813), and rabbit (Santa cruz rabbit polyclonal #sc-25761) antibodies.

first: Anil

last: Ozdemir

first: Lijia

last: Ma

first: Kewin

last: White

first: Angela


title: Differential microRNA expression and microRNA editing upon HP-PRRSV infection in vivo across different pig breeds

city: Beijing

first: Ning

last: Li

state: Beijing

address: Yuanmingyuan West Rd. 2,Haidian District

institute: China Agriculture University

summary:
Purpose: To characterize the differential microRNA expression profiles and microRNA editing upon PRRSV infection, using NGS techonology, we sequenced small RNAs of the lungs of Tongcheng and Landrace pigs before (0 dpi) and after (3, 5, 7 dpi) infection with high-pathogenic PRRSV (HP-PRRSV).
Methods: The miRNA expression profiles of the lungs of Tongcheng and Landrace pigs before (0 dpi) and after (3, 5, 7 dpi) HP-PRRSV infection were produced by using solexa platform. The raw reads with low qualities were filtered and the clean high quality reads were mapped to Ensembl Sus reference genome 10.2.71 using BWA. The unique mapped reads were retained for microRNA expression analysis. The raw reads counts of each microRNA were calculated by perl scripts and the differentially expressed microRNA (Fold change >2; FDR <0.05) were called using edgeR. The microRNA editing was identified using the methods described by Alon, S. and E. Eisenberg. Methods Mol Biol, 2013. Further analysis of microRNA editing was performed with perl scripts.

overall_design: Comparison of the microRNA expression profiles and microRNA editing profiles of lungs from two pig breeds: Tongcheng and Landrace, at 0, 3, 5, 7 dpi infected with HP-PRRSV.

first: Jia


title: Whole genome methylation maps of Wild Type (WT), mutant (ddm1) and epiRILs

city: PARIS CEDEX 05

first: Vincent

last: Colot

address: 46 rue d'Ulm

country: France

institute: Institut de Biologie de l'Ecole Normale Supérieure (IBENS) Section 3

type: Methylation profiling by high throughput sequencing

summary: DNA methylation profiling in Wild Type (WT), mutant (ddm1) and epiRILs  (060-098-202-260-344-480)

overall_design: 1 biological replicate per sample - Bisulfite-seq

first: Mohamed

last: Kassam

first: Evelyne

last: Duvernois-Berthet


title: The role of small RNAs on phenotypes in reciprocal hybrids between Solanum lycopersicum and S. pimpinellifolium

city: Hangzhou

first: Junxing

address: Yuhangtang Road 866

institute: Institute of Vegetable Science, Zhejiang University

summary: we found the expression levels of 76 known miRNAs were highly variable between the reciprocal hybrids through the high-throughput sequencing of small RNAs

sample_organism: Solanum lycopersicum x Solanum pimpinellifolium

overall_design: small RNA sequencing were performed in Solanum lycopersicum, S. pimpinellifolium and their reciprocal hybrids

first: Liping

last: Chen


title: Enhancers implicate new genes in QT interval below GWAS detection threshold

city: Cambridge

first: Xinchen

last: Wang

address: 32 Vassar St, D514

institute: MIT

summary: Our goal is to identify high-confidence candidate genes associated with sub-threshold QT interval loci. We predicted enhancer-promoter targets using two different methods.

overall_design:
1) We used the correlation in activity between enhancers and transcribed genes across 59 human cell lines and tissues to identify significantly correlated enhancer-promoter pairs that represent potential regulatory interactions.

2) We used chromosome conformation capture followed by high-throughput sequencing (4C-seq) to probe physical enhancer-promoter interactions.


title: Malaria Host Pathogen Interaction Center Experiment 13: Gene and exon transcript abundances of uninfected Macaca mulatta treated with pyrimethamine over 7 time points in a 100 day study

city: Atlanta

first: Mary

last: Galinski

state: GA

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

summary: The Malaria Host-Pathogen Interaction Center (MaHPIC) is a transdisciplinary malaria systems biology research program initially supported by an NIH/NIAID contract (# HHSN272201200031C, 2012-2017; see http://www.systemsbiology.emory.edu). The MaHPIC continues with ongoing support from the Defense Advanced Research Project Agency (DARPA) and others. The MaHPIC generates many data types (e.g., clinical, hematological, parasitological, metabolomics, functional genomics, lipidomics, proteomics, immune response, telemetry) and mathematical models, to iteratively test and develop hypotheses related to the complex host-parasite dynamics in the course of malaria in non-human primates (NHPs), and metabolomics data via collaborations with investigators conducting clinical studies in malaria endemic countries, with the overarching goal of better understanding human disease, pathogenesis, and immunity. Curation and maintenance of all data and metadata are the responsibility of the MaHPIC:  Mary Galinski mary.galinski@emory.edu (MaHPIC Program Director), Jessica Kissinger jkissinger@uga.edu (MaHPIC Co-Program Director), and Alberto Moreno alberto.moreno@emory.edu (MaHPIC Co-Program Director).

overall_design:
The experimental design of this pyrimethamine administration experiment with Macaca mulatta was approved by the Emory University Institutional Animal Care and Use Committee (IACUC) and is as follows. Five naive males (RCs13, RWr13, RUn13, RZe13 and RTi13) approximately 2 years of age were injected intravenously with a preparation of Anopheles dirus salivary gland material and then profiled for clinical and omic measurements over the course of a 100-day experiment. Samples were generated and analyzed as part of a multi-omic approach to understanding the effects that the anti-malarial drug pyrimethamine has on immune physiology in rhesus macaques (M. mulatta).  There was no infection with Plasmodium parasites during this study. Whole blood and bone marrow RNA-Seq and plasma have been obtained for seven time-points before, during and after three rounds of drug administration.  Samples are from either whole blood or bone marrow specimen types.  5 individuals were sampled for each specimen type, 7 times each over the 100 day experiment. 5 individuals * 2 specimen types * 7 time points = 70 samples.
Biological samples (Whole Blood or Bone Marrow) were collected at 7 time points during the 100 days.  These correspond to:
Time Point 1 = Day 0 (Baseline Sampling Point) Time Point 2 = Day 21 Time Point 3 = Day 27 Time Point 4 = Day 52 Time Point 5 = Day 59 Time Point 6 = Day 90 Time Point 7 = Day 98
Pyrimethamine was administered on Days 21, 52, 53, 54, 90, 91, and 92.

first: Greg

last: Gibson

first: Alberto

last: Moreno

last: Kissinger

first: Mark

last: Styczynski

first: Kevin

last: Lee

first: Suman

last: Pakala

first: Vishal

last: Nayak

first: Stacey

last: Lapp

first: ViLinh

last: Tran

first: Karan

last: Uppal

first: Dean

last: Jones

first: Dalia

last: Arafat

first: Esmeralda

last: Meyer

first: Monica

last: Cabrera

first: Yan

last: Tang

first: Weiwei

last: Yin

first: Jeremy

middle: D

last: DeBarry


title: Extensively Self-Renewing Erythroblasts Derived from Transgenic β-Yac Mice are a Novel Model System for Studying Globin Switching and Erythroid Maturation

status: Public on Oct 08 2014

city: Rochester

first: Laurie

last: Steiner

state: New York

address: 601 Elmwood Ave

department: Pediatrics

institute: University of Rochester

summary: Extensively Self Renewing Erythroblasts (ESREs) are cultured erythroid cells derived from yolk sack or fetal liver. Transcriptome analyses were conducted on ESREs using RNA-seq and compared to published transcriptome analyses of uncultured erythroid cells.

overall_design: RNA-seq was conducted on proliferating Extensively Self Renewing Erythroblasts (ESREs) and ESREs after one day of maturation.  Biologic duplicates were done at each time point.


title: Enhancer Activation Requires Trans-Recruitment of a Mega Transcription Factor Complex

status: Public on Oct 09 2014

city: La Jolla

first: Daria

last: Merkurjev

address: 9500 Gilman Drive, Mail Code 0648

department: Medicine

institute: UCSD

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

Enhancers provide critical information directing cell-type specific transcriptional programs, regulated by binding of signal-dependent transcription factors and their associated cofactors. Here we report that the most strongly activated estrogen (E2)-responsive enhancers are characterized by trans-recruitment and in situ assembly of a large 1-2MDa complex of diverse DNA-binding transcription factors by ERα at ERE-containing enhancers. We refer to enhancers recruiting these factors as mega transcription factor-bound in trans (MegaTrans) enhancers. The MegaTrans complex is a signature of the most potent functional enhancers and is required for activation of enhancer RNA transcription and recruitment of coactivators, including p300 and Med1. The MegaTrans complex functions, in part, by recruiting specific enzymatic machinery, exemplified by DNA-dependent protein kinase. Thus, MegaTrans-containing enhancers represent a cohort of functional enhancers that mediate a broad and important transcriptional program and provide a molecular explanation for transcription factor clustering and hotspots noted in the genome.

overall_design: Refer to individual Series


title: Enhancer Activation Requires Trans-Recruitment of a Mega Transcription Factor Complex (Gro-seq)

summary: Enhancers provide critical information directing cell-type specific transcriptional programs, regulated by binding of signal-dependent transcription factors and their associated cofactors. Here we report that the most strongly activated estrogen (E2)-responsive enhancers are characterized by trans-recruitment and in situ assembly of a large 1-2MDa complex of diverse DNA-binding transcription factors by ERα at ERE-containing enhancers. We refer to enhancers recruiting these factors as mega transcription factor-bound in trans (MegaTrans) enhancers. The MegaTrans complex is a signature of the most potent functional enhancers and is required for activation of enhancer RNA transcription and recruitment of coactivators, including p300 and Med1. The MegaTrans complex functions, in part, by recruiting specific enzymatic machinery, exemplified by DNA-dependent protein kinase. Thus, MegaTrans-containing enhancers represent a cohort of functional enhancers that mediate a broad and important transcriptional program and provide a molecular explanation for transcription factor clustering and hotspots noted in the genome.

overall_design: Global Run On (GRO) assay followed by high throughput sequencing (GRO-seq)

first: Zhijie

last: Liu

first: Michael

last: Rosenfeld


title: Mechanisms for U2AF to define 3′ splice sites and regulate alternative splicing in the human genome

city: Wuhan

first: Bo

last: Yang

state: Hubei

address: Luo-jia-shan, Wuchang

department: Biochemistry and Molecular Biology

institute: College of Life Sciences, Wuhan University

summary: The U2AF heterodimer has been well studied for its role in defining functional 3’ splice sites in pre-mRNA splicing, but many fundamental questions still remain unaddressed regarding the function of U2AF in mammalian genomes. Through genome-wide analysis of U2AF-RNA interactions, we report that U2AF has the capacity to directly define ~88% of functional 3’ splice sites in the human genome, but numerous U2AF binding events also occur in intronic locations. Mechanistic dissection reveals that upstream intronic binding events interfere with the immediate downstream 3’ splice site associated with either the alternative exon to cause exon skipping or with the competing constitutive exon to induce exon inclusion. We further demonstrate partial functional impairment with mutations in U2AF35, but not U2AF65, in regulated splicing. These findings reveal the genomic function and regulatory mechanism of U2AF in both normal and disease states.

overall_design: Examination of U2AF heterodimer regulated splicing in Hela cells with CLIP-seq (U2AF65), paired-end RNA-seq (si-NC and si-U2AF65) and RASL-seq (respective three biological replicates of WT, si-NC, si-U2AF65, si-U2AF35, si-NC + pcDNA3.0, si-U2AF65 + pcDNA3.0, and si-U2AF65 + Flag-U2AF35)

first: Changwei

last: Shao

first: Tongbin

last: Wu

first: Jie

last: Huang

first: Peng

first: Yu

last: Zhou

first: Jinsong

last: Qiu

first: Li

last: Jiang

first: Hairi

last: Li

first: Geng

last: Chen

first: Hui

last: Sun

first: Yi

last: Zhang

first: Alain

last: Denise

first: Dong-Er

first: Xiang-Dong

last: Fu


title: Enhancer Activation Requires Trans-Recruitment of a Mega Transcription Factor Complex (ChIP-seq)

first: Daria

overall_design: Chromatin Immunoprecipitation (ChIP) assay followed by high throughput sequencing (ChIP-seq)

first: Zhijie


title: Repeat elements study in pluripotent stem cells [RNA-seq]

city: Nantong

first: Gangcai

last: Xie

state: Jiangsu

address: Number 9, Se Yuan Road

department: Medical school

institute: Nantong University

summary: We surveyed RNA-Seq data to identify those TEs that are transcriptionally active uniquely in human pluripotent cells. We identified one endogenous retrovirus (HERV-H) family, uniquely found in primates as being unusually abundant in the transcriptome.

overall_design: Poly(A)+ RNA extraction and further sequencing library construction was done for two types of cells (iPS, HFF-1) and hiPSC-derived embryoid bodies following Illumina TruSeq RNA Sample Preparation Kit protocol, which was further sequenced on Illumina HiSeq machine with single-end 101 cycles.

first: Jichang

last: Wang

first: Manvedra

last: Singh

first: Avazeh

middle: T

last: Ghanbarian

first: Tamás

last: Raskó

first: Attila

last: Szvetnik

first: Huiqiang

last: Cai

first: Daniel

last: Besser

first: Alessandro

last: Prigione

first: Nina

last: Fuchs

first: Gerald

last: Schumann

first: Wei

first: Matthew

last: Lorincz

first: Zoltán

last: Ivics

first: Laurence

last: Hurst

first: Zsuzsanna

last: Izsvák


title: Repeat elements study in pluripotent stem cells

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


title: Musashi-2 HITS-CLIP sequencing in K562 cells

status: Public on Oct 07 2014

city: New York

first: Yuheng

last: Lu

state: NY

address: 417 East 68th Street

institute: Memorial Sloan Kettering Cancer Center

summary: Hematopoietic stem cells (HSCs) are maintained through the regulation of symmetric and asymmetric cell division. We report that conditional ablation of the RNA-binding protein Msi2 results in a failure of HSC maintenance and engraftment caused by a loss of quiescence and increased commitment divisions. Contrary to previous studies, we found that these phenotypes were independent of Numb. Global transcriptome profiling and RNA target analysis uncovered Msi2 interactions at multiple nodes within pathways that govern RNA translation, stem cell function, and TGF-β-signaling. Msi2-null HSCs are insensitive to TGF-β–mediated expansion and have decreased signaling output, resulting in a loss of myeloid-restricted HSCs and myeloid reconstitution. Thus, Msi2 is an important regulator of the HSC translatome and balances HSC homeostasis and lineage bias.

overall_design: One empty vector control– and two Flag-MSI2–overexpressing K562 cell samples were analyzed using HITS-CLIP protocol

first: Michael

middle: G

last: Kharas


title: Tracing the transcriptomic changes of synthetic trigenomic allohexaploid in Brassica by RNA-Seq approach

city: wuhan

first: Qin

last: Zhao

address: luojiashan

institute: wuhan university

summary: We explored the transcriptomic changes of synthetic Brassica allohexaploid by comparing to its parents using a high-throughput RNA-Seq method. A total of 35644409 sequence reads were generated, and 32642 genes were aligned from the data. There were 29260, 29060 and 29697 genes identified in Brassica rapa, Brassica carinata, and Brassica allohexaploid, respectively. We screened differentially expressed genes (DEGs) by a standard of two-fold or greater change in expression and false discovery rate (FDR) no more than 0.001. As a result, 7397 DEGs were detected between Brassica hexaploid and its parents. A large proportion of the 3184 DEGs between Brassica hexaploid and its paternal parent B. rapa was involved in biosynthesis of secondary metabolites, plant-pathogen interaction, photosynthesis, and circadian rhythm. Between Brassica hexaploid and its maternal parent B. carinata, 2233 DEGs were screened. A lot of them had functions of plant-pathogen interaction, plant hormone signal transduction, ribosome, limonene and pinene degradation, photosynthesis, and also biosynthesis of secondary metabolites. In addition, we found many transcription factor genes, methyltransferase and methylation genes that showed differential expression between Brassica hexaploid and its parents.

sample_organism:
Brassica rapa
Brassica carinata
Brassica carinata x Brassica rapa

overall_design: Leaf mRNA profiles of Brassica rapa, Brassica carinata, and Brassica allohexaploid

first: Jianbo


title: BCR-ABL1 promotes leukemia by converting p27 into a cytoplasmic oncoprotein

city: Portland

first: David

last: Ellison

state: OR

address: 3181 SW Sam Jackson Park Rd CR145

institute: Oregon Health and Science University

summary: Coordinated BCR-ABL1 kinase-dependent and -independent mechanisms convert p27 from a nuclear tumor suppressor to a cytoplasmic oncogene. Persistence of oncogenic p27 functions despite effective inhibition of BCR-ABL1 may contribute to resistance to tyrosine kinase inhibitors.

overall_design: BCR-ABL1 induced p27 versus knockout, controlling with Empty vector p27 versus knock out

last: Deininger

first: Anupriya

last: Agarwal


title: Charaterization of genetic alterations and gene expression signatures found in BCR-ABL inhibitor-resistant KCL-22 subpopulations and single clones

first: Joshua

middle: M

last: Korn

address: 250 Mass Ave

institute: Novartis

summary: KCL-22 is a chronic myeloid leukemia (CML) cell line derived from a patient in blast crisis phase and harbors the BCR-ABL translocation. The catalytic (ATP-competitive) BCR-ABL inhibitors imatinib and nilotinib have dramatically improved CML patient outcome, but the development of resistance remains a clinical challenge. The recent identification of allosteric BCR-ABL inhibitors, such as GNF-2, which target the enzyme by binding to the myristoyl pocket rather than catalytic site of ABL1, may provide a strategy to broadly overcome resistance to the class of ABL1 ATP competitive inhibitors. We therefore wanted to use the ClonTracer barcoding system to compare the clonal responses of KCL-22 to imatinib, nilotinib and GNF-2. RNA-seq was employed to characterize genetic alterations and gene expression signatures in the pooled cell populations resistant to BCR-ABL inhibitors as well as single clones showing differential response to the three inhibitors.

overall_design: mRNA profiling of the subpopulations and single clones of human CML cell line KCL-22 that contribute to BCR-ABL inhibitor resistance

first: Hyo-eun

last: Bhang

last: Ruddy

last: Rakiec

first: Frank

last: Stegmeier


title: CD161 defines a transcriptional and functional phenotype shared across distinct human T cell lineages (TCRgd)

city: Oxford

first: Joannah

last: Fergusson

state: select a state

address: South Parks Road

department: Peter Medawar Building for Pathogen Research

institute: University of Oxford

summary: T lymphocytes are conventionally divided into subsets based upon expression of co-receptors, cytokines and surface molecules.  By mRNA microarray analysis, T lymphocytes that express the C-type lectin CD161 were identified to share a transcriptional profile, which led to the identification of an innate function across these previously defined subsets, including CD8, CD4 and TCRgd T cells.

overall_design: Gene expression of sort purified, resting CD161+ and CD161- TCRgd T cells from peripheral blood was measured in 4 healthy donors.

first: Neil

last: Rajoriya

first: Helen

last: Lockstone

first: Emanuele

last: Marchi

first: Paul

last: Klenerman


title: CD161 defines a transcriptional and functional phenotype shared across distinct human T cell lineages


title: CD161 defines a transcriptional and functional phenotype shared across distinct human T cell lineages (CD4)

overall_design: Gene expression of magnetically enriched, resting CD161+ and CD161- CD4+ T cells from peripheral blood was measured in 3 healthy donors.

first: Vicki

last: Fleming


title: Mapping genome-wide binding sites of Kruppel-like factor-9 by ChIP-seq in human glioblastoma stem cells.

first: Mingya

last: Ying

summary: Kruppel-like factor-9 (KLF9), a member of the large KLF transcription factor family, has emerged as a regulator of oncogenesis, cell differentiation and neural development; however, the molecular basis for KLF9’s diverse contextual functions remains unclear. This study focuses on the functions of KLF9 in human glioblastoma stem-like cells. We establish for the first time a genome-wide map of KLF9-regulated targets in human glioblastoma stem-like cells, and show that KLF9 functions as a transcriptional repressor and thereby regulates multiple signaling pathways involved in oncogenesis and stem cell regulation. A detailed analysis of one such pathway, integrin signaling, shows that the capacity of KLF9 to inhibit glioblastoma cell stemness and tumorigenicity requires ITGA6 repression. These findings enhance our understanding of the transcriptional networks underlying cancer cell stemness and differentiation, and identify KLF9-regulated molecular targets applicable to cancer therapeutics.

overall_design: Two cell lines were used as biological replicates. Each cell line have one KLF9 ChIP-enriched DNA sample and one input genomic DNA sample.

first: John

last: Laterra

first: Mingyao

first: Hongkai

last: Ji

first: Yingying

last: Wei

first: Jessica

last: Tilghman


title: CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors [ChIP-Seq]

city: Boston

first: Michael

last: Talkowski

address: 185 Cambridge Street

institute: Massachusetts General Hospital

summary: Truncating mutations of CHD8, encoding a chromodomain helicase, and of many other genes with diverse functions, are strong-effect risk factors for autism spectrum disorder (ASD), suggesting multiple mechanisms of pathogenesis. We explored the transcriptional networks that CHD8 regulates in neural progenitor cells (NPCs) by reducing its expression and then integrating transcriptome sequencing (RNA-seq) with genome-wide CHD8 binding (ChIP-seq). Suppressing CHD8 to levels comparable with loss of a single allele caused altered expression of 1,756 genes, 64.9% of which were up-regulated.  CHD8 showed widespread binding to chromatin, with 7,324 replicated sites that marked 5,658 genes. Integration of these data suggests that a limited array of direct regulatory effects of CHD8 produced a much larger network of secondary expression changes. Genes indirectly down-regulated (i.e., without CHD8 binding sites) reflect pathways involved in brain development, including synapse formation, neuron differentiation, cell adhesion, and axon guidance, whereas CHD8-bound genes are strongly associated with chromatin modification and transcriptional regulation. Genes associated with ASD were strongly enriched among indirectly down-regulated loci (p = 1.01x10-9) and CHD8-bound genes (p = 4.34x10-3), which align with previously identified co-expression modules during fetal development. We also find an intriguing enrichment of cancer related gene-sets among CHD8-bound genes (p < 1.9x10-11). In vivo suppression of chd8 in zebrafish produced macrocephaly comparable to that of humans with inactivating mutations. These data indicate that heterozygous disruption of CHD8 precipitates a network of gene expression changes involved in neurodevelopmental pathways in which many ASD-associated genes may converge on shared mechanisms of pathogenesis.

overall_design: ChIP-seq for CHD8 using three different antibodies, and the related protein CHD7, in human iPSC-derived NPCs treated with shRNA targeting GFP (which were used as control cells for an shRNA knockdown RNA-seq experiment that was part of the overall study)

first: Aarathi

last: Sugathan

first: Marta

last: Biagioli

first: Christelle

last: Golzio

first: Serkan

last: Erdin

first: Ian

last: Blumenthal

first: Poornima

last: Manavalan

first: Ashok

last: Ragavendran

first: Harrison

last: Brand

first: Diane

last: Lucente

first: Judith

last: Miles

first: Steven

last: Sheridan

first: Alexei

last: Stortchevoi

first: Stephen

last: Haggarty

first: Nicholas

last: Katsanis

first: James

middle: F

last: Gusella


title: CD161 defines a transcriptional and functional phenotype shared across distinct human T cell lineages (CD 8)

first: Joannah

last: Fergusson

overall_design: Gene expression of sort purified, resting CD161++, CD161+ and CD161- CD8+ T cells from peripheral blood was measured in 4 healthy donors.

first: Yu-Hoi

last: Kang

first: Helen

last: Lockstone

first: Emanuele

last: Marchi

first: Paul

last: Klenerman


title: CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors [RNA-Seq]

first: Michael

last: Talkowski

overall_design: RNA-seq in NPCs treated with shRNAs targeting CHD8. For controls, NPCs were treated with shRNAs targeting GFP and LacZ. Infection and sequencing was carried out in two separate batches, with one GFP and one LacZ sample in each batch. All samples were sequenced in two technical replicates.

first: Aarathi

last: Sugathan

first: Marta

last: Biagioli

first: Christelle

last: Golzio

first: Serkan

last: Erdin


title: Transcriptional Pause Release Is a Rate-Limiting Step for Somatic Cell Reprogramming (ChIP-seq)

city: ShenZhen

first: Minghui

last: He

state: GuangDong

address: Beishan Industrial Zone, Yantian District

department: Cancer Research Department

institute: BGI-Shenzhen

summary: Reactivation of the pluripotency network during somatic cell reprogramming by exogenous transcription factors involves chromatin remodeling and the recruitment of RNA polymerase II (Pol II) to target loci. Here, we report that Pol II is engaged at pluripotency promoters in reprogramming but remains paused and inefficiently released. We also show that bromodomain-containing protein 4 (BRD4) stimulates productive transcriptional elongation of pluripotency genes by dissociating the pause release factor P-TEFb from an inactive complex containing HEXIM1. Consequently, BRD4 overexpression enhances reprogramming efficiency and HEXIM1 suppresses it, whereas Brd4 and Hexim1 knockdown do the opposite. We further demonstrate that the reprogramming factor KLF4 helps recruit P-TEFb to pluripotency promoters. Our work thus provides a mechanism for explaining the reactivation of pluripotency genes in reprogramming and unveils an unanticipated role for KLF4 in transcriptional pause release.

overall_design: Pol II ChIP-seq for MEFs, ESCs and bulk populations of OSKM reprogramming intermediates at two time points.

first: Longqi

last: Liu

first: Yan

last: Xu

first: Leina

last: Lu

first: Huating

last: Wang

first: Miguel

last: Esteban


title: Transcriptional Pause Release Is a Rate-Limiting Step for Somatic Cell Reprogramming

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

Reactivation of the pluripotency network during somatic cell reprogramming by exogenous transcription factors involves chromatin remodeling and the recruitment of RNA polymerase II (Pol II) to target loci. Here, we report that Pol II is engaged at pluripotency promoters in reprogramming but remains paused and inefficiently released. We also show that bromodomain-containing protein 4 (BRD4) stimulates productive transcriptional elongation of pluripotency genes by dissociating the pause release factor P-TEFb from an inactive complex containing HEXIM1. Consequently, BRD4 overexpression enhances reprogramming efficiency and HEXIM1 suppresses it, whereas Brd4 and Hexim1 knockdown do the opposite. We further demonstrate that the reprogramming factor KLF4 helps recruit P-TEFb to pluripotency promoters. Our work thus provides a mechanism for explaining the reactivation of pluripotency genes in reprogramming and unveils an unanticipated role for KLF4 in transcriptional pause release.


title: CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors


title: Transcriptional Pause Release Is a Rate-Limiting Step for Somatic Cell Reprogramming (RNA-seq)

overall_design: Examination of differential gene expression after overexpression of Cdk9-DN at 4 time points of somatic cell reprogramming


title: ETS1 is a genome-wide effector of RAS/ERK signaling in epithelial cells

city: North Chicago

first: Josh

last: Plotnik

state: IL

address: 1 North Waukegan Rd, AP10/210A

institute: AbbVie Inc.

overall_design: Refer to individual Series


title: Genome-wide quantification of microRNA processing efficiency from RNA-seq data

city: Berlin

first: Annalisa

last: Marsico

address: Ihnestraße 63-73

department: Computational Biology

institute: Max Planck Institute for Molecular Genetics

summary: Microprocessor is responsible for conversion of pri-miRNA transcripts into pre-miRNA hairpins in miRNA biogenesis. The in vivo properties of this process remain enigmatic. Here, we present the first study of in vivo transcriptome-wide pri-miRNA processing using next-generation sequencing of chromatin-associated pri-miRNAs. We identify a distinctive Microprocessor signature in the transcriptome profile, from which efficiency of the endogenous processing event can be accurately quantified. This analysis reveals differential susceptibility to Microprocessor cleavage as a key regulatory step in miRNA biogenesis. Processing is highly variable among pri-miRNAs and a better predictor of miRNA abundance than primary transcription itself. Processing is also largely stable across three cell lines, suggesting a major contribution of sequence determinants. Based on differential processing efficiencies we define functionality for short sequence features adjacent to the pre-miRNA hairpin. In conclusion, we identify Microprocessor as the main hub for diversified miRNA output and suggest a role for uncoupling miRNA biogenesis from host gene expression.

overall_design: We performed polyA independent deep sequencing of the chromatin-isolated RNA fraction for 5 samples: 2 replicates in HeLa cells, 1 Drosha knock down in HeLa cells, 1 sample for A549 cells and 1 sample for HEK293 cells. We also performed deep sequencing of the small RNA fraction in the same cell lines.

first: Thomas

last: Conrad

first: Maja

last: Gehre

first: Ulf

last: Orom


title: Charaterization of genetic alterations and gene expression signatures found in erlotinib-resistant and erlotinib/crizotinib dual-resistant HCC827 subpopulations

first: Joshua

last: Korn

summary: The non-small cell lung cancer (NSCLC) cell line HCC827 harbors an activating EGFR mutation (exon 19 deletion) that confers sensitivity to the FDA-approved EGFR inhibitor erlotinib. By applying the ClonTracer barcoding system, we were able to show the presence of pre-existing sub-populations in HCC827 that contribute to erlotinib resistance. Prior studies implicated that MET amplification confers resistance to erlotinib in this cell line. Therefore we examined the effects of the c-Met inhibitor crizotinib on the barcoded HCC827 population when treated either sequentially or simultaneously with both inhibitors. Despite the significant reduction in barcode complexity, the erlotinib/crizotinib combination treatment failed to eradicate all of the resistant clones implying the presence of an erlotinib/crizotinib dual resistant subpopulation. We performed transcriptome profiling (RNA-seq) to elucidate the potential resistance mechanisms of the dual resistant subpopulation in comparison to vehicle-treated or single agent erlotinib-resistant HCC827 cell populations as controls.

overall_design: mRNA profiling of the subpopulations of human NSCLC cell line HCC827 that contribute to EGFR inhibitor erlotinib and MET inhibitor crizotinib resistance

first: Hyo-eun

middle: C

last: Bhang

first: David

last: Ruddy

first: Daniel

last: Rakiec

first: Frank

last: Stegmeier


title: ETS1 is a genome-wide effector of RAS/ERK signaling in epithelial cells (RNA-Seq)

summary: ETS1 and RAS/ERK regulate a common gene expression program in establishing enviroment suitable for prostate cancer cell migration.

overall_design: mRNA profiles of luciferase knockdown (WT), ETS1 knockdown, and U0126 treated DU145 cells were generated using deep sequencing, in triplicate, using Illumina HiSeq. Knockdowns were stable shRNA expression from a lentiviral construct selected with puromycin.

first: Justin

last: Budka

first: Peter

last: Hollenhorst


title: ETS1 is a genome-wide effector of RAS/ERK signaling in epithelial cells (ChIP-Seq)

overall_design: ChIP-sequencing of various transcription factors


title: Hot spots of DNA double-strand breaks and genomic contacts of human rDNA units are involved in epigenetic regulation [DSBs]

status: Public on Oct 04 2014

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

summary: Eukaryotic chromosomes are subjected to spontaneous fragmentation even under quick isolation of DNA in a solid phase by strong treatment with 0.1 M EDTA, 1% SDS and proteinase K (1 mg/ml). The long DNA fragments of excised chromosomal DNA were denoted as forum domains. Mostly forum domains are of 50-200 kb in length, although larger domains, up to 500 - 700 kb, are also observed. The domains are delimited by hot spots of double-strand breaks (DSBs). We performed a genome-wide mapping of DSBs in human HEK293T cells cultured cells using Illumina deep sequencing of the termini of forum domains. We found that in rDNA units the hot spots of DSBs are distributed non-randomly. Mostly they are located in IGS.

overall_design: Genome-wide mapping of DNA DSBs in HEK293T cells

first: Yuri

middle: V

last: Kravatsky


title: Nuclear stability and transcriptional directionality separate functionally distinct RNA species.

city: Copenhagen N

first: Robin

last: Andersson

address: Ole Maaloes Vej 5

country: Denmark

institute: University of Copenhagen

type:
Expression profiling by array
Other


title: Vitamin d receptor-mediated stromal reprogramming suppresses pancreatitis and enhances pancreatic cancer therapy

status: Public on Oct 03 2014

first: Ruth

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

summary: The poor clinical outcome in pancreatic ductal adenocarcinoma (PDA) has been attributed to intrinsic resistance to chemotherapy and a growth-permissive tumor microenvironment.  Quiescent pancreatic stellate cells (PSCs) are neuroendocrine, nestin-positive, lipid-accumulating cells whose homologues in the liver are the principal repository of Vitamin A esters.  Upon activation, lipid droplets are lost and via transdifferentiation they become the key cell type responsible for driving the severe desmoplasia that characterizes PDA.  Despite their critical role in PDA progression and chemoresistance, therapeutic strategies targeting PSCs are lacking.  Here we identified the vitamin D receptor (VDR) as a master genomic regulator of PSC activation and function.  In vitro we demonstrate that VDR activation reduces expression in PSCs of genes implicated in activation, inflammation, and extracellular matrix production, as well as restoring lipid droplet integrity. In vivo, the VDR ligand calcipotriol enhances the anti-tumor effects of gemcitabine by increasing intratumoral concentration 5-fold, reducing tumor volume to near baseline and lowering metastases by more than 65%.  These findings implicate VDR as a master regulator of PSC activation and identify a novel therapeutic approach for the treatment of pancreatic cancer.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-Seq analyses was used to characterize cancer-associated changes between pre-activated (3-day culture) and activated (7-day culture) primary mouse PSCs, as well as control and PDA human PSCs.  RNA-Seq was also used to assess the impact of VDR activation (DMSO vs calcipotriol) in a human PSC line (MiaPaCa-2), the mouse primary PSCs

first: Mara

middle: H

last: Sherman

first: Ronald

last: Evans


title: GRO-seq in HeLa cells

summary: Mapping the nascent RNA transcriptome of HeLa cells with GRO-seq

overall_design: Standard GRO-seq assay from two replicates in HeLa cells

first: Leighton

last: Core

last: Anderson

first: Albin

last: Sandelin


title: Distinct structural transitions of chromatin topological domains coordinate hormone-induced gene regulation

status: Public on Oct 06 2014

city: Barcelona

first: Miguel

last: Beato

address: Aiguader 88

institute: CRG

summary: The three-dimensional (3D) organization of the genome within the cell nucleus contributes to cell-specific gene expression in different cell types1. High-throughput 3C–derived methods have revealed that the genome is segmented into contiguous topologically associating domains (TADs), which help to orchestrate gene expression changes during differentiation and development2-5. Using ChIP-Seq, Hi-C and 3D modelling techniques, we reveal that TADs regulate the rapid gene expression changes induced by progestin in T47D breast cancer cells. In response to the hormone, TADs maintain their borders and operate as discrete regulatory units in which the majority of the genes are either transcriptionally activated or repressed. Additionally, the epigenetic signatures of the TADs are coordinately modified by hormone in correlation with the transcriptional changes. Hormone-induced changes in gene activity and chromatin remodelling are accompanied by structural changes that are distinct for activated or repressed TADs. Integrative 3D modelling revealed that TADs are structurally expanded if active and compacted if repressed, and that this is accompanied by differential changes in accessibility. We thus propose that TADs function as “regulons” to enable spatially proximal genes to be coordinately transcribed in response to hormones.

overall_design: T47D-MTVL human breast cancer cells were incubated with the progestin R5020 for different times at 37ºC and prepared for ChIP-Seq or Hi-C according published protocols

first: François

last: Le Dily

first: Davide

last: Baù

first: Andy

last: Pohl

first: Guillermo

last: Vicent

last: Soronellas

first: Giancarlo

last: Castellano

last: Serra

first: Roni

last: Wright

first: Cecilia

last: Ballare

first: Guillaume

last: Filion

first: Marc

last: Marti-Renom


title: Circulating Dirofilaria immitis microRNAs in dog plasma

city: Sainte-Anne-de-Bellevue

first: Lucienne

last: Tritten

state: QC

address: 21111 Lakeshore Road

department: Institute of Parasitology

country: Canada

institute: McGill University

summary: We report the presence of circulating miRNAs released by the filarial nematode Dirofilaria immitis into the host (Canis familiaris) bloodstream.

overall_design: MiRNA deep-sequencing combined with bioinformatics revealed over 200 mature miRNA sequences of potential nematode origin in Dirofilaria immitis-infected dog plasma in two independent analyses

first: Timothy

last: Geary


title: ChIP-seq analyses of the Aspergillus fumigatus SREBP SrbA

city: Flagstaff

first: Bridget

middle: Marie

last: Barker

state: AZ

address: 3051 Shamrell Blvd

department: CFP

institute: TGEN-North

summary: The Aspergillus fumigatus sterol regulatory element binding protein (SREBP) SrbA belongs to the basic Helix-Loop-Helix (bHLH) family of transcription factors and is crucial for antifungal drug resistance and virulence.  The latter phenotype is especially striking, as loss of SrbA results in complete loss of virulence in murine models of invasive pulmonary aspergillosis (IPA). How fungal SREBPs mediate fungal virulence is unknown, though it has been suggested that lack of growth in hypoxic conditions accounts for the attenuated virulence. To further understand the role of SrbA in fungal infection site pathobiology, chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) was used to identify genes under direct SrbA transcriptional regulation in hypoxia. These results confirmed the direct regulation of ergosterol biosynthesis and iron uptake by SrbA in hypoxia and revealed new roles for SrbA in nitrate assimilation and heme biosynthesis. Moreover, functional characterization of an SrbA target gene with sequence similarity to SrbA identified a new transcriptional regulator of the fungal hypoxia response and virulence, SrbB. SrbB co-regulates genes involved in heme biosynthesis and demethylation of C4 sterols with SrbA in hypoxic conditions. However, SrbB also has regulatory functions independent of SrbA including regulation of carbohydrate metabolism. Loss of SrbB markedly attenuates A. fumigatus virulence, and loss of both SREBPs further reduces in vivo fungal growth. These data suggest that both A. fumigatus SREBPs are critical for hypoxia adaptation and virulence and reveals new insights into SREBP’s complex role in infection site adaptation and fungal virulence.

overall_design: 4 hour and 12 hour ChIP experiments were completed. Input control samples for each set were collected.

first: Robert

last: Cramer

first: Charles

last: Carey


title: BRD4 binding sites in transformed fibroblasts

status: Public on Oct 02 2014

city: Bethesda

first: Patricia

last: Fernandez Ferri

address: 41 Library Drive, B513

institute: NCI/NIH

summary:
Analysis of BRD4 ChIP-seq data of two types of human transformed fibroblasts (WT and HGPS) to identify specific and common binding sites for BRD4. Transformed cell lines were obtained by retroviral introduction of TERT (T), V12-HRAS (R) and SV40 large and small T antigens (S) of primary skin fibroblasts for HGPS patients (TRS-HGPS) and age-matched control wild-type individuals (TRS-WT)
Abstract: Advanced age and DNA damage accumulation are strong risk factors for cancer.  The premature-aging disorder Hutchinson Gilford Progeria Syndrome (HGPS) provides a unique opportunity to study the interplay between DNA damage and aging-associated tumor mechanisms, since HGPS patients do not develop tumors despite elevated levels of DNA damage. Here, we have used HGPS patient cells to identify a protective mechanism to oncogenesis. We find that HGPS cells are resistant to neo-plastic transformation. This resistance is mediated by the bromodomain protein BRD4, which exhibits altered genome-wide binding patterns in transformation-resistant cells leading to inhibition of oncogenic de-differentiation.  BRD4 also in-hibits, albeit to a lower extent, the tumorigenic potential of transformed cells from healthy individuals and BRD4-mediated tumor protection is clinically relevant, since a BRD4 gene signature predicts positive clinical outcome in breast and lung cancer.  Our results demonstrate a protective function for BRD4 and suggest tissue-specific functions for BRD4 in tumorigenesis.

overall_design: Examination of BRD4 binding events in TRS-WT and TRS-HGPS fibroblasts (2 independent cell lines in each group)

last: Fernandez

first: Tom

last: Misteli


title: Genomic discovery of potent chromatin insulators for human gene therapy

first: Matthew

last: Maurano

address: 435 East 30th Street

department: Institute for Systems Genetics

institute: NYU School of Medicine

summary: This data includes regulatory factor profiling using  ChIP-seq.

overall_design: Cells were grown according to the approved ENCODE cell culture protocols. Cells were crosslinked with 1% formaldehyde, and the reaction was quenched by the addition of glycine. Fixed cells were rinsed with PBS, lysed in nuclei lysis buffer, and the chromatin was sheared to 200-500 bp fragments using Fisher Dismembrator (model 500). Sheared chromatin fragments were immunoprecipitated with specific polyclonal antibodies at 4 degrees C with gentle rotation. Antibody-chromatin complexes were washed and eluted. The cross linking in immunoprecipitated DNA was reversed and treated with RNase-A. Following proteinase K treatment, the DNA fragments were purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. 20-50 ng of ChIP DNA was end-repaired, adenine ligated to Illumina adapters was added, and then a Solexa library was made for sequencing.  ChIP-seq affinity is directly reflected in raw tag density (Raw Signal), which is shown in the track as density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). ChIP-seq affinity zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004). 1.0% false discovery rate thresholds (FDR 0.01) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely mapping 36mers. ChIP-seq affinity (Peaks) were identified as signal peaks within FDR 1.0% hypersensitive zones using a peak-finding algorithm.

first: Mingdong

last: Liu

first: Hao

last: Wang

first: John

last: Stamatoyannopoulos

first: George


title: Hot spots of DNA double-strand breaks and genomic contacts of human rDNA units are involved in epigenetic regulation [rDNA units]

first: Nickolai

last: Tchurikov

summary: 4C procedure was used for analysis of genomic contacts of rDNA units in HEK 293T cells. The primers for 4C were selected inside IGS. Our data indicate that mostly rDNA units exhibit close proximity with pericentromeric regions in different chromosomes. We also detected the contacts within a rDNA unit and between rDNA units.

overall_design: Examination of rDNA genome-wide contacts in HEK 293T cells using 4C approach.

first: Yuri

last: Kravatsky

first: Olga

last: Kretova


title: Identification and characterization of miRNAs in oilseed rape (Brassica napus) responsive to the pathogenic fungus Verticillium longisporum infection using Brassica AA (B. rapa) and CC (B. oleracea) as reference genomes

city: Kiel

first: Dan

last: Shen

address: Hermann-Rodewald-Straße 9

institute: Kiel University

summary: we deep-sequenced two small RNA libraries made from V. longisporum infected/non-infected roots and employed Brassica rapa and Brassica oleracea genomes as reference for miRNA prediction and characterization as well. We identified 893 B. napus miRNAs representing 360 conserved and 533 novel miRNAs, and mapped 429 and 464 miRNAs to AA and CC genomes, respectively. Among them, 62 miRNAs were responsive to the V. longisporum infection.

overall_design: two small RNA libraries constructed from V. longsiporum infected and non-infected roots after 6 days were sequenced by  Illumina’s Solexa sequencing technology (BGI, China)

first: Daguang

last: Cai


title: Global gene expression profiling of mouse liver tissue samples after treated with various anti-HCV shRNAs

city: Stanford

first: Mark

middle: M.

last: Davis

address: 279 Campus Drive

department: Department of Microbiology and Immunology

institute: Stanford University

summary: RNA interference (RNAi) is becoming routine in scientific discovery and treating human disease. However, its applications are hampered by unwanted effects. The RNA-Seq analyses from mouse liver samples expressing various anti-HCV shRNAs show that weak base-pairing in both seed and 3’ regions is required to achieve minimal off-targeting effect.

overall_design: We created nine shRNAs against the HCV genome, and transfected shRNA-expressing plasmids into mouse liver via a hydrodynamic tail vein infusion. A plasmid backbone lacking the shRNA sequence was used as a negative control.  After 7 days, mouse liver RNAs were harvested and subject to RNA-Seq analysis (two biological repeats).

first: Shuo

last: Gu

last: Kay


title: RNA Expression Profiling of Human iPSC-Derived Cardiomyocytes in a Cardiac Hypertrophy Model

city: Milwaukee

first: Ulrich

last: Broeckel

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

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


title: hMeDIP-seq profiling of DNA hydroxymethylation in primary adipocytes from epididymal white adipose tissue (eWAT) of adult C57BL/6J mice

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

institute: CNRS

summary: DNA hydroxymethylation plays a crucial role in the regulation of gene transcription. In this study, using hMeDIP-seq experiment, we report the mapping of DNA hydroxymethylation in adipocytes from mouse eWAT

overall_design: Examination of DNA hydroxymethylation pattern in adipocytes from mouse eWAT

first: Frédérik

last: Oger

first: Philippe

last: Lefebvre


title: The CLE40 and CRN/CLV2 signaling pathways antagonistically control root meristem growth in Arabidopsis

city: Düsseldorf

first: Helge

last: Pallakies

address: Universitätsstrasse 1

department: Developmental Genetics

institute: CEPLAS / Heinrich-Heine-University Düsseldorf

summary: Differentiation processes in the primary root meristem are controlled by several signaling pathways that are regulated by phytohormones or by secreted peptides. Long term maintenance of an active root meristem requires that the generation of new root meristem cells and the loss of cells from the meristem due to differentiation is precisely coordinated. Via phenotypic and large scale transcriptome analyses of mutants, we show that the signalling peptide CLE40 and the receptor proteins CLV2 and CRN act in two genetically separable pathways that antagonistically regulate cell differentiation in the proximal root meristem. CLE40 inhibits cell differentiation throughout the primary root meristem by controlling genes with roles in abscisic acid, auxin and cytokinin signalling. CRN and CLV2 jointly control target genes that promote cell differentiation specifically in the transition zone of the proximal root meristem. While CRN and CLV2 are not acting in the CLE40 signaling pathway under normal growth conditions, both proteins are required when the levels of CLE40 or related CLE peptides increase. We show here that two antagonistically acting pathways controlling root meristem differentiation can be activated by the same peptide in a dosage dependent manner.

overall_design: 3 replicates reference(Col-0), clv2-gabi, cle40-2; 2 replicates crn-3

first: Rüdiger

last: Simon


title: ADAR2 reproducibly changes abundance and sequence of mature microRNAs in the mouse brain [RNA-Seq]

city: Vienna

first: Fritz

last: Sedlazeck

state: Vienna

address: Dr. Bohr-Gasse 9

department: CIBIV

country: Austria

institute: MFPL

summary:
Background: Adenosine deaminases that act on RNA (ADARs) bind to double-stranded and structured RNAs and deaminate adenosines to inosines. This A to I editing is widespread and required for normal life and development. Besides mRNAs and repetitive elements, ADARs can target miRNA precursors. Editing of miRNA precursors can affect processing efficiency and alter target specificity. Interestingly, ADARs can also influence miRNA abundance independent of RNA-editing. In mouse embryos where editing levels are low, ADAR2 was found to be the major ADAR protein that affects miRNA abundance. Here we extend our analysis to adult mouse brains where high editing levels are observed.
Results: Using Illumina deep sequencing we compare the abundances of mature miRNAs and editing events within them, between wild-type and ADAR2 knockout mice in the adult mouse brain. Reproducible changes in abundance of specific miRNAs are observed in ADAR2 deficient mice. Most of these quantitative changes seem unrelated to A to I editing events. However, many A to G transitions in cDNAs prepared from mature miRNA sequences, reflecting A to I editing events in the RNA, are observed with frequencies reaching up to 80%. About half of these editing events are primarily caused by ADAR2 while a few miRNAs show increased editing in the absence of ADAR2, suggesting preferential editing by ADAR1. Moreover, novel, previously unknown editing events were identified in several miRNAs. In general 64% of all editing events are located within the seed region of mature miRNAs. In one of these cases retargeting of the edited miRNA could be verified in reporter assays. Also, altered processing efficiency upon editing near a processing site could be experimentally verified.
Conclusions: ADAR2 can significantly influence the abundance of certain miRNAs in the brain. Only in a few cases changes in miRNA abundance can be explained by miRNA editing. Thus, ADAR2 binding to miRNA precursors, without editing them, may influence their processing and thereby abundance. ADAR1 and ADAR2 have both overlapping and distinct specificities for editing of miRNA editing sites. Over 60% of editing occurs in the seed region possibly changing target specificities for many edited miRNAs.

overall_design: Examination of the effect of ADAR2 on mature miRNA abundance and sequence in adult mouse brain.

first: Cornelia

last: Vesely

first: Stefanie

last: Tauber

middle: J

first: Mansoureh

last: Tajaddod

first: Arndt

last: von Haeseler

first: Michael

last: Jantsch


title: Genome-wide Twist1 occupancy in endocardial cushion cells, embryonic limb buds, and peripheral nerve sheath tumor cells

city: Cincinnati

first: Katherine

last: Yutzey

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Center

summary: The basic helix-loop-helix transcription factor Twist1 has a well-documented role in mesenchymal populations of the developing embryo, such as endocardial cushion (ECC) mesenchymal cells and limb buds, and during cancer development and progression.  Whether Twist1 regulates the same transcriptional targets in different cell types has yet to be investigated.  Through chromatin immunoprecipitation followed by sequencing (Chip-seq) analysis, the cell type-specific genome-wide occupancy of Twist1 was investigated in ECCs, limb buds and mouse peripheral nerve sheath tumor (PNST) cells.  Twist1 binds mainly in a cell type-specific manner, with very few common genomic regions occupied by Twist1 in different cell types.  Genes associated with binding peaks in each cell type are related to known Twist1 cellular functions in ECCs, limb buds, and cancer cells.  We found that cell type-specific binding of Twist1 may be influenced by histone modifications or co-factors.   Binding regions were located in several Wnt pathway associated genes, supporting a link between Twist1 and Wnt signalling in ECCs, limb buds, and PNST cells.  These data suggest that similar functions are regulated by Twist1 in ECCs, limb buds, and PNST cells in a cell type-specific manner, and provide insights into possible mechanisms utilized for cell type-specificity of Twist1 binding.

overall_design: We compare Twist1 genome occupancy in mouse embryonic day (E) 12.5 endocardial cushion mesenchymal cells, E10.5 forelimb buds, and a mouse peripheral nerve sheath tumor cell line.

first: Mary

last: Lee

first: Nancy

last: Ratner

middle: E


title: Global identification of target recognition and cleavage by the Microprocessor in human ESCs.

city: Seoul

first: Young-Soo

last: Kwon

address: Nungdongro 209, Gwangjingu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Sejong University

summary: The Microprocessor plays an essential role in canonical miRNA biogenesis by facilitating cleavage of stem-loop structures in primary transcripts to yield pre-miRNAs. Although miRNA biogenesis has been extensively studied through biochemical and molecular genetic approaches, it has yet to be addressed to what extent the current miRNA biogenesis models hold true in intact cells. To address the issues of in vivo recognition and cleavage by the Microprocessor, we investigate RNAs that are associated with DGCR8 and Drosha by using immunoprecipitation coupled with next-generation sequencing. Here, we present global protein-RNA interactions with unprecedented sensitivity and specificity. Our data indicate that precursors of canonical miRNAs and miRNA-like hairpins are the major substrates of the Microprocessor. As a result of specific enrichment of nascent cleavage products, we are able to pinpoint the Microprocessor-mediated cleavage sites per se at single-nucleotide resolution. Unexpectedly, a 2-nt 3’ overhang invariably exists at the ends of cleaved bases instead of nascent pre-miRNAs. Besides canonical miRNA precursors, we find that two novel miRNA-like structures embedded in mRNAs are cleaved to yield pre-miRNA-like hairpins, uncoupled from miRNA maturation. Our data provide a framework for in vivo Microprocessor-mediated cleavage and a foundation for experimental and computational studies on miRNA biogenesis in living cells.

overall_design: CLIP-seq for DGCR8 and Drosha, RIP-seq for DGCR8, sequencing of AGO2-assocated miRNA


title: HSF1 and HSF2 interactions with chromatin during the heat shock response in mouse spermatocytes

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

institute: University of Bergen

summary: Heat shock transcription factors HSF1 and HSF2 both are  necessary for proper spermatogenesis, which is disrupted at elevated temperatures. We studied how HSF1 and HSF2 cooperate during the heat shock response in mouse spermatocytes. For this purpose we used ChIP-sequencing. ChIP-Seq analyses revealed that the temperature elevation induces remodeling of HSF1 and HSF2 binding to chromatin. The highest HSF1-chromatin binding was observed at 43°C, when HSF2-chromatin binding was reduced. Many promoters (mainly Hsp genes) were occupied by both heat shock factors at physiological temperature of testes and/or at 38°C. In contrary at  43°C only HSF1 was bound. Obtained results suggest that HSF1 and HSF2 could cooperate in regulation of the transcription of some genes only at physiological temperatures and/or at 38°C. Alteration in HSFs interactions and their binding to chromatin could be one of the reason of increased spermatogenic cell death observed after heat shock.

overall_design: On Illumina platform we sequenced DNA immunoprecipitated from isolated spermatocytes using anti-HSF1 antibody or anti-HSF2 antibody. Cells were either untreated (control) or heat shocked for 5-20 minutes. Two PCR-verified ChIP replicates were collected per each sample, and three negative control samples with normal goat serum were included.

first: Joanna

last: Korfanty

first: Wieslawa

last: Widlak


title: Stage-specific binding profiles of cohesin in resting and activated B lymphocytes

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

summary: Binding profiles of cohesin in resting mature murine splenic B lymphocytes and at two stages after cell activation were elucidated by chromatin immunoprecipitation and deep sequencing.

overall_design: RAD21 binding profile in resting, 48h- and 96h-stimulated B cells were analyzed in three replicates and normalized to input DNA.

first: Gamze

last: Gunal-Sadik

first: Frank

last: Buchholz

first: Rolf

last: Jessberger


title: RNA Expression Profiling of Human iPSC-Derived Cardiomyocytes in a Cardiac Hypertrophy Model [miRNA expression]

first: Ulrich

last: Broeckel

summary:
Cardiac hypertrophy is an independent risk factor for cardiovascular disease and heart failure. There is increasing evidence that microRNAs (miRNAs) play an important role in the regulation of messenger RNA (mRNA) and the pathogenesis of various cardiovascular diseases. However, the ability to comprehensively study cardiac hypertrophy on a gene regulatory level is impacted by the limited availability of human cardiomyocytes. Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) offer the opportunity for disease modeling.
We utilized a previously established in vitro model of cardiac hypertrophy to interrogate the regulatory mechanism associated with the cardiac disease process. We performed miRNA sequencing and mRNA expression analysis on endothelin 1 (ET-1) stimulated hiPSC-CMs to describe associated RNA expression profiles. MicroRNA sequencing revealed over 250 known and 34 predicted novel miRNAs to be differentially expressed between ET-1stimulated and unstimulated control hiPSC-CMs. Messenger RNA expression analysis identified 731 probe sets with significant differential expression. Computational target prediction on significant differentially expressed miRNAs and mRNAs identified nearly 2000 target pairs.

overall_design: To characterize miRNA and mRNA expression patterns we utilized iCell Cardiomyocytes derived from human iPSCs (hiPSC-CMs). Based on preliminary dose-response and time-course studies, we stimulated these cells with ET-1 at 10-8M for 18h. We used unstimulated control (control-CM) and ET-1 stimulated (ET1-CM) hiPSCs from 3 separate experiments as triplicate data for this study. For the analysis of miRNA expression changes after ET-1 stimulation, single-end small RNA sequencing was performed using the Ion Torrent Personal Genome Machine (PGMTM) sequencing platform.

first: Praful

last: Aggarwal

first: Amy

last: Turner

first: Andrea

last: Matter

first: Steven

last: Kattman

first: Alexander

last: Stoddard

first: Rachel

last: Lorier

first: Bradley

last: Swanson

first: Donna

middle: K

last: Arnett


title: The cytoplasmic poly(A) polymerases GLD-2 and GLD-4 promote general gene expression via distinct mechanisms

first: Marco

last: Nousch

address: Pfotenhauerstrasse 108

institute: MPI-CBG

summary: Comparision of mRNA abundance and translation efficiency mediated by cytoplasmic poly(A) polymerases in C. elegans

overall_design: comparision of different adults treated with RNAi

first: Christian

last: Eckmann


title: Expression profile by RNA-seq of wild type or Caenorhabditis elegans mutant for the Werner syndrome gene ortholog treated with or without vitamin C

city: Quebec

first: Michel

last: Lebel

state: Qc

address: 2705 Laurier Blvd, Local T-2-04

department: Centre Hospitalier de l’Université Laval (CHUL)

institute: Centre de Recherche du CHU de Québec

summary: In this study, we analyzed the impact of a mutation in the wrn-1 gene compared to wild type worms and the dietary supplementation of vitamin C on the global mRNA expression of the whole C. elegans by the RNA-seq technology.

overall_design: Whole C. elegans mRNA profiles at the L4 stage of wild type and wrn-1(gk99) mutant animals treated with or without 10 mM ascorbate were generated by deep sequencing, in triplicate, using the HiSeq 2000 machine form Illumina. Detailed statistics on the quality of the reads were calculated with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The 50 base pairs raw sequences were aligned on the C. elegans ce10/W220 genome with TopHat using the Ensembl annotations provided with the Illumina iGenomes. The htseq-count software (http://www-huber.embl.de/users/anders/HTSeq) was used to count the number of reads aligned to each gene. These counts were then normalized relative to the sequencing depth with DESeq.


title: Transcriptome-wide analysis of gene expression in dark-grown WT and pif mutant seedlings

city: Albany

first: james

middle: m

last: tepperman

address: 800 Buchanan St.

department: Plant and Microbial Biology

institute: Plant Gene Expression Center/UC Berkeley

summary: We sequenced mRNA from WT and PhytochromeInteractingFactor (pif) mutant seedlings grown for 2d in darkness.

overall_design: Transcriptome profiles of the wild-type (WT), pif1, pif3, pif, pif5 monogenic mutants, pif3pif4pif5 (pif345), pif1pif4pif5(pif145), pif1pif3pif5 (pif135) and pif1pif3pif4 (pif134) triple mutants and pif1pif3pif4pif5 (pifq) quadruple mutant seedlings. Biological triplicate samples were analyzed from libraries constructed using a 3'-capture, 5' to 3' directional method.

first: James

last: Tepperman

first: Peter

last: Quail


title: Transcriptional changes in the aging mouse hippocampus (RNA-seq)

status: Public on Oct 01 2014

city: Cork

first: Roman

last: Stilling

address: Western Road

department: Anatomy and Neuroscience

country: Ireland

institute: University College Cork

summary: We sequenced mRNA from three age groups (3months (3M), 24 months (24M) and 29 months (29M)) from the full hippocampus

overall_design: There were two independent experiments: 3M vs 24M (n=5 to 6, single-end sequencing) and 3M vs 29M (n=3, paired-end sequencing))

first: Vincenzo

last: Capece

first: Stefan

last: Bonn

first: Andre

last: Fischer