title: Sequencing of First-strand cDNA Library Reveals Full-length Transcriptomes

city: Ann Arbor

first: Saurabh

last: Agarwal

state: Michigan

address: 1241 E. Catherine St. 5815 Medical Science II

department: Human Genetics

institute: University of Michigan

summary: We developed a new method of preparing libraries for strand-specific RNA sequencing (ssRNA-Seq). It employs Direct Ligation of Adaptors to First-strand cDNA (DLAF). We compared ssRNA-Seq libraries prepared using either the DLAF and dUTP methods from mouse embryonic stem cells (mES) and libraries were sequenced from one end or both ends. We also conducted a comparison of ssRNA-Seq libraries prepared using DLAF and ScriptSeq v2 kit (Epicenter) from mouse embryonic cortex (mECx).

overall_design: RNA was isolated using either Trizol or Qiagen Rneasy kit. rRNA is depleted using Eukaryote Ribominus v2 kit and libraries were prepared using one of the methods.

first: Todd

last: Macfarlan

first: Maureen

last: Sartor

first: Shigeki

last: Iwase


title: Next generation sequencing of Phaeodactylum tricornutum grown with and without nitrogen

status: Public on Jan 02 2015

city: New Brunswick

first: Orly

last: Levitan

state: NJ

address: 71 Dudley Road

country: USA

institute: Rutgers university

type: Expression profiling by high throughput sequencing

summary: We have done next generation sequencing of optically thin, exponentialy growing Phaeodactylum tricornutum cultures grown with and without nitrogen source to improve our undestanding of the pathways regulation under conditions that promote lipid accumulation (N-starvation).

overall_design: 3 biologically independent exponentially growing culture of Phaeodactylum tricornutum were pelleted and washed several times with N-free media. Each culture was devided to 2 replicates with initial cell concentration of 2X105 cells/mL, one with NaNO3 as nitrogen source and the other without any nitrogen source. The cuture were bubbled foro 48 hours and sampled for transcriptome together with other physiological parameters and lipid analysis.

first: Jorge

last: Dinamarca

first: Ehud

last: Zelzion

first: Desmun

last: Lun

first: Min

middle: K

last: Kim

first: Benjamin

last: Van Mooy

first: Joomi

first: Fedor

middle: I

last: Kuzminov

first: Debashish

last: Bhattacharya

first: Paul

middle: G

last: Falkowski


title: Stably-paused genes revealed through inhibition of transcription initiation by the TFIIH inhibitor Triptolide

status: Public on Jan 05 2015

city: Kansas City

first: Joan

last: Conaway

state: MO

institute: Stowers Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Transcription by RNA Polymerase II (Pol II) in metazoan is regulated in several steps, including  preinitiation complex (PIC) formation, initiation, Pol II escape, productive elongation, cotranscriptional  RNA-processing and termination. Genome-wide studies have demonstrated that  the phenomenon of promoter-bound Pol II pausing is widespread, especially for genes involved  in developmental and stimulus-responsive pathways. However, a mechanistic understanding of  the paused Pol II states at promoters is limited. For example, at a global level, it’s unclear to  what extent the engaged paused Pol II is stably tethered to the promoter or undergoes rapid  cycles of initiation and termination. Here we used the small molecule Triptolide (TPL), an  XPB/TFIIH inhibitor, to block transcriptional initiation followed by measuring Pol II occupancy  by ChIP-seq. This inhibition of initiation enables us to investigate different states of paused Pol  II. Specifically, our global analysis reveals that most genes with paused Pol II, as defined by  pausing index, show significant clearance of Pol II during the period of TPL treatment. Our  study further identifies a group of genes with unexpectedly stably-paused Pol II, with unchanged  Pol II occupancy even after one hour of inhibition of initiation. This group of genes constitutes a  small portion of all paused genes defined by the conventional criterion of pausing index. These  findings could pave the way for evaluating the contribution of different elongation/pausing  factors on different states of Pol II pausing in developmental and other stimulus-responsive  pathways.

overall_design: ChIP-Seq of total/Ser5P Pol II in HCT116 cells treated with DMSO or TPL in serum starvation/activation or normal conditions. Nascent RNA-seq in HCT116 cells treated with DMSO or TPL in starved condition.

first: Fei

last: Chen

first: Xin

last: Gao

first: Ali

last: Shilatifard


title: mRNA profiling of Col4a3-Knockout Alport Syndrome mouse model treated with inhibitor of miR-21 at 9 weeks of age

status: Public on Jan 01 2015

city: San Diego

first: Vivek

last: Kaimal

state: CA

address: 10614 Science Center Dr.

department: Bioinformatics

institute: Regulus Therapeutics

summary:
Purpose: MicroRNA-21 contributes to the pathogenesis of fibrogenic diseases in multiple organs including the kidney. To evaluate the therapeutic utility of antimiR-21 oligonucleotides in chronic kidney disease, we silenced miR-21 in mice that develop Alport Nephropathy due to a defect in the Col4a3 gene. The goals of this study to assess the effect of inhibiting miR-21 in the Col4a3-/- Alport Syndrome mouse model at 9 weeks of age.
Methods: Col4a3-/-, Col4a3+/-, and Col4a3+/+ mice in the 129X1/SvJ genetic background were obtained. Mice received anti–miR-21 (25 mg/kg) or control anti-miR (25mg/kg) in phosphate-buffered saline (PBS) by inter-scapular subcutaneous injection twice per week. In some experiments mice received a range of doses from 12.5mg/kg once a week to 50mg/kg once a week. Anti–miR-21 is a high-affinity oligonucleotide complementary to the active site of miR-21. Mice received injections starting at 24 days (3.5 weeks) after birth and ending at 5, 7, 9 or 16 weeks after birth depending on the study objectives. Total RNA from kidney tissue was extracted as per manufacturer’s instructions (miREASY kit, Qiagen). RNA quality was assessed using BioAnalyzer (Agilent). mRNA expression profiles were determined using next-generation sequencing (NGS) on the Illumina HiSeq 2000 platform producing 50bp paired-end reads. Bowtie/TopHat suites were used to align the reads to mouse genome or transcriptome and RSEM were used to quantify gene abundances. Gene level counts were then normalized with the R/Bioconductor package limma using the voom/variance stabilization method.
Results: Anti-miR-21 enhanced PPARα/RXR activity and associated downstream signaling pathways in glomerular, tubular and interstitial cells, enhanced mitochondrial function, which reduced mitochondrial ROS production and preserved tubular cell functions. In addition, inhibition of miR-21 reduced fibrogenic and inflammatory signaling in glomerular and interstitial cells, likely as a consequence of enhanced PPARα/RXR activity and mitochondrial function. Inhibition of miR-21 represents a novel therapeutic strategy for chronic kidney diseases including Alport Nephropathy.

overall_design: Whole kidney mRNA profiles of wild type and Col4a3-/- mice treated with either PBS or antimiR-21, ending at 9 weeks of age, were generated by Next Generation Sequencing in triplicate using Illumina HiSeq 2000

first: Ivan

last: Gomez

first: Deidre

last: MacKenna

first: Jeremy

last: Duffield


title: Anti-microRNA-21 prevents kidney failure in Alport syndrome by stimulating metabolic pathways

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

overall_design: Refer to individual Series


title: RNA-seq analysis of Mst1/2 deleted bronchiolar epithelial cells from adult mouse lungs

city: Cincinnati

first: Alexander

last: Lange

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Reseach Foundation

summary: Mst1 and Mst2 were conditionally deleted from non-ciliated bronchiolar epithelial cells in the mature lung.  Bronchiolar epithelial cells from control and Mst1/2 deleted mice were isolated by cell sorting and used for RNA-seq analysis.

overall_design: Scgb1a1-rtTA/tetO-Cre/Mst1;2-flx/flx (Mst1/2 D/D) mice were generated to conditionally delete Mst1 and Mst2 from non-ciliated, secretory bronchiolar epithelial cells.  Adult mice were maintained on doxycycline food for 16 days to induce deletion of Mst1/2.  Lin-/CD326+/CD24-intermediate cells were isolated by fluorescence cell sorting to enrich for the targeted airway epithelial cells.  mRNA isolated from Lin-/CD326+/CD24-intermediate cells from control and Mst1/2 D/D mice was pooled and analyzed by RNA-seq to identify transcriptional changes following deletion of Mst1 and Mst2 from mature lung bronchiolar epithelial cells.

middle: W

first: Jeffrey

middle: A

last: Whitsett


title: PIAS1 is a target gene selective androgen receptor coregulator in prostate cancer cell chromatin

city: Kuopio

first: Sari

last: Toropainen

address: Yliopistonranta 1 E

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: To study the importance of PIAS1 (protein inhibitor of activated STAT1) for the androgen-regulated transcriptome of VCaP prostate cancer cells, we silenced its expression by RNAi. Transcriptome analyses revealed that a subset of the androgen-regulated genes is significantly influenced, either activated or repressed, by PIAS1 depletion. The depletion also exposed a completely new set of genes to androgen regulation, suggesting that PIAS1 can mask genes from androgen receptor (AR). Pathway analyses of gene expression data suggest involvement of PIAS1 in VCaP cell proliferation. According to genome-wide ChIP-seq analyses, PIAS1 interacts with the AR on chromatin harboring also SUMO2/3, as androgen exposure multiplied the occupancy of PIAS1 in the chromatin, and resulted in nearly complete overlap with AR chromatin binding events. PIAS1 interacted also with pioneer factor FOXA1 in the chromatin. Our results strongly suggest that PIAS1 is a genuine chromatin-bound coregulator of AR which functions in a target gene selective fashion in prostate cancer cells.

overall_design: All ChIP-seq samples were collected from cells treated with vehicle (EtOH) or 10 nM R1881 (synthetic androgen methyltrienolone) for 2 h. In addition, AR and FOXA1 ChIP-seq samples were collected from cells exposed to control siRNA (siNON, Dharmacon Non-targeting pool) or PIAS1 siRNA (siPIAS1, Dharmacon ON-TARGETplus SMARTpool for human PIAS1). IgG sample was collected from EtOH- and R1881-treated cells (siNON and siPIAS1 cells) and used as background control. Biological duplicate samples of the AR (siNON-R1881), PIAS1 (vehicle- and R1881-treated), FOXA1 (vehicle- and R1881-treated), RNA polymerase 2 (Pol2) (R1881-treated) and SUMO2/3 (R1881-treated) ChIP-seq samples were analyzed by using Solexa/Illumina 1.5 System and AR (siPIAS1-R1881), FOXA1 (siNON-R1881- and siPIAS1-R1881-treated) and SUMO2/3 (vehicle-treated) samples were analyzed using Illumina HiSeq 2000 platform. Single IgG sample was analyzed using Solexa/Illumina 1.5 System and single H3K4me2 (R1881-treated) sample with Illumina HiSeq 2000 platform 1.9.

first: Marjo

last: Malinen

first: Sanna

last: Kaikkonen

first: Miia

last: Rytinki

first: Tiina

last: Jääskeläinen

first: Biswajyoti

last: Sahu

first: Olli

last: Jänne

first: Jorma

middle: J

last: Palvimo


title: mRNA profiling of Col4a3-Knockout Alport Syndrome mouse model treated with inhibitor of miR-21 at 5.5 weeks of age

summary:
Purpose: MicroRNA-21 contributes to the pathogenesis of fibrogenic diseases in multiple organs including the kidney. To evaluate the therapeutic utility of antimiR-21 oligonucleotides in chronic kidney disease, we silenced miR-21 in mice that develop Alport Nephropathy due to a defect in the Col4a3 gene. The goals of this study to assess the effect of inhibiting miR-21 in the Col4a3-/- Alport Syndrome mouse model at 5.5 weeks of age.
Methods: Col4a3-/-, Col4a3+/-, and Col4a3+/+ mice in the 129X1/SvJ genetic background were obtained. Mice received anti–miR-21 (25 mg/kg) or control anti-miR (25mg/kg) in phosphate-buffered saline (PBS) by inter-scapular subcutaneous injection twice per week. In some experiments mice received a range of doses from 12.5mg/kg once a week to 50mg/kg once a week. Anti–miR-21 is a high-affinity oligonucleotide complementary to the active site of miR-21. Mice received injections starting at 24 days (3.5 weeks) after birth and ending at 5, 7, 9 or 16 weeks after birth depending on the study objectives. Total RNA from kidney tissue was extracted as per manufacturer’s instructions (miREASY kit, Qiagen). RNA quality was assessed using BioAnalyzer (Agilent). mRNA expression profiles were determined using next-generation sequencing (NGS) on the Illumina HiSeq 2000 platform producing 50bp paired-end reads. Bowtie/TopHat suites were used to align the reads to mouse genome or transcriptome and RSEM were used to quantify gene abundances. Gene level counts were then normalized with the R/Bioconductor package limma using the voom/variance stabilization method.
Results: Anti-miR-21 enhanced PPARα/RXR activity and associated downstream signaling pathways in glomerular, tubular and interstitial cells, enhanced mitochondrial function, which reduced mitochondrial ROS production and preserved tubular cell functions. In addition, inhibition of miR-21 reduced fibrogenic and inflammatory signaling in glomerular and interstitial cells, likely as a consequence of enhanced PPARα/RXR activity and mitochondrial function. Inhibition of miR-21 represents a novel therapeutic strategy for chronic kidney diseases including Alport Nephropathy.

overall_design: Whole kidney mRNA profiles of Col4a3+/- (triplicate) and Col4a3-/- (quadruplicates) mice treated with either PBS or antimiR-21, ending at 5.5 weeks of age, were generated by Next Generation Sequencing using Illumina HiSeq 2000


title: Mst1/2-Yap in lung epithelial progenitor cells

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: RNA-seq analysis of bronchosphere cultures of primary human bronchiolar epithelial cells

summary: Primary human bronchial epithelial cells were transduced with control or hYAP(S127A) lentivirus in sphere forming conditions. Bronchospheres were harvested on day 18-20 for RNAseq analysis

overall_design: Passage 1 Primary HBECs from 2 independent donors were transduced with control or hYAP lentivirus. 48 hours post infection, cells were plated on transwell inserts in a 50-50 mixture of ALI medium-Cultrex BME reduced growth factor (RGF) to form spheres. Well differentiated bronchospheres were harvested for RNA-seq analysis on day 18-20 by combining 3 wells of each group for each donor.

first: Anusha

last: Sridharan


title: RNA-Seq analysis of mouse small intestine enteroendocrine cells

city: Boston

first: Gustavo

last: Mostoslavsky

state: MA

address: 670 Albany, Suite 209

department: Medicine

institute: Boston University School of Medicine

summary: We generated knock-in mice expressing GFP under the control of the endogenous GIP (Glucose-dependent Insulinotropic Polypeptide) promoter that enable the isolation of a purified population of small intestine K cells. Using RNA-Seq, we comprehensively characterized the transcriptomes of GIP-GFP cells as well as the entire enteroendocrine lineage derived from Neurogenin3 (Ngn3)-expressing progenitors.

overall_design: We interrogated the whole transcriptome of FACS-isolated small intestine GIPGFP cells using high-throughput mRNA sequencing. We also obtained the global gene expression patterns of the entire enteroendocrine cell lineage as well as the non-enteroendocrine cell population, comprising enterocytes, goblet cells and Paneth cells. To achieve this, small intestine epithelial cells from male mice resulting from the breeding of Neurogenin3 (Ngn3)-Cre mice with ROSA26-LoxP-STOP-LoxP-tomato indicator mice were isolated based on Tomato fluorescence and negative staining for CD45. Due to the small cell numbers, we constructed each of the three RNA-Seq libraries (GIPGFP, Ngn3TOMATO, and Ngn3-) using a pool of equal amounts of individual RNA samples without RNA amplification.

first: Cesar

last: Sommer


title: SMYD2 specificly regulate BIX-01294 induced TP53 target genes revealed by RNA-Seq

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

summary: We characterized expression profilings of SMYD2 knockdown and control cells treated by BIX-01294 and Rapamycin.

overall_design: We used siRNAs to knockdown SMYD2 in HCT116 cells, and NC as control. We treated those cell lines with BIX-01294 and Rapamycin, and the expression profilings were perfomed by Illumina high throughput sequencing.

first: Jiadong

last: Fan

first: Pinji


title: Genome-wide analysis of microRNAs and their targets involving in leaf senescence of rice

city: Hangzhou

first: bo

last: shen

address: Cangqian  road

country: China

institute: Hangzhou normal university

type: Non-coding RNA profiling by high throughput sequencing

summary: Enhancing grain production of rice (Oryza sativa L.) is a top priority in ensuring food security for human being. One approach to increase yield is to delay leaf senescence and to extend the available time for photosynthesis. microRNAs (miRNAs) are key regulators for aging and cellular senescence in eukayotes. However, miRNAs and their roles in rice leaf senescence remain unexplored. Here, we report identification of miRNAs and their putative target genes by deep sequencing of six small RNA libraries, six RNA-seq libraries and two degradome libraries from the leaves of two super hybrid rice, Nei-2-You 6 (N2Y6, age-resistant rice) and Liang-You-Pei 9 (LYP9, age-sensitive rice). Totally 372 known miRNAs and 162 miRNA candidates were identified, and 1145 targets were identified. Compared with the expression of miRNAs in the leaves of LYP9, the numbers of miRNAs up-regulated and down-regulated in the leaves of N2Y6 were 47 and 30 at early stage of grain-filling, 21 and 17 at the middle stage, and 11 and 37 at the late stage, respectively. Six miRNA families, osa-miR159, osa-miR160 osa-miR164, osa-miR167, osa-miR172 and osa-miR1848, targeting the genes encoding APETALA2 (AP2), zinc finger proteins, salicylic acid-induced protein 19 (SIP19), Auxin response factors (ARF) and NAC transcription factors, respectively, were found to be involved in leaf senescence through phytohormone signaling pathways. These results provided valuable information for understanding the miRNA-mediated leaf senescence of rice, and offered an important foundation for rice breeding.

overall_design:
[miRNA] sample 1:The flag leaves at early stage of grain-filling of N2Y6 rice; sample 2: The flag leaves at middle stage of grain-filling of N2Y6 rice;sample 3:The flag leaves at late stage of grain-filling of N2Y6 rice; sample 4:The flag leaves at early stage of grain-filling of LYP9 rice; sample 5: The flag leaves at middle stage of grain-filling of LYP9 rice;sample 6:The flag leaves at late stage of grain-filling of LYP9 rice.
[DGE]: samples 7-12
[degradome (targets)]: samples 13:The flag leaves at mixed stages of grain-filling of N2Y6 rice; sample 14:The flag leaves at mixed stages of grain-filling of LYP9 rice

first: Bo

last: Shen

first: Jieyun

last: Zhuang


title: Sublethal Concentrations of Carbapenems Alter Cell Morphology and Genomic Expression of Klebsiella pneumoniae Biofilms

city: Cambridge

first: Tsute

last: Chen

address: 245 First Street

department: Microbiology

institute: The Forsyth Institute

summary: K. pneumoniae, a Gram-negative bacterium, is normally associated with pneumonia in patients with weakened immune systems. However, it is also a prevalent nosocomial infectious agent that can be found in infected surgical sites and combat wounds. Many of these clinical strains display multi-drug resistance. We have worked with a clinical strain of K. pneumoniae that was initially isolated from a wound of an injured soldier. This strain demonstrated resistance to many commonly used antibiotics, but sensitivity to carbapenems. This isolate was capable of forming biofilms in vitro, contributing to its increased antibiotic resistance and impaired clearance. We were interested in determining how sublethal concentrations of carbapenem treatment specifically affect K. pneumoniae biofilms both in morphology and genomic expression. Scanning electron microscopy showed striking morphological differences between untreated and treated biofilms, including rounding, blebbing, and dimpling of treated cells. Comparative transcriptome analysis using RNA sequencing technology identified a large number of open reading frames (ORFs) differentially regulated in response to carbapenem treatment at 2 and 24 hours. ORFs upregulated with carbapenem treatment included genes involved in resistance, antiporters, and autoinducers. ORFs downregulated included metal transporters, membrane biosynthesis proteins, and motility proteins. Quantitative real time PCR validated the general trend of some of these differentially regulated ORFs. Treating K. pneumoniae biofilms with sublethal concentrations of carbapenems induced a wide-range of phenotypic and gene expression changes. This study reveals some of the mechanisms underlying how sublethal amounts of carbapenems could affect the overall fitness and pathogenic potential of K. pneumoniae biofilm cells.

overall_design: Treat K. pneumoniae biofilm with carbapenem at 2 and 24 hour and compared to biofilm without treatment

first: Tricia

last: Van Laar

first: Tao

last: You

first: Kai

middle: P

last: Leung


title: Wax and Wane of genome-wide DNA methylation during monkey preimplantation embryogenesis

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

institute: Agricultural Genomes Institute at Shenzhen

summary: This study reports, for the first time, the genome scale methylome of nonhuman primate preimplantation development and proposes a perspective of DNA methylation dynamic equilibrium involving both DNA demethylation and de novoremethylation during primate early embryogenesis.

overall_design: we collected rhesus monkey sperms and around 100 cells of MII-stage oocytes, zygotes, as well as 2 cell, 8 cell, morula stage embryos and inner cell mass (ICM) of the blastocysts to perform single-base resolution whole genome bisulfite sequencing (WGBS). A previously described transposase-based library preparation method (T-WGBS) was applied.

first: Fei

last: Gao

last: Tan

first: Hanlin

last: Lu


title: Orsay Virus infection is neither systemic nor transgenerational

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

country: United Kingdom

institute: Imperial College London

summary: Small RNA sequencing of Orsay virus infected animals and their progeny

overall_design: Sequencing of small RNAs (18-30nt)

first: Eric

last: Miska


title: ChIP-seq and RNA-seq analysis of PRC2 core subunits in primary human erythroid progenitor cells

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital


title: A comparison of control samples for ChIP-seq of histone modifications

city: Parkville

first: Marnie

last: Blewitt

state: VIC

address: 1G Royal Parade

department: Molecular Medicine Division

country: Australia

institute: WEHI

summary:
The advent of high-throughput sequencing has allowed genome wide profiling of histone modifications by Chromatin ImmunoPrecipitation (ChIP) followed by sequencing (ChIP-seq). In this assay the histone mark of interest is enriched through a chromatin pull-down assay using an antibody for the mark. Due to imperfect antibodies and other factors, many of the sequenced fragments do not originate from the histone mark of interest, and are referred to as background reads. Background reads are not uniformly distributed and therefore control samples are usually used to estimate the background distribution at any given genomic position. The Encyclopedia of DNA Elements (ENCODE) Consortium guidelines suggest sequencing a whole cell extract (WCE, or “input”) sample, or a mock ChIP reaction such as an IgG control, as a background sample. However, for a histone modification ChIP-seq investigation it is also possible to use a Histone H3 (H3) pull-down to map the underlying distribution of histones.
In this paper we generated data from a hematopoietic stem and progenitor cell population isolated from mouse foetal liver to compare WCE and H3 ChIP-seq as control samples. The quality of the control samples is estimated by a comparison to pull-downs of histone modifications and to expression data. We find minor differences between WCE and H3 ChIP-seq, such as coverage in mitochondria and behaviour close to transcription start sites. Where the two controls differ, the H3 pull-down is generally more similar to the ChIP-seq of histone modifications. However, the differences between H3 and WCE have a negligible impact on the quality of a standard analysis.

overall_design: WCE and histone H3 ChIP-seq samples are compared to H3K27me3 ChIP-seq and RNA-seq.

first: Sarah

last: Kinkel

first: Andrew

last: Keniry


title: RNA-seq transcriptional profiling in primary human erythroid progenitor cells upon shRNA-mediated knockdown of PRC2 core subunits

summary: Polycomb Repressive Complex 2 (PRC2) plays crucial roles in transcriptional regulation and stem cell development. However, the context-specific functions associated with alternative subunits remain largely unexplored. Here we show that the related enzymatic subunits EZH1 and EZH2 undergo an expression switch during hematopoiesis. We examine the in vivo stoichiometry of the PRC2 complexes by quantitative proteomics and reveal the existence of an EZH1-SUZ12 sub-complex lacking EED. We provide evidence that EZH1 together with SUZ12 form a non-canonical PRC2 complex, occupy active chromatin domains in the absence of H3K27me3, and positively regulate gene expression. Loss of EZH2 expression leads to global repositioning of EZH1 chromatin occupancy to EZH2 targets. Moreover, we demonstrate that an erythroid-specific enhancer mediates transcriptional activation of EZH1, and a switch from GATA2 to GATA1 controls the developmental EZH1/2 switch by differential association with EZH1 enhancers during erythropoiesis. Thus, the lineage- and developmental stage-specific regulation of PRC2 expression and subunit composition leads to a switch from canonical silencing to non-canonical PRC2 functions during blood stem cell specification.

overall_design: Transcriptional profiling in primary human fetal liver proerythroblasts upon lentiviral shRNA-mediated knockdown of EZH1, EZH2, EED, or SUZ12 by RNA-seq analysis.

first: Zhen

last: Shao

first: Stuart

middle: H

last: Orkin


title: Endogenous germline nuclear RNAi-mediated transcriptional silencing and histone H3 lysine 9 methylation in defined regions of the Caenorhabditis elegans genome

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

summary: We describe the identification and characterization of genomic regions that are targeted by germline nuclear RNAi in C. elegans for transcriptional silencing and heterochromatic response.

overall_design: We compared the wild type and germline nuclear Argonaute protein hrde-1 mutant for their RNA polymerase II ChIP-seq, H3K9 trimethylation ChIP-seq, pre-mRNA seq, mRNA-seq, and small RNA-seq profiles.

first: Julie

middle: Z

last: Ni

first: Esteban


title: Comparative FAIRE-seq analysis reveals distinguishing features of the chromatin structure of ground state- and primed pluripotent cells

city: New York

first: Matthew

last: Murtha

state: NY

address: 550 First Ave

institute: NYU School of Medicine

summary: We utilized FAIRE-seq to identify accesible chromatin in mouse embryonic-, epiblast-, and neural- stem cells in addition to mouse embryonic fibroblasts. Analysis of these data sets reveal cell type specific chromatin signatures that differentiate naïve and primed pluripotency. Functional analysis of type-specific peaks revealed cell-type specific enhancers.

overall_design: FAIRE-seq of mESC, EpiSC, NSC and MEF

first: Lisa

last: Dailey


title: Gene expression analysis of Candida albicans hyphae in interaction with PK E6/E7 vaginal epithelial cell line

city: Morahalom

first: Balazs

last: Horvath

address: Vallalkozok u. 7.

department: NGSP

country: Hungary

institute: SeqOmics Biotechnology Ltd.

summary: Identification of genes differentially expressed in Candida albicans upon hyphal growth

overall_design: To better understand the molecular events during vulvovaginal candidiasis, we established an in vitro system based on immortalized vaginal epithelial cells infected with C. albicans. As control, a low glucose cell culture medium was used, which robustly induced yeast to hyphae transition. RNA-seq approach was used to find major and significant changes in our in vitro system at the transcriptional level.

first: Máté

last: Manczinger

first: Gabriella

last: Kocsis-Fodor

first: Andrea

last: Vörös

first: Zoltán

last: Hegedűs

first: Lilla

last: Ördögh

first: Éva

last: Kondorosi

first: Lajos

last: Kemény

first: István

last: Nagy

first: Lóránt

last: Lakatos


title: An angiogenic role for the aryl hydrocarbon receptor in choroidal neovascularization

city: Palo Alto

first: Dmitri

last: Kazmin

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

summary: We report that decreased expression and activity of AhR exacerbates murine neovascular age-related macular degeneration, and increases cell migration and tube formation. The mechanism involves increased expression of pro-angiogenic mediators and altered matrix degradation. The results of our study suggest that the AhR signaling pathway may be important in multiple AMD related pathways.

overall_design: Gene expression analysis in the retinal pigment epithelium (RPE)-choroid tissue from AhR knockout mice contrasted against wild-type age-matched controls.

first: Mayur

last: Choudhary

first: Peng

last: Hu

first: Russell

middle: S

last: Thomas

first: Donald

last: McDonnell

first: Goldis

last: Malek


title: Transcriptome analysis of threespine sticklebacks acclimated in different salinities

city: College Station

first: James

last: Cai

state: TX

address: TAMUS 4458

department: Veterinary Integrative Biosciences

institute: Texas A&M University

summary: RNA sequencing was used to measure global gene expression in wild caught threespine sticklebacks. Native freshwater and marine fish were acclimated in water of different salinities before the gene expression in kidney was measured. The comparative transcriptomic analysis allowed the identification of salt-responsive genes.

overall_design: We acclimated native freshwater (FW) and saltwater (SW) threespine sticklebacks to fresh (salinity: 0 g/L), brackish (salinity: 11 g/L), and sea water (salinity: 33 g/L) for 30 days, and then measured the global gene expression in fish kidneys.


title: Scl specifies hemogenic endothelium and inhibits cardiogenesis via primed enhancers [RRBS]

city: Tartu

first: Tõnis

last: Org

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

type: Methylation profiling by high throughput sequencing

summary: Scl/Tal1 confers hemogenic competence and prevents cardiomyogenesis in embryonic endothelium. Here we show that Scl both directly activates a broad gene regulatory network required for hematopoietic stem/progenitor cell (HS/PC) development, and represses transcriptional regulators required for cardiogenesis. Cardiac repression occurs during a short developmental window through Scl binding to distant cardiac enhancers that harbor H3K4me1 at this stage. Scl binding to hematopoietic regulators extends throughout HS/PC and erythroid development and spreads from distant enhancers to promoters. Surprisingly, Scl complex partners Gata 1 and 2 are dispensable for hematopoietic versus cardiac specification and Scl binding to the majority of its target genes. Nevertheless, Gata factors co-operate with Scl to activate selected transcription factors to facilitate HS/PC emergence from hemogenic endothelium. These results uncover a dual function for Scl in dictating hematopoietic versus cardiac fate choice and suggest a mechanism by which lineage-specific bHLH factors direct the divergence of competing fates.

overall_design: Examination of Scl and Gata 1 & 2 target genes in ES cell derived day4.75 EB (embryoid body) Tie2+CD31+CD41- endothelial cells

first: Tonis

first: Dan

last: Duan

first: Roberto

last: Ferrari

first: Amelie

last: Montel-Hagen

first: Ben

last: Van Handel

first: Marc

last: Kerényi

first: Rajkumar

last: Sasidharan

first: Ludmilla

last: Rubbi

first: Yuko

last: Fujiwara

first: Matteo

last: Pellegrini

first: Stuart

last: H. Orkin

first: Siavash

last: Kurdistani

first: Hanna

last: Mikkola


title: KLF1 null neonates display hydrops fetalis and a deranged erythroid transcriptome

city: Brisbane

first: Graham

middle: William

last: Magor

state: Queensland

address: 37 Kent St

institute: Mater Research

summary: We describe a case of severe neonatal anemia with kernicterus due to compound heterozygosity for null mutations in KLF1, each inherited from asymptomatic parents. One of the mutations is novel. This is the first described case of a KLF1 null human. The phenotype of severe DAT-negative non-spherocytic hemolytic anaemia (NSHA), jaundice, hepato-splenomegaly, and marked erythroblastosis is more severe than that present in CDA type IV due to dominant mutations in the second zinc-finger of KLF1. There was a very high level of HbF expression into childhood (>70%), consistent with a key role for KLF1 in human hemoglobin switching. We performed RNA-seq on circulating erythroblasts and found human KLF1 acts like mouse Klf1 to coordinate expression of many genes required to build a red cell including those encoding globins, cytoskeletal components, AHSP, heme synthesis enzymes, cell cycle regulators, and blood group antigens. We identify novel KLF1 target genes including KIF23 and KIF11 which are required for proper cytokinesis. We also identify new roles for KLF1 in autophagy, global transcriptional control and RNA splicing. We suggest loss of KLF1 should be considered in otherwise unexplained cases of severe neonatal NSHA or hydrops fetalis.

overall_design: mRNA sequencing on peripheral blood from a family trio (mother, father and proband) where parents were asymptomatic and proband had severe neonatal anemia.

first: Andrew

middle: C

last: Perkins


title: Seedling transcriptomes of Arabidopsis thaliana HULK mutants

city: Salt Lake City

first: Richard

middle: M

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

summary: We produced RNA-seq reads from messenger RNA isolated from aerial seedling tissue for Arabidopsis thaliana mutants in the HULK gene family. The read data were generated with biological replication (two replicates). The resulting RNA-seq data provide a resource to assess the function of HULK genes in the control of downstream gene expression in A. thaliana.

overall_design: Examination of RNA transcript levels in HULK T-DNA mutants (and mutant combinations therein) in Arabidopsis thaliana.

first: Joshua

last: Steffen


title: Transcriptome and gene expression analysis during flower blooming in Rosa chinensis ‘Pallida’

city: Kunming

first: huijun

last: yan

address: Kunming, Yunnan, P. R. China

institute: Flower Research Institute of Yunnan Academy of Agricultural Sciences

summary: Rosa chinensis ‘Pallida’ (Rosa L.) is one of the most important ancient rose cultivars originating from China. It contributed the ‘tea scent’ trait to modern roses. However, little information is available on the gene regulatory networks involved in scent biosynthesis and metabolism in Rosa. In this study, the transcriptome of R. chinensis ‘Pallida’ petals at different developmental stages, from flower buds to senescent flowers, was investigated using Illumina sequencing technology. De novo assembly generated 89,614 clusters with an average length of 428 bp. Based on sequence similarity search with known proteins, 62.9% of total clusters were annotated. Out of these annotated transcripts, 25,705 and 37,159 sequences were assigned to gene ontology and clusters of orthologous groups, respectively. The dataset provides information on transcripts putatively associated with known scent metabolic pathways. Digital gene expression (DGE) was obtained using RNA samples from flower bud, open flower and senescent flower stages. Comparative DGE and quantitative real time PCR permitted the identification of five transcripts encoding proteins putatively associated with scent biosynthesis in roses. The study provides a foundation for scent-related genes discovery in roses.

overall_design: Examination of transcriptome of  Rosa chinensis 'Pallida' by RNA-seq.

first: Huijun

last: Yan

first: Hao

last: Zhang

first: Min

last: Chen

first: Hongying

last: Jian

first: Sylvie

last: Baudino

first: Jean-Claude

last: Caissard

first: Mohammed

last: Bendahmane

first: Shubin

last: Li

first: Ting

first: Ningning

last: Zhou

first: Xianqin

last: Qiu

first: Qigang

last: Wang

first: Kaixue

last: Tang


title: Redefinition of Human Androgen Responsive Elements [LNCaP_ChIP-exo]

city: Stanford

first: Xun

last: Lan

address: 318 Campus Dr. Room S240

department: Genetics

summary: The androgen receptor (AR) mediates the action of androgens by binding to androgen-responsive elements (AREs) and subsequently regulating target genes involved in prostate carcinogenesis. The precise locations, true nature, and functional roles of AREs in human prostate cancer are still unknown. Here we redefine AREs by motif-resolution AR chromatin immunoprecipitation-exonuclease (ChIP-exo) assay in human prostate cancer cells and tumors. Surprisingly, we find that, in addition to canonical full-length AREs and half-site-like AREs, a significant portion of the four redefined ARE categories comprises non-canonical full-length AREs. The redefined AREs in enhanced AR binding regions in prostate tumors versus paired non-malignant adjacent tissues regulate a prostate cancer-relevant gene network not only centered on AR, but more interestingly, on novel AR target genes mTOR, BIRC5 and BCL2L1 involved in prostate cancer cell growth and survival. The precise redefinition of AREs has important implications for understanding how AR contributes to prostate carcinogenesis.

overall_design: To accurately define ARE in human genome and identify cancer related AR binding site, AR ChIP-exo is performed in LNCaP cells before/after androgen stimulation. Each experiment includes two replicates. Please see the PROTOCOLS section for detailed information.

first: Qianben

first: Zhong


title: Uncover small RNAs in citrus somatic embryogenesis

city: Wuhan

first: Xiaomeng

last: Wu

state: Hubei

address: Shizishan No.1

department: College of Horticulture & Forestry Sciences

institute: HuaZhong Agricultural University

summary: To uncover the involvement of miRNAs and siRNAs in somatic embryogenesis of the perennial woody crop citrus, we carried out high-throughput (Illumina) sequencing (HTS) of sRNAs and RNA degradome tags in non-embryogenic and embryogenic tissue of Valencia sweet orange. A total of 191 stem-loop structures were identified, emanating 50 known and 45 novel miRNAs, 130 miniature inverted-repeat transposable elements (MITEs) derived small interfering RNAs (siRNAs) and 94 other siRNAs. Combining with the result of degradome sequencing, a total of 235 phased siRNAs (phasiRNAs), and 195 cleaved target genes were identified for miRNAs/siRNAs.

overall_design: Small RNA and degradome libraries of nonembryogenic callus (NEC), embryogenic callus (EC) and embryogenic callus exposed to  somatic embryo induction for 1, 2, 3, 4 weeks (E1-4) of Valencia sweet orange (Citrus sinensis) were sequenced by Illumina platform, one biological replicates

first: Wenwu

last: Guo


title: ALDH2, CCNE1 and SMAD3 are Potential Prognostic Markers for Upper Tract Urothelial Carcinoma Revealed by Massively Parallel Sequencing.

first: Gaille

last: Joo

address: Beishan Industrial Zone, Yantian District

institute: BGI

summary:
Purpose: upper tract urothelial carcinoma (UTUC) is the predominant subtype of the renal pelvis carcinoma but current knowledge about the molecular properties and prognostic markers is sparse. In this study, we examined the genome-wide mRNA expression spectrum of UTUC aiming to characterize the molecular basis of this cancer, and identify potential prognostic markers and thus facilitate the clinical practices.
Experimental Design: we compared the whole mRNA expression spectrum of cancer and matched normal tissues in 10 patients with UTUC using massively parallel sequencing, thereafter the protein levels and prognostic roles of ALDH2, CCNE1 and SMAD3 were evaluated under an independent validation set comprising of 104 patients.
Results: mRNA down-regulation of ALDH2 and up-regulation of SMAD3 and CCNE1 in UTUC were revealed by expression profiling. And low protein expression of ALDH2 was associated with an adverse outcome for patients (p < 0.0001). Whereas high CCNE1 and SMAD3 were associated with adverse clinical outcome (p < 0.0001). And multivariate analysis revealed that all these three molecular markers were independent prognostic predictors. Besides, compared to the pathological TNM classification, All ALDH2, CCNE1 and SMAD3 were more competent in identifying patient subgroup with high mortality risk, and the molecular markers were able to predict the survival difference in the patients of T2 and T3 subgroup (p < 0.001), which could not be achieved by TNM staging.
Conclusions: This is the ﬁrst prospective study that characterizes genome-wide mRNA expression profile of UTUC. We revealed the prognostic significance of ALDH2, CCNE1 and SMAD3, and these molecular marker were more robust than TNM system in clinical outcome prediction.

overall_design: Whole mRNA expression spectrum of cancer and matched normal tissues in 10 patients with UTUC was obtained by using massively parallel sequencing

first: Jiahao

first: Jialou

last: Zhu


title: Scl specifies hemogenic endothelium and inhibits cardiogenesis via primed enhancers [RNA-seq]

first: Tõnis

last: Org

first: Tonis

first: Dan

last: Duan

first: Roberto

last: Ferrari

first: Amelie

last: Montel-Hagen

first: Ben

last: Van Handel

first: Rajkumar

last: Sasidharan

first: Marc

last: Kerényi

first: Ludmilla

last: Rubbi

first: Yuko

last: Fujiwara

first: Matteo

last: Pellegrini

first: Stuart

last: Orkin

first: Siavash

last: Kurdistani

first: Hanna

last: Mikkola


title: A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation

city: Montpellier Cedex 5

first: Laurent

last: Journot

address: 141 rue de la cardonille

department: Institut de Genomique Fonctionnelle

country: France

institute: Centre National de la Recherche Scientifique

summary: We used the 3T3-L1 preadipocyte cell line (Green and Kehinde. Cell 5:19-25, 1974; ATCC CL-173), in which adipogenic differentiation is experimentally induced when quiescent 3T3-L1 cells are incubated with serum and IDX (insulin, dexamethasone, isobutylmethylxanthine). Following IDX addition, the cells retract and re-enter the cell cycle in the so-called clonal expansion phase. Two to three days later the cells definitively exit the cell cycle, express adipocyte-specific genes, and accumulate lipids to form lipid droplets.

overall_design: 3T3-L1 cells were grown in DMEM/FBS 10% until they reached confluence and entred quiescence following contact inhibition. The cells were kept confluent in the same medium for 2 days. The medium was renewed and supplemented with IDX for 48 hours. The medium was supplemented with insulin and renewed every 2 days until the adipogenic differentiation was completed.

first: Hala

last: AL ADHAMI

first: Brendan

last: EVANO

first: Anne

last: LE DIGARCHER

first: Charlotte

last: GUEYDAN

first: Emeric

last: DUBOIS

first: Hugues

last: PARRINELLO

first: Christelle

last: DANTEC

first: Tristan

last: BOUSCHET

first: Annie

last: VARRAULT

last: JOURNOT


title: Scl specifies hemogenic endothelium and inhibits cardiogenesis via primed enhancers [ChIP-seq]

first: Tõnis

last: Org

overall_design: ChIP-seq with Scl, Hand1, Lsd1, Ezh2, H3K4me1 and H3K27ac in different cell types with mesodermal origin. Scl ChIP-seq in WT, SclKO, SclKO-iScl and Gata12KO mES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells, SclKO-iScl ES cells and MEL cells; Hand1 ChIP-seq in WT mES cell derived day4 EB Flk1+ mesodermal cells; Lsd1 and Ezh2 ChIP-seq in WT and SclKO mES cell derived day4 EB Flk1+ mesodermal cells. ChIP-seq of histone modifications H3K4me1 and H3K27ac in WT, SclKO and Gata12KO mES cell derived day4 EB Flk1+ mesodermal cells, HPC7 hematopoietic progenitor cells and HL1 cardiomyogenic cells

first: Tonis

first: Dan

last: Duan

first: Roberto

last: Ferrari

first: Amelie

last: Montel-Hagen

first: Ben

last: Van Handel

first: Marc

last: Kerényi

first: Rajkumar

last: Sasidharan

last: Rubbi


title: ICOS coreceptor signaling inactivates the transcription factor FOXO1 to promote Tfh cell differentiation

city: La Jolla

first: Carol

last: Katayama

address: 9500 Gilman Dr.

department: BIO/CMM

institute: UC San Diego

summary: T follicular helper (Tfh) cells are essential in the induction of high-affinity, class-switched antibodies. The differentiation of Tfh cells is a multi-step process that depends upon the co-receptor ICOS and the activation of phosphoinositide-3 kinase leading to the expression of key Tfh cell genes. We report that ICOS signaling inactivates the transcription factor FOXO1, and a Foxo1 genetic deletion allowed for generation of Tfh cells with reduced dependence on ICOS ligand. Conversely, enforced nuclear localization of FOXO1 inhibited Tfh cell development even though ICOS was overexpressed. FOXO1 regulated Tfh cell differentiation through a broad program of gene expression exemplified by its negative regulation of Bcl6. Final differentiation to germinal center Tfh cells (GC-Tfh) was instead FOXO1 dependent as the Foxo1(-/-) GC-Tfh cell population was substantially reduced. We propose that ICOS signaling transiently inactivates FOXO1 to initiate a Tfh cell contingency that is completed in a FOXO1-dependent manner.

overall_design: Performed ChIP-seq analysis to examine the role of foxo1 in the development of Tfh cells

first: Erica

middle: L

last: Stone

first: Marion

last: Pepper

middle: D

first: Yann

last: Kerdiles

first: Chen-Yen

last: Lai

first: Elizabeth

last: Emslie

first: Yin

last: Lin

first: Edward

last: Yang

first: Ananda

last: Goldrath

first: Ming

middle: O

last: Li

first: Doreen

last: Cantrell

first: Stephen

last: Hedrick


title: Deep transcriptome profile analysis reveals different expression patterns of Xanthomonas oryzae pv. oryzae strains

city: beijing

first: Zhenglin

last: Du

address: NO.1 Beichen West Road, Chaoyang District, Beijing 100101, China

institute: Beijing Institute of Genomics

summary: An attempt has been made to investigate gene expression patterns of three Xoo strains in XOM2, PXO99 (P6) and PXO86 (P2) from Phillipines, and GD1358 (C5) from China, which exhibited different virulence in 30 rice varieties, with putative virulence factors using deep sequencing. In total, 4759 transcripts were identified in this study, and 1151 and 3076 genes were differentially expressed when P6 compared with P2 and P6 compared with C5, respectively. Our results indicated that Xoo strains from different regions exhibited distinctly different expression patterns of putative virulence-revelent genes. Interestingly, all genes involved in chemotaxis and motility exhibited higher transcript alteration in C5 compared with P6 and P2, while the most other genes associated with the virulence, including expolysaccharide (EPS) synthesis, Hrp genes and type III effectors, including Xop effectors and transcription activator-like (TAL) effectors, down-regulation differentially expressed in C5 compared with P6 and P2. The data were confirmed by real-time quantitative RT-PCR and test experiment of bacterial motility and enzyme activity analysis of EPS and xylanase. These results highlight the complexity of the Xoo and offer new avenues for improving our understanding of Xoo-rice interactions and evolutionary of Xoo virulence.

overall_design: Analyzing the transcriptome profile of 3 Xanthomonas oryzae pv. oryzae strains cultured in XOM2

first: Yongli

last: Zhou

first: Fan

last: Zhang

first: Liyu

last: Huang

first: Zhikang


title: Extensive remodeling of DC function by rapid maturation-induced epigenetic gene silencing

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

summary: Dendritic-cell (DC) maturation involves substantial remodeling of their gene-expression program. Most research has focused on inducible gene-expression networks promoting the acquisition of new functions, such as cytokine production and enhanced T-cell-stimulatory capacity. In contrast, mechanisms that modulate DC-function by inducing gene silencing remain poorly understood. Here we describe a novel primary epigenetic-silencing response that makes major contributions to the DC-maturation process. The repressed genes function in pivotal processes - including antigen-presentation, extracellular-signal detection, signal-transduction and lipid-mediator biosynthesis - underscoring the central contribution of the silencing mechanism to rapid reshaping of DC-function. Interestingly, promoters of the repressed genes exhibit a surprisingly high frequency of PU.1-occupied sites, suggesting a novel role for this transcription factor in marking genes poised for inducible repression

overall_design: Analysis of PU.1 binding sites in mo-DC

first: Queralt

last: Seguín-Estévez

first: Isabelle

last: Dunand-Sauthier

last: Lemeille

first: Christian

last: Iseli

first: Mark

last: Ibberson

first: Vassilios

last: Ioannidis

first: Emmanuèle

last: Barras

first: Antoine

last: Geinoz

first: Christoph

last: Schmid


title: ChIP-seq analysis of PRC2 core subunits in primary human erythroid progenitor cells

city: Memphis

first: Jian

last: Xu

address: 262 Danny Thomas Place, MS 345

institute: St. Jude Children's Research Hospital

summary: Polycomb Repressive Complex 2 (PRC2) plays crucial roles in transcriptional regulation and stem cell development. However, the context-specific functions associated with alternative subunits remain largely unexplored. Here we show that the related enzymatic subunits EZH1 and EZH2 undergo an expression switch during hematopoiesis. We examine the in vivo stoichiometry of the PRC2 complexes by quantitative proteomics and reveal the existence of an EZH1-SUZ12 sub-complex lacking EED. We provide evidence that EZH1 together with SUZ12 form a non-canonical PRC2 complex, occupy active chromatin domains in the absence of H3K27me3, and positively regulate gene expression. Loss of EZH2 expression leads to global repositioning of EZH1 chromatin occupancy to EZH2 targets. Moreover, we demonstrate that an erythroid-specific enhancer mediates transcriptional activation of EZH1, and a switch from GATA2 to GATA1 controls the developmental EZH1/2 switch by differential association with EZH1 enhancers during erythropoiesis. Thus, the lineage- and developmental stage-specific regulation of PRC2 expression and subunit composition leads to a switch from canonical silencing to non-canonical PRC2 functions during blood stem cell specification.

overall_design: Analysis of genomic occupancy of EZH1, EZH2, EED, SUZ12, various histone marks and transcription factors in primary human fetal liver proerythroblasts by ChIP-seq. Sample GSM970262 was used as the input DNA sample.

first: Zhen

last: Shao

first: Stuart

last: Orkin


title: Scl specifies hemogenic endothelium and inhibits cardiogenesis via primed enhancers

first: Tõnis

last: Org

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

overall_design: Refer to individual Series

first: Tonis

first: Dan

last: Duan

first: Roberto

last: Ferrari

first: Amelie

last: Montel-Hagen

first: Ben

last: Van Handel

first: Marc

last: Kerényi

first: Rajkumar

last: Sasidharan

first: Ludmilla

last: Rubbi

first: Yuko

last: Fujiwara

first: Matteo

last: Pellegrini

first: Siavash

middle: K

last: Kurdistani

first: Hanna

last: Mikkola


title: Redefinition of Human Androgen Responsive Elements [ChIP-Seq, RNA-Seq]

first: Xun

last: Lan

overall_design: To accurately define ARE in human genome and identify cancer related AR binding site, AR ChIP-exo is performed in LNCaP cells before/after androgen stimulation, malignant prostate tumors and non-malignant adjacent tissues. Each experiment includes two replicates.

first: Qianben

last: Wang

first: Zhong

last: Chen


title: Redefinition of Human Androgen Responsive Elements [MNase-Seq, ChIP_seq]

overall_design: To examine the differential AR binding in LNCaP cells before and after androgen stimulation, ChIP-Seq of androgen receptor is performed in LNCaP cells under the two conditions. To profile histone modification status in control LNCaP cells, MNase-Seq is performed with five different antibodies specific to certain histone marks. Each experiment includes two replicates.


title: NA-Seq reveals dynamic changes of gene expression in key stages of intestine regeneration in the sea cucumber Apostichopus japonicus.

city: Qingdao

first: Lina

last: Sun

address: Nanhai Road 7

institute: Institute of Oceanology, Chinese Academy of Sciences

summary: Sea cucumbers (Holothuroidea; Echinodermata) have the capacity to regenerate lost tissues and organs.We used RNA-Seq to determine gene expression profiles associated with  intestinal regeneration in A. japonicus at 3, 7, 14 and 21 days post evisceration (dpe)

overall_design: At least 15 individuals per stage, at 3, 7, 14 and 21 days post evisceration (dpe) were used for our experiments.

first: Hongsheng

last: Yang


title: Redefinition of Human Androgen Responsive Elements [FOX_ChIP_exo]

overall_design: FOXA1 ChIP-exo


title: RNA-Seq of the BA9, BA40 and AMY for one typically developing individual #5407

status: Public on Dec 31 2014

first: Jingjing

last: Li

address: 3165 Porter Drive

summary: We performed RNA-Seq for the BA9/40/AMY for a typically developing individual #5407. The samples were dissected from the frozen postmortem brain.

first: Minyi

last: Shi

first: Zhihai

last: Ma

first: Michael

last: Snyder


title: RNA-Seq of the corpus callosum from 12 individuals

summary: We performed RNA-Seq for the corpus callosum sampled from 12 individuals. The samples were dissected from the frozen postmortem brain. The 12 individuals were matched by their age, sex and ethnicity for the postmortem brain samples, but differed in their disease status with half of the subjects were diagnosed with autism spectrum disorders.


title: Ascorbic acid enhances Tet-mediated 5-methylcytosine oxidation and promotes DNA demethylation in mammals.

city: Beijing

first: Zechen

last: Chong

address: NO. 7 Beitucheng West Road

summary: DNA demethylation occurs in multiple cellular processes but its regulation is poorly understood. Here we report that a vital nutrient factor ascorbic acid (AA), or vitamin C (Vc), induces DNA demethylation in mammalian cells. The levels of active 5mC oxidation products, 5-formylcytosine and 5-carboxylcytosine, increase by more than one magnitude of order in mouse ES cells when cultured in the presence of AA. In cells deleted of Tet1 and Tet2 dioxygenase genes, AA does not facilitate 5mC oxidation. The AA effect is however restored when Tet2 was re-expressed in the mutant cells. The enhancing effect of AA on 5mC oxidation and DNA demethylation was also observed in a mouse model deficient in AA synthesis. Our results thus reveal a role of AA in the regulation of DNA modification, which might mediate a plethora of functions of AA.

overall_design: Examination of 5hmC levels with or without AA in mouse ES cells

first: Yun-Gui

first: Guoliang

last: Xu

first: Hailin


title: A triple-HLH/bHLH Cascade Controls Cell Elongation Downstream of Multiple Hormonal and Environmental Signaling Pathways

city: Jinan

first: Mingyi

last: Bai

state: Shandong

address: 27 Shandananlu

department: Life of Scienec

institute: Shandong University

summary: The environmental and endogenous signals, light, temperature, brassinosteroid (BR), and gibberellin (GA), regulate cell elongation largely by controlling the expression of the PRE family helix-Loop-helix (HLH) factors, which promote cell elongation by interacting antagonistically with another HLH factor, IBH1. But the molecular mechanism by which PREs and IBH1 regulate gene expression has remained unknown. Here we show that IBH1 interacts with and inhibits a DNA-binding bHLH protein HBI1. Overexpression of HBI1 increased hypocotyl and petiole elongation, whereas dominant inactivation of HBI1 and its homologs caused a dwarf phenotype, indicating that HBI1 is a positive regulator of cell elongation. In vitro and in vivo experiments showed that HBI1 directly bound to the promoters and activated two EXPANSIN genes encoding cell wall-loosening enzymes; HBI1’s DNA-binding and transcriptional activities were inhibited by IBH1, but the inhibitory effects of IBH1 were abolished by PRE1. The results indicate that PREs activate the DNA-binding bHLH factor HBI1 by sequestering its inhibitor IBH1. Altering each of the three factors affected plant sensitivities to BR, GA, temperature, and light. Our study demonstrates that PREs, IBH1 and HBI1 form a chain of antagonistic switches that controls cell elongation downstream of multiple external and endogenous signals.

overall_design: Compare the transcriptome of IBH1 and PRE1

first: Zhiyong


title: An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations

city: Vancouver

first: Matthew

last: Lorincz

state: British Columbia

address: 2350 Health Sciences Mall

department: Medical Genetics

country: Canada

institute: University of British Columbia

summary: The development of combined chromatin immunoprecipitation and next generation sequencing (ChIP-seq) technologies has enabled genome-wide epigenetic profiling of numerous cell lines and tissue types. A major limitation of ChIP-seq, however, is the large number of cells required to generate high quality datasets, precluding the study of rare cell populations. Here, we present an ultra-low-input micrococcal nuclease-based native ChIP (ULI-NChIP) and sequencing method, to generate genome-wide histone mark profiles with high resolution and reproducibility from as few as one thousand cells. Using ULI-NChIP, we generated high quality maps of several covalent histone marks from 10^3-10^6 embryonic stem cells. To further validate our procedure we demonstrate that genome-wide H3K27me3 profiles generated from 10^3 E13.5 primordial germ cells (PGCs) using ULI-NChIP-seq show high similarity to recently generated datasets using 50-180× more material, illustrating the utility of this method for generating high quality libraries with improved complexity from rare cell populations.

overall_design: Low input H3K9me3, H3K27me3 H3K4me3 and expression profiles in mouse ES cells.

first: Julie

last: Brind'Amour

first: Sheng

last: Liu

last: Hudson

first: Carol

first: Mohammad

last: Karimi


title: Transcriptional Profiling of Sorted Mouse Cortical Projection Neuron Subtypes

city: Baltimore

first: Loyal

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

summary: Neuronal development requires a complex choreography of transcriptional decisions to obtain specific cellular identities. Realizing the ultimate goal of identifying genome-wide signatures that define and drive specific neuronal fates has been hampered by enormous complexity in both time and space during development. Here, we have paired high-throughput purification of pyramidal neuron subclasses with deep profiling of spatiotemporal transcriptional dynamics during corticogenesis to resolve lineage choice decisions. We identified numerous features ranging from spatial and temporal usage of alternative mRNA isoforms and promoters to a host of mRNA genes modulated during fate specification. Notably, we uncovered numerous long non-coding RNAs with restricted temporal and cell type specific expression. To facilitate future exploration, we provide an interactive online database to enable multidimensional data mining and dissemination. This multi-faceted study generates a powerful resource and informs understanding of the transcriptional regulation underlying pyramidal neuron diversity in the neocortex.

overall_design: 24 distinct samples analyzed. 2 replicates each of 3 distinct sorted mouse cortical projection neuron subtypes at 4 developmental time points.


title: Gene expression profiling of TGF-B/PDGF-induced CAF

city: Shanghai

first: Jun

last: Mi

address: 280 South Chongqing Rd.

institute: Shanghai Jiao Tong University School of Medicine

summary: We have found aerobic glycolysis is increased in cancer-associated fibroblasts (CAF). To explore the mechanism by which glucolysis was switched from oxidative phosphorylation, two in vitro CAF models were successfully established. To screen genes potentially regulate aerobic glysolysis, we analyzed gene expression profiling of CAF, and compared with control fibroblasts.

overall_design: Primary fibroblasts separately treated with PDGF or TGF-B for 96 hours to induce CAF formation, control fibroblast were treated with 1% BSA. mRNA profiling were analyzed by deep sequencing.

first: Qiong

first: Zhimin


title: Potential functions of microRNAs in starch metabolism and development revealed by miRNA transcriptome profiling of cassava cultivars and their wild progenitor

city: Saint Louis

first: Weixiong

last: Zhang

address: Campus Box 1045 One Brookings Drive

institute: Washington university in St Louis

summary: Six small RNA and six mRNA libraries from leaves and roots of the two cultivars, KU50 and Arg7, and their wild progenitor, W14, were subjected to NGS. Analysis of the sequencing data revealed 29 conserved miRNA families and 33 novel miRNA families. Together, these miRNAs potentially targeted a total of 360 putative target genes. Whereas 16 miRNA families were highly expressed in cultivar leaves, another 13 miRNA families were highly expressed in storage roots of cultivars. Co-expression analysis revealed that the expression level of some targets had negative relationship with their corresponding miRNAs in storage roots and leaves; these targets included MYB33, ARF10, GRF1, RD19, APL2, NF-YA3 and SPL2, which are known to be involved in plant development, starch biosynthesis and response to environmental stimuli.

sample_organism:
Manihot esculenta
Manihot esculenta subsp. flabellifolia

overall_design:
Six small RNA libraries from leaves and roots of the two cultivars, KU50 and Arg7, and their wild progenitor, W14, were subjected to NGS.
All materials were planted in natural condition

first: Xin

last: Chen

first: Jing

last: Xia

first: Zhiqiang

first: Wenquan

last: Wang


title: From mouse to humans: detecting preventing vaccination targets associated to melanoma cancer stem cells

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino


title: DNA methylation variation in Arabidopsis has a genetic basis and appears to be involved in local adaptation

city: Salt Lake City

first: Richard

last: Clark

summary: We investigated DNA methylation variation in Swedish Arabidopsis thaliana accessions. We found that methylation of transposable elements is temperature sensitive and associated with genetic polymorphism in both cis and trans, whereas gene body methylation is associated with genetic polymorphism in trans. Additionally, complementary RNA-Seq data for the Arabidopsis accessions were used to correlate methylation changes with gene expression across environments.

overall_design: mRNA-sequencing (mRNA-Seq) of 160 Arabidopsis thaliana accessions grown at 10 C and 163 grown at 16 C. The source tissue for RNA collection was whole rosette at the 9-leaf stage.

first: Edward

last: Osborne

first: Pei

first: Marie

last: Remigereau

first: Philipp

last: Drewe

first: Gunnar

last: Rätsch

first: Magnus

last: Nordborg


title: From mouse to humans: detecting preventing vaccination targets associated to melanoma cancer stem cells. Gene-level analysis: B16

summary: The efficacy of cancer treatments has improved constantly in the last decade. However, therapeutic resistance and the lack of curative treatments in metastatic disease, raises the question if conventional anticancer therapies target the right cells. Indeed, these treatments might miss cancer stem cells (CSCs), which might also represent a more chemoresistant and radioresistant subpopulation within cancer. In this view using vaccines in tertiary prevention of cancer, i.e. residual disease treatment, might be particularly effective if vaccine-elicited immune response is directed against CSC oncoantigens (OAs) — proteins required for the neoplastic process — the chance that the tumour will evade the vaccine should be reduced. An important task to devise effective CSC preventive vaccines is therefore the identification of CSC OAs. We used gene-level transcription profiling of B16 mouse melanoma epithelial cell and one mammosphere passage (P1). This analysis allowed the identification of some interesting CSC OAs which are undergoing further studies.

overall_design: B16 cell line (E) was compared to passage 1 (P1) mammospheres (tw independent experiments for each experimental condition). Transcription profiling was done using pair ends RNA-seq analysis. Reads were mapped with STAR (version 2.3.0e). Mapped reads were converted in exon-level counts using the python script provided as part of DEXSeq (version 1.6.0) Bioconductor package and UCSC mm9 annotation. Exon-level counts were then collapsed in gene-level counts using the geneCountsTable function from DEXSeq (version 1.6.0). Differential gene expression was evaluated by DESeq2 package (version 1.0.19) using default settings. Differentially expressed genes were selected using a FDR < 0.1 and |log2FC|>1

first: Stefania

last: Lanzardo

first: Laura

last: Conti

first: Federica

last: Riccardo

first: Matteo

last: Carrara

first: Maddalena

last: Arigoni

last: Cavallo


title: From mouse to humans: detecting preventing vaccination targets associated to melanoma cancer stem cells. Gene-level analysis: CT26

summary: The efficacy of cancer treatments have improved constantly in the last decade. However, therapeutic resistance and the lack of curative treatments in metastatic disease, raises the question if conventional anticancer therapies target the right cells. Indeed, these treatments might miss cancer stem cells (CSCs), which might also represent a more chemoresistant and radioresistant subpopulation within cancer. In this view using vaccines in tertiary prevention of cancer, i.e. residual disease treatment, might be particularly effective if vaccine-elicited immune response is directed against CSC oncoantigens (OAs) — proteins required for the neoplastic process — the chance that the tumour will evade the vaccine should be reduced. An important task to devise effective CSC preventive vaccines is therefore the identification of CSC OAs. We used gene-level transcription profiling of CT26 mouse colon carcinoma epithelial cell and one spheroid passage (P1). This analysis allowed the identification of some interesting CSC OAs which are undergoing further studies.

overall_design: CT26 cell line (E) was compared to passage 1 (P1) spheroids (two independent experiments for each experimental condition). Transcription profiling was done using pair ends RNA-seq analysis. Reads were mapped with STAR (version 2.3.0e). Mapped reads were converted in exon-level counts using the python script provided as part of DEXSeq (version 1.6.0) Bioconductor package and UCSC mm9 annotation. Exon-level counts were then collapsed in gene-level counts using the geneCountsTable function from DEXSeq (version 1.6.0). Differential gene expression was evaluated by DESeq2 package (version 1.0.19) using default settings. Differentially expressed genes were selected using a FDR < 0.1 and |log2FC|>1


title: Genomewide binding of Sulfolobus solfataricus transcription factor MerR

city: Davis

first: Marc

middle: T

last: Facciotti

state: Ca

address: 451 Health Sciences Drive

department: Biomedical Engineering

institute: University of California, Davis

summary: We report the in vivo binding of transcription factor MerR in the presence and absence of mercury as measured by ChIPSeq.

overall_design: Examining the binding of MerR in the presence and absence of mercury.

first: Paul

last: Blum


title: The Sweden Canceromics Analysis Network - Breast (SCAN-B) Initiative: a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine [RNA-Seq]

city: Lund

first: Lao

last: Saal

address: Scheelevägen 2, MV404B2

department: Department of Oncology and Pathology

country: Sweden

institute: Lund University

summary:
Breast cancer exhibits significant molecular, pathological, and clinical heterogeneity. Current clinicopathological evaluation is imperfect for predicting outcome, which results in overtreatment for many patients, and for others, leads to death from recurrent disease. Therefore, additional criteria are needed to better personalize care and maximize treatment effectiveness and survival. To address these challenges, the Sweden Cancerome Analysis Network - Breast (SCAN-B) consortium was initiated in 2010 as a multicenter prospective study with longsighted aims to 1) analyze breast cancers with next-generation genomic technologies for translational research in a population-based manner and integrated with healthcare; 2) decipher fundamental tumor biology from these analyses; 3) utilize genomic data to develop and validate new clinically-actionable biomarker assays; and 4) build the infrastructure for real-time clinical implementation of molecular diagnostic, prognostic, and predictive tests. In the first phase, we focus on molecular profiling by next-generation RNA-sequencing on the Illumina platform. In the three years from August 30, 2010 through August 31, 2013, we have consented and enrolled 3,979 patients with primary breast cancer at the seven hospital sites in South Sweden, representing approximately 85% of eligible patients in the catchment area. Pre-operative blood samples have been collected for 3,942 (99%) patients and primary tumor specimens collected for 2,929 (74%) patients. Herein we describe the study infrastructure and present initial proof of concept results from prospective RNA-sequencing including tumor molecular subtyping and detection of driver gene mutations. We demonstrate that large-scale population-based collection and RNA-sequencing analysis of breast cancer is feasible. The SCAN-B Initiative should significantly reduce the time to discovery, validation, and clinical implementation of novel molecular diagnostic and predictive tests. We welcome the participation of additional comprehensive cancer treatment centers.

Due to privacy concerns, submitters were not allowed to release the actual sequencing reads

overall_design: 55 RNA samples (49 tumors, 6 as technical replicates) were sequenced (paired-end Illumina) and in parallel analyzed on Human HT12 v4 BeadChip microarrays following the manufacturer’s standard protocol (Illumina). Intrinsic subtypes were determined for both platforms using the gene lists PAM50, Sorlie and Hu. Mutation calling was performed on the RNA-seq data of the 49 tumors.

first: Johan

last: Vallon-Christersson

first: Jari

last: Häkkinen

first: Cecilia

last: Hegardt

first: Dorthe

last: Grabau

first: Christof

last: Winter

first: Christian

last: Brueffer

first: Man-Hung

middle: E

last: Tang

first: Christel

last: Reuterswärd

first: Ralph

last: Schulz

first: Anna

last: Karlsson

last: Ehinger

first: Janne

last: Malina

first: Jonas

last: Manjer

first: Martin

last: Malmberg

first: Christer

last: Larsson

first: Lisa

last: Rydén

first: Niklas

last: Loman

first: Åke

last: Borg


title: Extensive remodeling of DC function by rapid maturation-induced epigenetic gene silencing

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

institute: SIB Swiss Institute of Bioinformatics

type: Genome binding/occupancy profiling by genome tiling array


title: From mouse to humans: detecting preventing vaccination targets associated to melanoma cancer stem cells. Gene-level analysis: TUBO

first: Raffaele

last: Calogero

summary: The efficacy of cancer treatments have improved constantly in the last decade. However, therapeutic resistance and the lack of curative treatments in metastatic disease, raises the question if conventional anticancer therapies target the right cells. Indeed, these treatments might miss cancer stem cells (CSCs), which might also represent a more chemoresistant and radioresistant subpopulation within cancer. In this view using vaccines in tertiary prevention of cancer, i.e. residual disease treatment, might be particularly effective if vaccine-elicited immune response is directed against CSC oncoantigens (OAs) — proteins required for the neoplastic process — the chance that the tumour will evade the vaccine should be reduced. An important task to devise effective CSC preventive vaccines is therefore the identification of CSC OAs. We used gene-level transcription profiling of TUBO mouse breast cancer epithelial cell and one mammosphere passage (P1). This analysis allowed the identification of some interesting CSC OAs which are undergoing further studies.

overall_design: TUBO cell line (E) was compared to passage 1 (P1) mammospheres (two independent experiments for each experimental condition). Transcription profiling was done using pair ends RNA-seq analysis. Reads were mapped with STAR (version 2.3.0e). Mapped reads were converted in exon-level counts using the python script provided as part of DEXSeq (version 1.6.0) Bioconductor package and UCSC mm9 annotation. Exon-level counts were then collapsed in gene-level counts using the geneCountsTable function from DEXSeq (version 1.6.0). Differential gene expression was evaluated by DESeq2 package (version 1.0.19) using default settings. Differentially expressed genes were selected using a FDR < 0.1 and |log2FC|>1

first: Stefania

last: Lanzardo

first: Laura

last: Conti

first: Federica

last: Riccardo

first: Matteo

last: Carrara

first: Maddalena

last: Arigoni

last: Cavallo


title: Extensive remodeling of DC function by rapid maturation-induced epigenetic gene silencing [RNA-Seq]

summary: Dendritic-cell (DC) maturation involves substantial remodeling of their gene-expression program. Most research has focused on inducible gene-expression networks promoting the acquisition of new functions, such as cytokine production and enhanced T-cell-stimulatory capacity. In contrast, mechanisms that modulate DC-function by inducing gene silencing remain poorly understood. Here we describe a novel primary epigenetic-silencing response that makes major contributions to the DC-maturation process. The repressed genes function in pivotal processes - including antigen-presentation, extracellular-signal detection, signal-transduction and lipid-mediator biosynthesis - underscoring the central contribution of the silencing mechanism to rapid reshaping of DC-function. Interestingly, promoters of the repressed genes exhibit a surprisingly high frequency of PU.1-occupied sites, suggesting a novel role for this transcription factor in marking genes poised for inducible repression

overall_design: Transcriptional changes induced by one hour LPS treatment in monocyte derived dendritic cells.

first: Queralt

last: Seguín-Estévez

first: Isabelle

last: Dunand-Sauthier

first: Sylvain

last: Lemeille

first: Christian

last: Iseli

first: Vassilios

last: Ioannidis

first: Emmanuèle

last: Barras

first: Antoine

last: Geinoz

first: Christoph

last: Schmid

first: Philippe

last: Rousseau

first: Ioannis

last: Xenarios

first: Hans

last: Acha-Orbea

first: Walter

last: Reith


title: Correction of a Genetic Disease by CRISPR-Cas9-Mediated Gene Editing in Mouse Spermatogonial Stem Cells

first: Xiaoying

last: Fan

state: Beijing

address: 5 Yiheyuan Road

department: College of Life Sciences

institute: Peking University

summary: We used CRISPR/Cas9 mediated gene editing technology to rescue a mutant gene in mouse spermatogenic stem cell(SSC). To evaluate the whole gemome off-target ratio and check the impact on imprinting methylation level by this gene editing method, We built libraries of WGBS from both mutant SSCs and rescued SSCs. We analyzed these data using bioinformatics .All the 12 imprinting locus the WGBS data coverd showed no difference between the two samples(sample name WGBS_**), with expected methylation patterns at each locus.

overall_design: 3 WGBS libraries from 2 SSC cell sample

first: Jinsong

last: Li

first: Ligang

last: Wu

first: Fuchou

last: Tang


title: Methylome sequencing identifies potential epigenetic prognostic biomarker signature that stratifies triple negative breast cancer

city: Darlinghurst

first: Aaron

last: Statham

state: NSW

address: 384 Victoria St

department: Cancer Department

institute: Garvan Institute of Medical Research

summary: Triple negative breast cancers (TNBCs) comprise a heterogeneous group of cancers with varying prognoses, presenting a challenge for effective clinical management. Epigenetic alterations in the cancer methylome are common in breast cancer and provide novel options for tumor stratification on the basis of prognosis.  Advances in genome-wide DNA methylation technology have enabled more comprehensive identification of potential epigenetic diagnostic and prognostic cancer biomarkers. Here, we use MBDCap-Seq to perform genome-wide DNA methylation profiling from archival TNBC and matched normal DNA samples. We identified 822 differentially methylated regions (DMRs) comprising 308 genes affected by cancer-specific promoter hypermethylation. Notably, 51 of these genes are also recurrently mutated in breast cancer, seven of which include members of the axon guidance pathway recently implicated in tumor initiation and progression.  Using TCGA methylation data as an independent validation cohort for TNBCs (n= 73), we showed that 36 genomic regions were specific for TNBCs, including both promoter and gene body hypermethyled loci. Importantly, we stratified TNBCs into three distinct methylation clusters associated with better or worse prognosis. Furthermore, we identified a “survival” methylation signature consisting of 17 DMRs that show strong regional association with overall survival, 16 of which overlap DNase1 hypersensitive sites. Notably three of these “survival” DMRs are located in the bi-directional promoter and gene bodies of WT1 gene and its anti-sense counter-part WT1-AS.  Together, our data identifies for the first time a cancer DNA methylation diagnostic and prognostic signature that promises to stratify TNBCs for more personalized management.

overall_design: Genome-wide methylation profiling of 19 TNBC tumor and 6 matched normal samples was carried out with MBDCap-Seq. In addition,  fully methylated control sample was profiled to identify regions of the genome assayable by the MBDCap-Seq technology.

first: Elena

last: Zotenko


title: mRNA profiling of Drosophila midguts treated by uracil

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

country: South Korea

institute: POSTECH

summary: We performed an mRNA-sequencing experiment using Drosophila midgut to find uracil-induced signaling pathways and biological processes in response to uracil. The sequenced reads from Illumina Hiseq2000 that passed quality filters were mapped to Drosophila genome (NCBI build 5.3) using Tophat and then quantitatively analyzed by HTseq at the gene level. By comparing uracil-treated and non-treated samplesl,  we profiled uracil-dependent gene expression changes.

overall_design: mRNA expression profiles of uracil-treated Drosophila midgut and control Drosophila midgut were examined by Illumina Hiseq2000.

first: Won-Jae

last: Lee

first: Daehee

last: Hwang

first: Kyung-Ah

first: Jinhyuk

last: Bhin


title: Next-generation sequencing facilitates quantitative analysis of hepatic sex-differences in ZSF1 rats

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: The aim of this study was to identify sex-specific hepatic genes in Zucker spontaneously hypertensive fatty rats (ZSF1), a rat model for diabetic nephropathy.

overall_design: Comparison of gene expression in liver samples between 6 female and 6 male obese ZSF1 rats. Each sample were analyzed as a separate sample.

first: M

last: Henjakovic

first: B

last: Burckhardt

first: C

last: Pommerenke

first: G

last: Salinas-Riester


title: Wheat (Triticum aestivum L.) transcriptome profiling

city: Wuhan

first: Qiang

state: Saskatchewan

address: #1 Shizishan Street

institute: Huazhong Agricultural University

summary: Transcript changes in response to low temperature

overall_design: Total RNA for RNA-seq analysis were extracted from wheat leaf tissues with three biological replicates for each growth condition.

first: Jitao

last: Zou


title: Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast

city: San Francisco

first: Courtney

last: Onodera

state: CA

address: 1450 Third St, HD374

institute: University of California, San Francisco

summary: The pluripotent mammalian epiblast undergoes unusually fast cell proliferation. This rapid growth is expected to generate a high transcriptional demand, but the underlying mechanisms remain unknown. We report that the chromatin remodeler Chd1, which binds the activating histone mark H3K4me3 and is associated with transcription, is required for development of the mouse epiblast. Chd1-/- embryos exhibit proliferation defects and increased apoptosis, are smaller than controls by E5.5, and fail to grow, become patterned or gastrulate. We show that Chd1-/- ES cells have a self-renewal defect and a genome-wide reduction in transcriptional output that is associated with losses in RNA Pol II elongation at growth-promoting genes, including ribosomal proteins. We also report that Chd1 directly regulates ribosomal RNA transcription and that both Chd1-/- epiblast cells in vivo and ES cells in vitro express significantly lower levels of ribosomal RNA. Single cell analyses reveal abnormal nucleolar morphology in mutants in vivo and in vitro. These data indicate that Chd1 promotes a globally elevated transcriptional output required to sustain the distinct rapid growth of the mouse epiblast.

overall_design: Cell-number normalized RNA-seq from wild-type and Chd1-/- mouse embryonic stem cells.

first: Marcela

last: Guzman-Ayala

first: Michael

last: Sachs

first: Fong

last: Koh

first: Aydan

last: Bulut-Karslioglu

first: Chih

last: Lin

first: Priscilla

last: Wong

first: Rachel

last: Nitta

first: Jun

last: Song

first: Miguel

last: Ramalho-Santos


title: mRNA profiling of JHDM2 knockdown Drosophila midguts post-infection with Ecc15

first: Bhin

last: Jin-hyuk

summary: We performed an mRNA-sequencing experiment using Drosophila midgut to find JHDM2-dependent signaling pathways in response to bacterial challenge and downstream target genes that are epigenetically regulated across genome. The sequenced reads from Illumina Hiseq2000 that passed quality filters were mapped to Drosophila genome (dm3) using Tophat and then quantitatively analyzed by Cufflinks at the gene level. By comparing Wild type and JHDM2 knock-down samples post-infection with Ecc15,  we profiled JHDM2-dependent gene expression changes induced by Ecc15 infection.

overall_design: mRNA expression profiles of JHDM2 knockdown Drosophila midgut and control Drosophila midgut at 4 and 16hr post-infection with Ecc15 were examined by Illumina Hiseq2000.

first: Sung

last: Baek

first: Won-Jae

last: Lee

first: Daehee

last: Hwang

first: Hyunkyung

last: Kim

first: Jinhyuk

last: Bhin


title: Genome wide analysis of the direct and indirect consequences on gene expression of a thyroid hormone receptor alpha 1 mutation restricted to Sertoli cells

city: Oullins

first: Fabrice

last: Chatonnet

address: 165 Chemin du Grand Revoyet

institute: INSERM

summary: A dominant negative allele of TRα1 (TRαAMI) has been introduced only in Sertoli cells using the Cre/lx system and the AmhCre mouse line. Testes were isolated at P3 and RNA was extracted. MRNA were enriched by oligo-dT purification and submitted to Illumina HiSeq2000 sequencing. Reads were aligned on the mouse mm9 genome, gene counts were obtained with the HTSeq-count script and differential expression was investigated with the DESeq2 R package.

overall_design: Examination of thyroid hormone target genes in testes after disruption of the receptor in only the Sertoli cells.

first: Sophie

last: Fouchecourt

first: Frédéric

last: Flamant


title: Transcriptome analysis during seed development provides insights into co-regulated and altered gene expression between a seeded wine grape variety and it seedless somatic variant.

city: San Michele all'Adige

first: Laura

last: Costantini

state: Trento

address: Via E. Mach 1

department: Genomics and Biology of Fruit Crops

institute: Fondazione Edmund Mach

summary: We report the application of Illumina mRNA sequencing technology for high-throughput profiling of the transcriptome of a seeded wine cultivar (wild-type) and its seedless somatic variant (mutant), sampled at three key growth stages of grapevine: E-L 15 (single flowers in compact groups), E-L 27 (young berries enlarging) and E-L 38 (berries harvest-ripe). By obtaining over 126 to 143 million and 102 to 127 million reads of 100-bp in length for the wild-type and mutant respectively, we have for the first time provided a holistic view of the transcriptional landscape during seed development in both phenotypes. We found that comparison of differentially expressed (DE) genes, gene patterns and gene enrichment between the wild-type and mutant distinguished transcriptional events in the two lines. For example, differential expression analysis in the pairwise comparison between developmental stages identified DE genes specific to the wild-type background, DE genes specific to the mutant background and DE genes commonly shared in both backgrounds. The analysis of differential expression patterns and functional category enrichment of DE genes highlighted specific and common significant coordination and enrichment of various biological processes during seed development which have lead to the identification of candidate genes for seedlessness that have altered expression in wild-type and mutant. In conclusion, we have shown here a logical approach to identify possible regulators and processes required for normal seed development that may be altered in the seedless phenotype, and highlighted the importance of somatic variants as a resources.

overall_design: Examination of absolute expression count for every gene at three key time-points in a seeded grapevine variety and its seedless somatic variant.

first: Chinedu

last: Nwafor

first: Ivana

last: Gribaudo

first: Anna

last: Schneider

first: Ron

last: Wehrens

first: Maria

last: Grando


title: Analysis of genes that control fur color formation in domestic rabbits using Solexa sequencing

city: Yangzhou

first: Lizhi

last: Qin

state: Jiangsu

address: No.48 Wenhui East Road

department: College of Animal Science and Technology

institute: Yangzhou University

summary: We used Solexa sequencing technology to probe the gene expression of dorsal skin tissues from three full-sib Rex rabbits of different colors. The number of expressed genes in each sample was approximately 14,700. Compared with the chinchilla Rex rabbit control sample, the numbers of genes that exhibited greater than a 2-fold change in expression with a false discovery rate of ≤0.001 in the black rabbit sample and white rabbit sample were 1,809 and 460, respectively, and the number of common differentially expressed genes was 257.Of the 257 genes, 32 genes that were upregulated in sample B and downregulated in sample W. The FABP7 gene was the only gene that was downregulated in the B sample and upregulated in the W sample

overall_design: The samples collected with three full-sib individual and they were raised under the same conditions for 42 days(at the first molt). The fur colors of them were characterized as black (B), white (W), and chinchilla (C).

first: L

first: W

last: Wang

last: Shi

first: X

middle: Y

last: Wan

middle: R

last: Yan

first: Q

middle: Q

last: Weng

last: Wu


title: Redefinition of Human Androgen Responsive Elements

city: Stanford

first: Xun

last: Lan

address: 318 Campus Dr. Room S240

department: Genetics

institute: Stanford University

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

overall_design: Refer to individual Series


title: Marked methylation changes of intestinal genes in the neonatal period of preterm neonates

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

institute: Agricultural Genomes Institute at Shenzhen

summary: We hypothesized that the immature pig intestine would be highly sensitive to gene methylation changes in the immediate prenatal and neonatal periods. We performed a Reduced Representation Bisulfite Sequencing (RRBS) to assess the DNA methylation differences occurring during the last 10 days prenatally (PN, 0d-term vs. 0d-preterm), neonatally after 4 days (NN, 4d-preterm vs. 0d-preterm) and after NEC development (4d-preterm-NEC vs. 4d-preterm) in pigs (each group n=2-3). Differentially methylated gene regions (DMRs) between the groups were identified, subjected to KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis and selected genes were chosen for further validation of gene expression levels by RT-PCR (n= 6 for each group). Consistent with the need to increase expression of many intestinal genes in the perinatal period, methylation levels of most genes decreased during the prenatal and neonatal periods. We identified four intestinal genes (CYP2W1, GPR146, TOP1MT, CEND1), related to intestinal metabolism, that were significantly hyper-methylated in their promoter CGIs, and transcriptionally down-regulated in the 4 d-old preterm pigs. This down-regulation of intestinal metabolism may predispose to intestinal dysfunction and NEC. The first enteral feeds and bacterial colonization are critical factors for NEC sensitivity and it remains to be investigated whether these factors affect intestinal gene methylation and thereby predispose to, or prevent from, disease more long term.

first: Fei

last: Gao


title: Small RNA Solexa sequencing of multiple tissues of papaya, Carica papaya

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

summary: The tissues of male flowers, female flowers and hermaphrodite are collected and stored in liquid nitrigen immediately. Total RNA was isolated from male, hermaphrodite, and female flowers using the Trizol reagent (Invitrogen USA). Low molecular weight RNA was enriched from the total RNA by precipitating with 0.4M NaCl and polyethylene glycol (PEG). The enriched low molecular weight RNA was then separated on a denaturing 15% polyacrylamide gel. The band corresponding to the RNA standard of 18-30 nucleotides was then excised from the gel and eluted overnight in 0.4M NaCl at 4 degrees Celsius, and subsequently ligated with 5’ and 3’ Illumina small RNA adapters. The adapter ligated library was converted into cDNA and amplified by using PCR and sequenced by Illumina Genome Analyzer II.

overall_design: Examination of small RNA transcriptomes in multiple tissues of papaya using Illumina Genome Analyzer II sequencer.

first: Ramanjulu

last: Sunkar


title: Flexible multiplatform RNA profiling at the single cell level applied to enriched cancer initiating cells: RNA-Seq MCF7 and MCF10A single cell data

city: Manchester

first: Ged

last: Brady

address: Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Rd

department: Clinical and Experimental Pharmacology

institute: Caner Research UK Manchester Institute

summary: Accurate profiling of RNA expression of single cells is a valuable approach for broadening our understanding of cancer biology and mechanisms of dissemination, but requires the development of reliable methods for their molecular characterization. Here we evaluate a single cell methodology which generates microgram amounts of cDNA suitable for next generation sequencing (RNA-Seq), high throughput RT-qPCR and Affymetrix array analysis. The approach was tested by comparing expression profiles of amplified single MCF7 and MCF10A cells to profiles generated from unamplified RNA. The expression profiles were compared by Affymetrix-U133 arrays, RNA-Seq and high-density qPCR.  There were strong cross-platform correlations of >80% and concordance between single cell and unamplified material of >70%. We exemplify the approach through analysis of rare sorted cancer initiating cells (CICs) derived from a NSCLC patient-derived xenograft. Populations of 10 cells from total tumour and two distinct subsets of CIC, putatively involved in primary tumor maintenance or metastasis formation were FACS sorted then directly amplified. CIC expression profiles strongly correlated with published stem-cell and epithelial-mesenchymal transition (EMT) signatures. Our results confirm the utility of the amplification system and our methodology to detect and distinguish RNA profiles in rare cell populations that inform on EMT and stem-cell characteristics. This GEO dataset comprises the RNA-Seq data for MCF7 and MCF10A single cell samples.

overall_design: 10 samples. 5 biological replicates each of MCF7 cDNA generated from amplified RNA from a single cell and MCF10A cDNA generated from amplified RNA from a single cell (cDNA generated from the same single cells used to generate the single cell cDNA samples used for Affymetrix array analysis in this super series, i.e. the same set of cDNA samples analysed using both platforms). SOLiD RNA-Seq expression data was compared to the Affymetrix microarray gene expression data for the same samples and to a reference sample set generated from Affymetrix arrays of 10μg of unamplified RNA for each cell line (Bitton, D.A., Okoniewski, M.J., Connolly, Y. and Miller, C.J. (2008) Exon level integration of proteomics and microarray data. BMC Bioinformatics, 9, 118).

first: Dominic

middle: G

last: Rothwell

first: Yaotong

last: Li

first: Gillian

last: Newton

first: Yvonne

last: Hey

first: Mahmood

last: Ayub

first: Catriona

last: Tate

first: Louise

last: Carter

first: Suzanne

last: Faulkner

first: Stuart

last: Pepper

first: Crispin

last: Miller

first: Fiona

last: Blackhall

first: Giulia

last: Bertolini

first: Luca

last: Roz

first: Caroline

last: Dive


title: Flexible multiplatform RNA profiling at the single cell level applied to enriched cancer initiating cells: RNA-Seq CIC data

summary: Accurate profiling of RNA expression of single cells is a valuable approach for broadening our understanding of cancer biology and mechanisms of dissemination, but requires the development of reliable methods for their molecular characterization. Here we evaluate a single cell methodology which generates microgram amounts of cDNA suitable for next generation sequencing (RNA-Seq), high throughput RT-qPCR and Affymetrix array analysis. The approach was tested by comparing expression profiles of amplified single MCF7 and MCF10A cells to profiles generated from unamplified RNA. The expression profiles were compared by Affymetrix-U133 arrays, RNA-Seq and high-density qPCR.  There were strong cross-platform correlations of >80% and concordance between single cell and unamplified material of >70%. We exemplify the approach through analysis of rare sorted cancer initiating cells (CICs) derived from a NSCLC patient-derived xenograft. Populations of 10 cells from total tumour and two distinct subsets of CIC, putatively involved in primary tumor maintenance or metastasis formation were FACS sorted then directly amplified. CIC expression profiles strongly correlated with published stem-cell and epithelial-mesenchymal transition (EMT) signatures. Our results confirm the utility of the amplification system and our methodology to detect and distinguish RNA profiles in rare cell populations that inform on EMT and stem-cell characteristics. This GEO dataset comprises the RNA-Seq data for total tumour, MCIC and RCIC samples.

overall_design: 12 samples. 4 biological replicates each of total tumour cDNA generated from amplified RNA from a volume equivalent to 10 single cells, metastasis associated cancer-initiating cell cDNA generated from amplified RNA from a volume equivalent to 10 single cells, and resident cancer initiating cell cDNA generated from amplified RNA from a volume equivalent to 10 single cells. RNA-Seq data for these 3 groups (total tumour, metastasis associated cancer initiating cells and resident cancer initiating cells) were compared.


title: Flexible multiplatform RNA profiling at the single cell level applied to enriched cancer initiating cells