title: Autophagy regulator DRAM1 functions downstream of MYD88 in defense against tuberculosis (RNA-seq)

summary: MyD88 is an adaptor protein in Toll-like receptor and interleukin 1 receptor mediated signaling pathways that plays an essential role in activation of immune responses following pathogen recognition. We investigate that role in the zebrafish embryo model by using a zebrafish mutant line that contains a premature stop condon in the gene encoding MyD88, leading to a truncated protein that lacks domains important for its normal function. We infected these MyD88 mutants and wildtype individuals with Mycobacterium marinum to compare the resulting immune response by transcriptome profiling on total RNA isolated from single embryos. Autophagy regulator dram1 was identified as one of the MyD88-dependent genes.

overall_design: This RNAseq analysis was used to determine the effect of a truncation of the MyD88 protein on the innate immune response of zebrafish embryos during infection with Mycobacterium marinum. Myd88 mutant and wild type embryos were derived by incrossing homozygous myd88 mutant parents (allele hu3568, van der Vaart et al., 2013, Disease models & mechanisms 6, 841-854) or their wildtype siblings. RNA was isolated from pools of 20 embryos at 4 days post infection (4 dpi).  The following treatment groups were used: homozygous mutants mock-injected with PBS/2%PVP 4 dpi, (2) wildtype siblings mock-injected with PBS/2%PVP 4dpi, (3) M. marinum-infected homozygous mutants 4dpi, (4) M. marinum-infected wildtype siblings 4dpi. Embryos were grown at 28.5–30°C in egg water and manually dechorionated at 24 hours post fertilization (hpf). Subsequently, embryos were infected at 28 hpf by micro-injecting 200 colony forming units (CFU) of Mycobacterium marinum Mma20 bacteria into the caudal vein, or were mock-injected with buffer (PBS/2%PVP) as a control.  After injections embryos were transferred into fresh egg water and incubated for 4 days at 28°C. After the incubation period, single embryos were snap-frozen in liquid nitrogen and RNA was isolated for RNAseq analysis.

first: M

last: van der Vaart

first: H

middle: P

last: Spaink

first: A


title: High-Resolution Profiling of Novel Transcribed Regions During Rat Spermatogenesis

status: Public on Jun 01 2014

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

type: Expression profiling by high throughput sequencing

summary: Mammalian spermatogenesis is a complex and highly orchestrated combination of processes in which male germline proliferation and differentiation result in the production of mature spermatozoa. If recent genome-wide studies have contributed to the in-depth analysis of the male germline protein-coding transcriptome, little effort has yet been devoted to the systematic identification of novel unannotated transcribed regions expressed during mammalian spermatogenesis. We report high-resolution expression profiling of male germ cells in the rat using Illumina next-generation sequencing technology and highly enriched testicular cell populations. Among 20,424 high-confidence transcripts reconstructed, we defined a stringent set of 1,419 long multi-exonic unannotated transcripts expressed in the testis, named TUTs. These were classified into seven groups with different expression patterns. The vast majority of TUTs share many of the characteristics of vertebrate long non-coding RNAs (lncRNAs). We also markedly reinforced the finding that TUTs and known lncRNAs accumulate during the meiotic and postmeiotic stages of spermatogenesis in mammals, and that X-linked meiotic TUTs do not escape the silencing effects of meiotic sex chromosome inactivation. Importantly, we discovered that TUTs and known lncRNAs with a peak expression during meiosis define a distinct class of non-coding transcripts that exhibit exons twice as long as those of other transcripts. Our study provides new insights in transcriptional profiling of the male germline and represents a high-quality resource of novel loci expressed during spermatogenesis that significantly contributes to the rat genome annotation. A graphical display of the data is conveniently accessible through the ReproGenomics Viewer (RGV) at http://rgv.genouest.org.

overall_design: Genome-wide expression profiling analysis using Illumina next-generation sequencing technology

first: Aurélie

last: Lardenois

first: Bertrand

last: Evrard

first: Antoine

middle: D

last: Rolland

first: Olivier

last: Sallou

first: Marie-Charlotte

last: Dumargne

first: Isabelle

last: Coiffec

last: Collin

first: Michael

last: Primig

first: Bernard

last: Jégou


title: LncRNA DEANR1 facilitates human endoderm differentiation by activating FOXA2 expression

city: Brookline

first: Yuting

last: Liu

state: MA

address: 82 Walnut St. Unit 3

department: Department of Genetics

country: USA

institute: Harvard Medical School

summary: Long non-coding RNAs (lncRNAs) regulate diverse biological processes including cell lineage specification. Here we report transcriptome profiling of human endoderm and pancreatic cell lineages using purified cell populations. Analysis of the data sets allowed the identification of hundreds of lncRNAs exhibiting differentiation stage-specific expression patterns. As a first step in characterizing these lncRNAs, we focus on an endoderm-specific lncRNA DEANR1 (Definitive Endoderm Associated long Non-coding RNA1) and demonstrate that it plays an important role in human endoderm differentiation. DEANR1 contributes to endoderm differentiation by positively regulating endoderm factor FOXA2 expression. Importantly, overexpression of FOXA2 is able to rescue endoderm differentiation defects caused by DEANR1 depletion. Mechanistically, DEANR1 facilitates FOXA2 activation by helping SMAD2/3 recruitment to the FOXA2 promoter. Thus, our study not only reveals a large set of differentiation stage-specific lncRNAs, but also characterizes a novel lncRNA important for endoderm differentiation.

overall_design: Here we perform RNA-seq based transcriptome profiling using undifferentiated human ESCs (one sample), definitive endoderm (two replicates), pancreatic progenitors(three replicates) as well as sorted human primary alpha cells (two replicates), beta cells (two replicates) and exocrine cells (one sample). Moreover, we perform RNA-seq based transcriptome profiling for WT, FOXA2 knockdown, and DEANR1 knockdown of differentiated definitive endoderm samples (two replicates for each).

first: Wei

last: Jiang

first: Yi

last: Zhang


title: RNA at 92 °C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi.

status: Public on May 31 2014

city: Gif-sur-Yvette

first: Claire

last: Toffano-Nioche

address: Avenue de la Terrasse, b. 21

department: UFR des Sciences

institute: CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay

type: Non-coding RNA profiling by high throughput sequencing

summary: The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi is investigated using the RNA-seq technology. A dedicated computational pipeline analyzes RNA-seq reads and prior genome annotation to identify small RNAs, untranslated regions of mRNAs, and cis-encoded antisense transcripts. Unlike other archaea, such as Sulfolobus and Halobacteriales, P. abyssi produces few leaderless mRNA transcripts. Antisense transcription is widespread (215 transcripts) and targets protein-coding genes that are less conserved than average genes. We identify at least three novel H/ACA-like guide RNAs among the newly characterized non-coding RNAs. Long 5' UTRs in mRNAs of ribosomal proteins and amino-acid biosynthesis genes strongly suggest the presence of cis-regulatory leaders in these mRNAs. We selected a high-interest subset of non-coding RNAs based on their strong promoters, high GC-content, phylogenetic conservation, or abundance. Some of the novel small RNAs and long 5' UTRs display high GC contents, suggesting unknown structural RNA functions. However, we were surprised to observe that most of the high-interest RNAs are AU-rich, which suggests an absence of stable secondary structure in the high-temperature environment of P. abyssi. Yet, these transcripts display other hallmarks of functionality, such as high expression or high conservation, which leads us to consider possible RNA functions that do not require extensive secondary structure.

overall_design: directional RNA-seq, Illumina GA-IIx

first: Alban

last: Ott

first: Estelle

last: Crozat

first: An

middle: N

last: Nguyen

first: Matthias

last: Zytnicki

first: Fabrice

last: Leclerc

first: Patrick

last: Forterre

first: Philippe

last: Bouloc

first: Daniel

last: Gautheret


title: Small RNA profiling of KSHV-miRNA-expressing and KSHV-infected B cell lines

status: Public on Jun 02 2014

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

summary: Micro (mi)RNAs are small non-coding RNAs with key regulatory functions. Recent advances in the field allowed researchers to identify their targets. However, much less is known regarding the regulation of miRNA themselves. The accumulation of these tiny regulators can be modulated at various levels during their biogenesis from the transcription of the primary transcript (pri-miRNA) to the stability of the mature miRNA. Here, we studied the importance of the pri-miRNA secondary structure for the regulation of mature miRNAs accumulation. To this end, we used the Kaposi’s sarcoma herpesvirus, which encodes a cluster of twelve pre-miRNAs. Using small RNA profiling and quantitative northern blot analysis, we measured the absolute amount of each mature miRNAs in different cellular context. We found that the difference in expression between the least and most expressed viral miRNA could be as high as 60-fold. Using high-throughput selective 2’-hydroxyl acylation analyzed by primer extension (hSHAPE), we then determined the secondary structure of the long primary transcript. We found that highly expressed miRNAs derived from optimally structured regions within the pri-miRNA. Finally, we confirmed the importance of the local structure by swapping stem-loops for highly and lowly expressed miRNAs, which resulted in a perturbed accumulation of the mature miRNA.

overall_design: Examination of sRNA profiles in 3 independent B cell lines expressing KSHV miRNAs or infected with KSHV, without replicate

first: Maud

last: Contrant

first: Aurélie

last: Fender

first: Béatrice

last: Chane-Woon-Ming

first: Ramy

last: Randrianjafy

first: Valérie

last: Vivet-Boudou

first: Delphine

last: Richer


title: Streptomyces hygroscopicus 5008 Transcriptome or Gene expression

city: Shanghai

first: Gao-Yi

last: Tan

address: 800 Dongchuan Road

country: China

institute: Shanghai Jiao Tong University

summary:
The RNA sequencing approach was utilized to carry out a comparative transcriptome analysis between Streptomyces hygroscopicus 5008 wild-type and a genetically engineered strain.
The A-factor-like cascade play an important role in the regulation of validamycin biosynthesis by Streptomyces hygroscopicus 5008, and the pleiotropic regulator AdpA-H may positively regulate the transcription of gene cluster for the biosynthesis. shbR1 and shbR3 as the A-factor receptor homolog genes,  could repress the transcription of AdpA-H. By tandem deletions of these genes, the production and productivity of validamcyin was significantly enhanced.  To explore the effects of the shbR1/R3 double deletion of the overall cellular metabolism, the RNA sequencing approach was utilized to carry out a comparative transcriptome analysis between wild-type and shbR1/shbR3 double mutant (genetically engineered strain).

sample_organism: Streptomyces hygroscopicus subsp. jinggangensis 5008

overall_design: The trancriptome analysis between 5008 and DM98 was carried out respectively.

first: Linquan

last: Bai

first: Jian-Jiang

last: Zhong


title: Study of the cross-talk between two distant tumors

city: East Melbourne

first: Jason

last: Li

address: St Andrews Pl

country: Australia

institute: Peter MacCallum Cancer Centre

summary: We demonstrated that a visceral immunosuppressive tumor can influence a distant, normally-responsive tumor, located in the skin and rend it resistant to a particular immunotherapy.

overall_design: Examination of the transcriptome of sub-cutaneous tumors that were growing in a mouse model, in the presence or in the absence of a concomitant intra-kidney immunosuppressive tumor

first: Christel

last: Devaud

first: Liza

middle: B

last: John

first: Jennifer

middle: A

last: Westwood

first: Carmen

middle: S

last: Yong

first: Paul

last: Beavis

first: Phillip

middle: K

last: Darcy

first: Michael

last: Kershaw


title: Study of Foxp3 expression in tumor-associated macrophages

summary: Using 5 differents approaches, including RNA sequencing, we demonstrated that macrophages that specifically infiltrate renal tumors, express the immunosuppressive transcription factor Foxp3.

overall_design: Examination of the Foxp3 mRNA expression in 3 different cell subsets (including CD4 T cells (CD4), type-1 macrophages (M1) and type-2 macrophages (M2))

first: Connie

last: Duong

first: Colin

middle: M

last: House

last: Denoyer


title: Jarid2, a Polycomb member and target of miR-155, regulates the fates of Th17 and Treg cells

city: Dallas

first: Gokhul

middle: Krishna

last: Kilaru

state: TEXAS

address: 6000 Harry Hines Boulevard

department: Department of Neuroscience

institute: University of Texas Southwestern Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genome-wide analysis of Jarid2, Suz12, and c-Maf binding and H3K27me3 profiling in miR-155 KO and WT Th17 performed by ChIP-seq. We found that Jarid2 and c-Maf is differentially expressed in absence of miR-155 and they compete for binding to the Il22 promoter. We highlight  targets of Jarid2 and Suz12 in miR-155 KO Th17 cells that are epigenetically silenced by increased H3K27me3 status. Furthermore, genome-wide analysis through Suz12 ChIP-exo in WT and Jarid2fl/fl;CD4cre Th17 reveals defects in PRC2 recruitment in abscence of Jarid2 that results in derepression of genes in Th17 cells. Thus, one main function of miR-155 is to curb epigenetic silencing by targeting Jarid2.

overall_design: Examination of Jarid2, Suz12, c-Maf binding and H3K27me3 changes in miR-155 KO and WT Th17.

first: Thelma

last: Escobar

first: Stefan

last: Muljo


title: Differential RISC association of endogenous human microRNAs predicts their inhibitory potential

status: Public on May 30 2014

city: Durham

first: Adam

middle: Wesley

last: Whisnant

state: NC

address: 213 Research Drive 427 CARL Bldg

department: Molecular Genetics and Microbiology

institute: Duke University

summary: It has previously been assumed that the generally high stability of microRNAs (miRNAs) reflects their tight association with Argonaute (Ago) proteins, essential components of the RNA-induced silencing complex (RISC). However, recent data have suggested that the majority of mature miRNAs are not, in fact, Ago associated. Here, we demonstrate that endogenous human miRNAs vary widely, by >100-fold, in their level of RISC association and show that the level of Ago binding is a better indicator of inhibitory potential than is the total level of miRNA expression. While miRNAs of closely similar sequence showed comparable levels of RISC association in the same cell line, these varied between different cell types. Moreover, the level of RISC association could be modulated by overexpression of complementary target mRNAs. Together, these data indicate that the level of RISC association of a given endogenous miRNA is regulated by the available RNA targetome and predicts miRNA function.

overall_design: This series includes microRNA sequencing data for human cell lines 293, C8166, A549, SH-SY5Y, and an EBV-transformed LCL line.  For each cell line, total small RNA isolated by TRIzol was sequenced for comparison to RISC-associated microRNAs as determined by sequencing small RNAs from an Argonaute immunoprecipitation.

first: Omar

last: Flores

first: Edward

last: Kennedy

first: Rebecca

middle: L

last: Skalsky

first: Bryan

middle: R

last: Cullen


title: Genomic Determinants of Gene Regulation by 1,25-Dihydroxyvitamin D3 During Osteoblast-Lineage Cell Differentiation

city: Madison

first: Mark

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

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

overall_design: Refer to individual Series


title: Gene expression profiles of blood vascular endothelial cells (BECs) in response to larminar shear flow [RNA-Seq]

city: Los Angeles

first: Young-Kwon

last: Hong

state: CA

address: 1450 Biggy St. NRT6501

institute: University of Southern California

summary: RNA sequencing (RNA-seq) analysis of a genome-wide gene expression change in primary human neonatal dermal BECs when subjected to laminar flow-induced shear stress

overall_design: Primary human neonatal dermal BECs were subjected to low level laminar flow (2 Dyne/cm2) -induced shear stress for 12 hours. Total RNA were isolated from these cells as well as from the equivalent cells cultured under the static condition as a control.

first: Dongwon

last: Choi


title: HBI1 integrates hormonal and environmental signals to regulate the trade-off between growth and immunity (RNA-seq)

city: Jinan

first: Mingyi

last: Bai

state: Shandong

address: 27 Shandananlu

department: Life of Scienec

institute: Shandong University

summary: The trade-off between growth and immunity is crucial for survival in plants. An antagonistic interaction has been observed between the growth-promoting hormone brassinosteroid and pathogen associated molecular pattern (PAMP) signals, which induce immunity but inhibit growth, however the underlying molecular mechanism has remained unclear. The PRE-IBH1-HBI1 triple helix-loop-helix/basic helix-loop-helix (HLH/bHLH) cascade has been shown to mediate growth responses to several hormonal and environmental signals, but its downstream targets and role in immunity remain unknown. Here, we performed genome-wide analyses of HBI1 target genes in Arabidopsis. The results show that HBI1 regulates a set of genes that largely overlaps with targets of PIFs, but displays both similar and unique transcriptional activities compared to PIFs, supporting a role in fine-tuning the network through cooperation and antagonism with other DNA-binding factors of the network. Furthermore, HBI1 also negatively regulates a subset of defense response genes. Two PAMPs, flagellin and elongation factor, repressed HBI1 expression, whereas overexpression of HBI1 reduced the PAMP-induced growth inhibition, defense gene expression, reactive oxygen species (ROS) production, and flg22-induced resistance to Pseudomonas syringae pathovar tomato DC3000. These data indicate that HBI1 is a node for crosstalk between hormone and immune pathways. This study demonstrates that the PRE-IBH1-HBI1 module integrates hormone and pathogen signals, and thus plays a central role in the balance between growth and immunity in plants.

overall_design: Compare the transcriptome of HBI1-Ox and wild type.

first: Zhiyong

last: Wang


title: HBI1 integrates hormonal and environmental signals to regulate the trade-off between growth and immunity (ChIP-seq)

overall_design: Genome wide analysis the HBI1 binding target


title: HBI1 integrates hormonal and environmental signals to regulate the trade-off between growth and immunity


title: The Osteoblast to Osteocyte Transition: Epigenetic Changes and Response to the Vitamin D3 Hormone [ChIP-seq]

summary: Osteocytes are derived from osteoblast lineage cells that become progressively embedded in mineralized bone.  Development of the osteocytogenic cell line IDG-SW3 has enabled a temporal and mechanistic investigation of this process.  Through RNA-seq analyses, we show that while substantial changes in gene expression occur during the osteoblast to osteocyte transition, the majority of the transcriptome remains qualitatively osteoblast-like.  Genes either up-regulated or expressed uniquely in the osteocyte include local and systemic factors such as Sost and Fgf23 as well as genes implicated in neuronal, muscle, vascular, or regulatory function. As assessed by ChIP-seq, numerous changes in epigenetic histone modifications also occur during osteocytogenesis; these are largely qualitative rather than quantitative.  Specific epigenetic changes correlate with altered gene expression patterns that are observed during the transition.  These genomic changes likely influence the highly restricted transcriptomic response to 1,25(OH)2D3 that occurs during differentiation.  VDR binding in osteocytes revealed an extensive cistrome co-occupied by RXR and located predominantly at sites distal to regulated genes.  Although sites of VDR binding were apparent near many 1,25(OH)2D3-regulated genes, the expression of others adjacent to VDR binding sites were unaffected; lack of VDR binding was particularly prevalent at down-regulated genes.  Interestingly, 1,25(OH)2D3 was found to induce the Boc and Cdon co-receptors that are active in hedgehog signaling in osteocytes.  We conclude that osteocytogenesis is accompanied by changes in gene expression that may be driven by both genetic and epigenetic components.  These changes are likely responsible for the osteocyte phenotype and may contribute to reduced sensitivity to 1,25(OH)2D3.

overall_design: ChIP-seq was performed on differentiated IDGSW3 cells at day 35 for VDR and RXR following 3 hour vehicle or 1,25(OH)2d3 treatment in biological replicate.  ChIP-seq was also performed for H3K4me1, H3K4me2, H3K4me3, H3K27Ac, H4K5Ac, H3K9Ac, H4K20me1, H3K36me3, or H3K9me3 at day 3 and day 35 of differentiation in the basal condition.

first: Hillary

middle: C

first: J

middle: W

last: Pike


title: Interplay of TRIM28 and DNA methylation in controlling human endogenous retroelements

status: Public on May 29 2014

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

summary: Reverse transcription-derived sequences account for at least half of the human genome. Although these retroelements are formidable motors of evolution, they can occasionally cause disease, and accordingly are inactivated during early embryogenesis through epigenetic mechanisms. In the mouse, at least for endogenous retroviruses, important mediators of this process are the tetrapod-specific KRAB-containing zinc finger proteins (KRAB-ZFPs) and their cofactor TRIM28. The present study demonstrates that KRAB/TRIM28-mediated regulation is responsible for controlling a very broad range of human-specific endogenous retroelements (EREs) in human embryonic stem (ES) cells and that it exerts, as a consequence, a marked effect on the transcriptional dynamics of these cells. It further reveals reciprocal dependence between TRIM28 recruitment at specific families of EREs and DNA methylation. It finally points to the importance of persistent TRIM28-mediated control of ERE transcriptional impact beyond their presumed inactivation by DNA methylation.

overall_design: Analyses of epigentic effectors and marks in KAP1 WT and KD human embryonic stem cells

first: Priscilla

last: Turelli

first: Nathaly

last: Castro-Diaz

first: Flavia

last: Marzetta

first: Adamandia

last: Kapopoulou

first: Didier

last: Trono


title: Gene expression profiling in allele replacement panel strains containing all combinations of four sporulation QTN in S. cerevisiae

city: St. Louis

first: Barak

last: Cohen

state: Missouri

address: Campus Box 8510, Department of Genetics

department: Genetics

institute: Washington University School of Medicine

summary: We study the effect of four QTN in RME1, IME1 & RSF1 that are causative for variation in sporulation efficiency. We investigate the relationship between genotype, gene expression and phenotype and whether the amount of gene expression variation explained by the sporulation QTN is predictive of the amount of phenotypic variation explained by them.

overall_design: RNA-Seq analysis of 4 replicates each of 16 allele replacement panel strains containing all combinations of the four sporulation QTN after 2 hours in sporulation medium.

first: Priya

last: Sudarsanam


title: Targeting c-MYC by antagonizing PP2A inhibitors in breast cancer

status: Public on May 28 2014

city: Portland

first: Rosalie

last: Sears

state: OR

address: 3181 S.W. Sam Jackson Park Rd

department: MMG

institute: OHSU

summary: Inhibition of SET by siRNA or SET antagonist and CIP2A by siRNA can downregulate c-MYC and c-MYC target genes.

overall_design: Cells were treated with a SET antagonist (1μMOP449) for 12 hours, or siRNA for 48 hours.

first: Mahnaz

last: Janghorban

first: Carl

last: Pelz


title: High-throughput integration of metabolic and transcriptional profiles reveals major metabolic regulators of macrophage polarization

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: Macrophages polarize to divergent functional phenotypes depending on their microenvironment in a highly coordinated process of metabolic and transcriptional rewiring that is still poorly understood. We developed an Integrated Metabolomics and Gene Expression (IMAGE) profiling and analysis pipeline and applied it to extensively characterize global metabolic programs of macrophage polarization. IMAGE analysis identified 7 major (novel and known) regulatory modules responsible for metabolic rewiring during polarization, which we validated through extensive carbon and nitrogen labeling experiments. M1-specific modules included:  inflammatory variant of the aspartate-arginosuccinate shunt; TCA cycle break at Idh expression accompanied by citrate accumulation and production of itaconate and fatty acid synthesis.  In M2 macrophages we discovered significant role of glutamine in polarization, providing nitrogen for UDP-GlcNAc synthesis. Consistently, glutamine deprivation results in significant M2-specific defect in polarization. Our data provide, for the first time, a global view of the integrated transcriptional and metabolic changes that result in M1 and M2 polarization.

overall_design: Bone-marrow derived macrophages were generated from C57BL/6 mice were plated at ~100k cells per well in 96-well plate and stimulated with either Il4 or combination of LPS&IFNg or left unstimulated for 24 h mRNA was derived from lysates using Invitrogen oligo-dT beads


title: Trophoblast giant cell underrepresentation (sequencing)

city: Stanford

first: Roberta

last: Hannibal

address: 300 Pasteur Drive

institute: Stanford University

summary: We characterized the mouse trophoblast giant cell epigenome and gene expression profiles.  We then compared these data to our data on underrepresentation in the polyploid trophoblast giant cells.

overall_design: We profiled 5 histone modifications (+ chromatin input) using ChIP-Seq, and digital expression profiles (3' RNA-Seq) for trophoblast giant cells derived from mouse.  Furthermore, we profiled digital expression profiles (3' RNA-Seq) for in vivo trophoblast giant cells samples from e9.5 wildtype mouse trophoblast giant cells.  We found that underrepresented domains in trophoblast giant cells are enriched for repressive marks and anti-correlate with active marks and transcription.

first: Edward

last: Chuong

first: Julie

last: Baker


title: Trophoblast giant cell underrepresentation

type: Expression profiling by genome tiling array

type: Genome variation profiling by genome tiling array

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

The BioProject ID on this superSeries record also encompasses a genome sequencing project under BioProject PRJNA213010.


title: Comparison of expression data of  2 & 4- months old  CRYAAN101D versus CRYAAWT lenses

city: Birmingham

first: David

last: Crossman

state: AL

address: 720 20th Street South

institute: University of Alabama at Birmingham

summary: To understand the global view of dysregulated genes and pathwyas in CRYAAN101D lenses,  RNA sequencing of 2 & 4  months old CRYAAWT and CRYAAN101D lenses was carried out.

overall_design: Determination of differential gene expression between CRYAAWT and CRYAAN101D in 2 & 4 months old lenses

first: Shylaja

last: Hegde

first: Om

last: Srivastava

first: Michael

last: Crowley


title: Integrated analysis of DNA methylation and RNA transcriptome during the differentiation of human pluripotent stem cells into retinal pigment epithelial cells

first: Kevin

last: Huang

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

department: Human Genetics

institute: UCLA

type: Methylation profiling by high throughput sequencing

summary: Using the paradigm of in vitro differentiation of hESCs/iPSCs into retinal pigment epithelial (RPE) cells, we have recently profiled mRNA and miRNA transcriptomes to define a set of RPE mRNA and miRNA signature genes implicated in directed RPE differentiation. In this study, in order to understand the role of DNA methylation in RPE differentiation, we profiled genome-scale DNA methylation patterns using the method of reduced representation bisulfite sequencing (RRBS). We found dynamic waves of de novo methylation and demethylation in four stages of RPE differentiation. Integrated analysis of DNA methylation and RPE transcriptomes revealed a reverse-correlation between levels of DNA methylation and expression of a subset of miRNA and mRNA genes that are important for RPE differentiation and function. Gene Ontology (GO) analysis suggested that genes undergoing dynamic methylation changes were related to RPE differentiation and maturation. We further compared methylation patterns among human ESC- and iPSC-derived RPE as well as primary fetal RPE (fRPE) cells, and discovered that specific DNA methylation pattern is useful to classify each of the three types of RPE cells. Our results demonstrate that DNA methylation may serve as biomarkers to characterize the cell differentiation process during the conversion of human pluripotent stem cells into functional RPE cells.

overall_design: Study of DNA methylation patterns during RPE differentiation of pluripotent stem cells.

first: Zhenshan

last: Liu

first: Guoping

last: Fan


title: Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: Different Library Sample Preparation (LSP) allow the detection of a large common set of isoforms. However, each LSP also detects a smaller set of isoforms which are characterized both by lower coverage and lower FPKM than that observed for the common ones among LSPs. This characteristic is particularly critical in case of low input RNA NuGEN v2 LSP. The effect of statistical detection of alternative splicing considering low input LSP (NuGEN v2) with respect to high input LSP (TruSeq) was studied using a benchmark dataset, in which both synthetic reads and reads generated from high and low input LSPs were spiked-in. Statistical detection of alternative splicing was done using prototypes of bioinformatics analysis for isoform-reconstruction and exon-level analysis.

overall_design: Each available sample contains a total of 5 paired end replicates. 3 samples contain increasing numbers of spiked-in reads (20, 40, 80 millions) from NuGENv2 library preparation kit on a common TruSeq 1000ng background. 3 additional samples were built with the same approach, but spiked-in reads were collected from a TruSeq-based experiment. The remaining 6 samples follow the same approach of the previous 6, but the common background is based on a TruSeq library preparation on 100ng of material

first: Matteo

last: Carrara

first: J

last: Lum

first: Francesca

last: Cordero

first: Marco

last: Beccuti

first: M

last: Poidinger

first: Susanna

last: Donatelli

last: Zolezzi


title: The coding and noncoding architecture of the Caulobacter crescentus genome

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

summary: Caulobacter crescentus undergoes an asymmetric cell division controlled by a genetic circuit that cycles in space and time.  We provide a universal strategy for defining the coding potential of bacterial genomes by applying ribosome profiling, RNA-seq, global 5’-RACE, and liquid chromatography coupled with tandem mass spectrometry (LC-MS) data to the 4-megabase C. crescentus genome.  We mapped transcript units at single base-pair resolution using RNA-seq together with global 5’ RACE.  Additionally, using ribosome profiling and LC-MS, we mapped translation start sites and coding regions with near complete coverage.  We found most start codons lacked corresponding Shine-Dalgarno sites although ribosomes were observed to pause at internal Shine-Dalgarno sites within the ORF.  These data suggest a more prevalent use of the Shine-Dalgarno sequence for ribosome pausing rather than translation initiation in C. crescentus.  Overall 19% of the transcribed and translated genomic elements were newly identified or significantly improved by this approach providing a valuable genomic resource to elucidate the complete C. crescentus genetic circuitry that controls asymmetric cell division.

overall_design: Ribosome profiling and RNA-seq data were collected in Caulobacter crescentus NA1000 cells grown in M2G and PYE media to map transcript and ORF features in the genome.

first: Gene-Wei

last: Li

first: Jonathan

last: Weissman

first: Lucy

last: Shapiro


title: Deletion of RING1A/B and loss of H2AK119ub1 affects PRC2 occupancy and H3K27me3 genome-wide

status: Public on May 27 2014

city: London

first: Hamish

last: King

address: 4 Newark St

department: Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

summary: The chromatin modifying activities inherent to polycomb repressive complexes PRC1 and PRC2 play an essential role in gene regulation, cellular differentiation, and development. However, the mechanisms by which these complexes recognize their target sites and function together to form repressive chromatin domains remain poorly understood. Recruitment of PRC1 to target sites has been proposed to occur through a hierarchical process, dependent on the prior nucleation of PRC2 and placement of H3K27me3. Here, using a de novo targeting assay in mouse embryonic stem cells we unexpectedly discover that PRC1-dependent H2AK119ub1 leads to the recruitment of PRC2 and H3K27me3 to effectively initiate a polycomb domain. Genetic ablation of catalytic subunit of the PRC1 complex (RINGA/B) and ChIP-seq analysis of PRC1 and PRC2 components confirmed genome-wide decreases in PRC2 occupancy and H3K27me3 levels at PRC target sites. This activity is restricted to variant PRC1 complexes and genetic ablation experiments reveal that targeting of the variant PCGF1/PRC1 complex by KDM2B to CpG islands is required for polycomb domain formation and normal development. Together these observations provide a surprising new PRC1-dependent logic for PRC2 occupancy and polycomb domain formation.

overall_design: RING1A-/-;RING1Bfl/fl ES cells were treated with 800µM tamoxifen for 48hours and compared to untreated control cells by ChIP-seq for RING1B, SUZ12, EZH2 and H3K27me3.

first: Anca

last: Farcas

first: Neil

last: Blackledge

first: Rob

middle: J

last: Klose


title: RNA-seq analysis revealed novel genes and signaling pathway associated with disease resistance to avian influenza virus infection in chickens

city: Davis

first: Huaijun

last: Zhou

address: 2247 Meyer hall, One shield AVE

department: Animal Science

institute: University of California Davis

summary: Three-week-old chickens were inoculated with low pathogenic H5N3 AIV and tissues were harvested 4 d pos tinoculation. Four lung cDNA libraries (1 library each for infected and noninfected Leghorn, and infected and noninfected Fayoumi) were prepared and sequenced by Illumina Genome Analyzer II, which yielded a total of 116 million, 75-bp single-end reads.

overall_design: The objective of this study was to identify genes and signal pathways associated with resistance to AIV infection in 2 genetically distinct highly inbred chicken lines (Fayoumi, relatively resistant to AIV infection, and Leghorn, susceptible to AIV infection).

first: Ying

last: Wang

first: Blanca

last: Luipiani

first: Sanjay

last: Reddy

first: Susan

last: Lamont


title: RNA-seq based characterization of long non-coding RNA involved in respiratory viruses pathogenesis

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: This dataset includes both whole transcriptome (WT) and mRNA-seq data for interferon-treated mouse samples. This is part of a larger study (GSE52405), where these interferon datasets were used as validation.

overall_design: 6-week-old C57BL/6J mice were treated with 10,000 U of recombinant interferon (Universal Type I IFN, Recombinant Human IFN-alpha A/D [BglII], R&D Systems) dissolved in endotoxin-free phosphate-buffered saline (EF-PBS), or with EF-PBS alone. For this study, the mice at 12 hours post-treatment were used.

first: Laurence

last: Josset

first: Nicolas

last: Tchitchek

first: Lisa

middle: E

last: Gralinski

first: Martin

middle: T

last: Ferris

first: Richard

last: Green

first: Matthew

last: Thomas

first: Fernando

last: Pardo-Manuel de Villena

first: Ralph

last: Baric

first: Mark

last: Heise

first: Xinxia

last: Peng

middle: G


title: The Osteoblast to Osteocyte Transition: Epigenetic Changes and Response to the Vitamin D3 Hormone [RNA-seq]

middle: B

last: Meyer

overall_design: Two sets of IDG-SW3 differentitiation mRNA-seq experiments are presented here in biological triplicate.  One a differentiation time course in the basal condition at days 3, 7, 14, 21, 28, 35.  The second experiment is IDG-SW3 cells differentiated to day 3 or day 35 and treated with vehicle or 100nM 1,25(OH)2D3 for 24 hours prior to mRNA isolation and sequencing.

first: Hillary

first: J

last: Pike


title: The Osteoblast to Osteocyte Transition: Epigenetic Changes and Response to the Vitamin D3 Hormone

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

overall_design: Refer to individual Series


title: Molecular mechanism of action of plant DRM de novo DNA methyltransferases

first: Christopher

middle: Joel

last: Hale

address: 1959 NE Pacific St., HSC H-458

department: Pathology

summary: DNA methylation is a conserved epigenetic gene regulation mechanism. DOMAINS REARRANGED METHYLTRANSFERASE (DRM) is a key de novo methyltransferase in plants, but how DRM acts mechanistically is poorly understood. Here, we report the crystal structure of the methyltransferase domain of tobacco DRM (NtDRM) and reveal a molecular basis for its rearranged structure. NtDRM forms a functional homo-dimer critical for catalytic activity. We also show that Arabidopsis DRM2 exists in complex with the siRNA effector ARGONAUTE4 (AGO4) and preferentially methylates one DNA strand, likely the strand acting as the template for non-coding Pol V RNA transcripts. This strand-biased DNA methylation is also positively correlated with strand-biased siRNA accumulation. These data suggest a model in which DRM2 is guided to target loci by AGO4-siRNA and involves base-pairing of associated siRNAs with nascent RNA transcripts.

overall_design: Whole-genome bisulfite sequencing was done for a wildtype line (ecotype Col) as well as various transgenic lines in a drm2 mutant background (ecotype Col). Each transgenic line expressed a version of the DRM2 protein that was either wildtype or carried induced mutations in order to test the function of various domains in the DRM2 protein. Two sets of whole-genome bisulfite were performed (130615 or 131216) and comparisons were mainly done within sets although comparisons can also be done between sets. The drm2 mutant methylome was also analyzed in this study using a previously published whole-genome bisulfite library (GSE39901).


title: RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome [RNA-Seq]

city: Boston

first: Lillian

last: Zwemer

address: 800 Washington St, Box 394

department: Mother Infant Research Institute

institute: Tufts Medical Center

summary:
The second trimester fetal transcriptome can be assessed based on cell-free RNA found within the amniotic fluid supernatant. The objective of this study was to compare the suitability of two technologies for profiling the human fetal transcriptome: RNA-Seq and expression microarray. Comparisons were based on total numbers of gene detected, rank-order gene expression, and functional genomic analysis.
Fewer gene transcripts were observed using RNA-Seq than microarray (4,158 vs 8,842). Correlation of total expression within each sample ranged from R=0.43 to R=0.57. On average, there was 59% concordance in gene identity among the top 10% of genes ranked by expression. The RNA-Seq data yielded more significant pathways enrichment within the ?Physiological Systems Development and Function? categories of IPA. Alternative splicing of many well-known genes, including those previously studied in fetal development, such as H19 and IGF2  is detected by RNA-Seq. Also included in this paper is discussion of the technical challenges inherent to working with cell-free fetal RNA and possible solutions.

overall_design: Cell-free fetal RNA from the amniotic fluid supernatant of five second trimester fetuses was divided and prepared in tandem for analysis using either the Illumina HiSeq 2000 or Affymetrix HG-U133 Plus 2.0 GeneChip microarray.

last: Hui

first: Heather

last: Wick

first: Diana

last: Bianchi


title: RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome


title: Discovery of the p53 targetome in MCF7 cells from RNA-seq data

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 box 602

department: Department of Human Genetics

country: Belgium

institute: KU Leuven

summary: RNA-seq and ChIP-seq on MCF-7 breast cancer cell line upon activation of p53 by the non-genotoxic small molecule Nutlin-3a

overall_design: RNA-seq on MCF7 without (NS) or with Nutlin-3a stimulation (S), in duplicate, using illumina HiSeq 2000

first: Annelien

last: Verfaillie

first: Stein

last: Aerts


title: Discovery of the p53 targetome in MCF7 cells from ChIP-Seq data

overall_design: ChIP-seq on p53 in MCF7 with Nutlin-3a stimulation (S) in triplicate, and the control (input), in stimulated and non stimulated, using illumina HiSeq 2000


title: Deletion of KDM2B DNA-binding domain affects RING1B and SUZ12 occupancy

first: Hamish

last: King

summary: The histone lysine demethylase protein, KDM2B, associates with the PCGF1/PRC1 complex and binds to non-methylated DNA through its ZF-CxxC domain, providing a possible molecular link between CpG island elements and polycomb nucleation (Farcas et al., 2012, Wu et al., 2013). Here, a novel genetic system was designed in which PCGF1/PRC1 targeting could be disrupted in vivo through the ablation of KDM2B-mediated DNA binding. To ablate PCGF1/PRC1 targeting, an exon that encodes most of the KDM2B ZF-CxxC domain and is shared by both the long and short form of the protein was flanked by loxP sites (Kdm2bfl/fl). Homozygous mouse ES cell lines were derived that also stably express a tamoxifen inducible form of CRE-recombinase. CRE induced deletion of the ZF-CxxC domain by the addition of tamoxifen yields KDM2B long and short form proteins that are incapable of binding to CpG island DNA but still remain associated with the PCGF1/PRC1 variant complex. We then assessed genome-wide occupancy of the PRC1 component RING1B and the PRC2 component SUZ12 to examine the impact of losing KDM2B-dependent targeting of polycomb.

overall_design: KDM2Bfl/fl ES cells were treated with 800µM tamoxifen for 72hours and compared to untreated control cells by ChIP-seq for KDM2B, RING1B and SUZ12, and RNA-seq.

first: Anca

last: Farcas

first: Neil

middle: P

last: Blackledge

first: Rob

last: Klose


title: Identification and characterization of microRNAs involved in growth of blunt snout bream (Megalobrama amblycephala) by Solexa sequencing

status: Public on May 25 2014

city: WuHan

first: Yi

middle: Shao

last: Kui

state: HuBei

address: No.1,Shizishan Street · Hongshan District · Wuhan · Hubei Province

institute: Huazhong Agricultural University

summary: The present study provides the first large-scale characterization of miRNAs in M. amblycephala and miRNA profile of M. amblycephala with different growth performance. The discovery of miRNA resource from this study is expected to contribute to a better understanding of the miRNAs roles playing in regulating the growth biological processes in fish and the study of miRNA function and phenotype-associated miRNA identification in fish.

overall_design: To investigate the functions of miRNAs associated with growth of M. amblycephala, we adopted the Solexa sequencing technology to sequence two small RNA libraries prepared from four growth related tissues (brain, pituitary, liver and muscle) of M. amblycephala using individuals with relatively high and low growth rates.

last: Shaokui

first: Gao

last: Zexia


title: A novel post-translational mechanism controlling the oncogenic activity of c-Myc is enhanced in poor outcome breast cancer

first: Rosalie

last: Sears

summary: Examination of Pin1-regulated Myc target genes in a human breast epithelial cell line.

overall_design: Two samples: control GFP-expressing MCF10A-Myc cells and Pin1-expressing MCF10A-Myc cells.

first: Amy

middle: S

last: Farrell


title: Global analysis of the nuclear processing of unspliced U12-type introns by the exosome

status: Public on May 26 2014

city: Helsinki

first: Marco

last: Savarese

address: Topeliuksenkatu 20

department: Samfundet Folkhälsan i svenska Finland r.f.

country: Finland

institute: Folkhälsan Research Center

summary: we analyzed globally the effect of exosome processing on the nuclear pre-mRNA transcripts by inactivating either the RRP41 or DIS3 subunit of the exosome. Using SOLiD RNA sequencing technology, we report 30-120 million mapped cellular compartment specific reads per sample allowing the detection of unspliced pre-mRNAs. We show that RRP41 and DIS3 knockdowns stabilize an overlapping set of U12-type introns.

overall_design: Studying the global effect of the exosome (Rrp41 or Dis3 subunit) knockdown comparing to the control sample.

first: Elina

middle: H

last: Niemelä

first: Ali

last: Oghabian

first: Raymond

last: Staals

first: Dario

last: Greco

first: Ger

last: Pruijn

first: Mikko

last: Frilander


title: Variant PRC1 complex dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation


title: Cell cycle transition from S-phase to G1 in Caulobacter is mediated by ancestral virulence regulators

city: Geneva

first: Antonio

last: Frandi

address: rue michel servet 1

department: Microbiology and Molecular Medicine

institute: University of Geneva

summary: We report that ancestral zinc-finger-domain transcriptional regulators, previously  reported to control virulence/symbiosis, implement a cell cycle (S→G1) transcriptional  switch. To unravel how this G1-phase transcriptional program is reinstated during a  primitive cell cycle, we first defined G1-specific promoters in the model bacterium  Caulobacter crescentus by comparative ChIP-Seq analysis. We then exploited one  such promoter as genetic proxy, to identify two conserved developmental regulator  paralogs, MucR1/2, that constitute a quadripartite and homeostatic regulatory module  directing the switch from S→G1-phase transcription. Surprisingly, MucR orthologs that  regulate virulence and symbiosis gene transcription in Brucella, Agrobacterium or  Sinorhizobium support the G1 transcriptional switch in Caulobacter. Pan-genomic  ChIP-Seq analyses in Sinorhizobium and Caulobacter show that this module targets  orthologous genes. Thus, this ancestral bacterial lineage from which eukaryotic  organelles descended may coordinate virulence/symbiosis with other cell cycle  functions using a primordial transcription factor fold that is now primarily found in the  eukaryotic domain of life.

sample_organism:
Sinorhizobium fredii
Caulobacter vibrioides

overall_design: Examination of 5 transcripton factor binding in two different species

first: Coralie

last: Fumeaux

first: Sunish

middle: K

last: Radhakrishnan

first: Silvia

last: Ardissone

first: Laurence

last: Théraulaz

first: Daniel

last: Martins

first: Jutta

last: Nesper

first: Sören

last: Abel

first: Urs

last: Jenal

first: Patrick

last: Viollier


title: Genome-wide identification and functional analysis of Apobec-1 mediated C-to-U RNA editing in mouse small intestine and liver

status: Public on May 23 2014

city: Irvine

first: Eddie

last: Park

address: 2300 Biological Sciences 3

department: DevCell

institute: UCI

summary: The genome-wide identification, tissue-specificity and functional implications of Apobec-1 mediated C-to-U RNA editing remains incomplete. Deep sequencing, data filtering and validation from wild-type and Apobec-1 deficient mice revealed 56 novel editing sites in 54 intestinal mRNAs and 22 novel sites in 17 liver mRNAs (74-81% true-positive), all within 3' untranslated regions.  Eleven of 17 liver RNAs shared editing sites with intestinal RNAs, while 6 sites were unique to liver. Changes in RNA editing led to corresponding changes in intestinal mRNA and protein levels in 11 genes. We found distinctive polysome profiles for several editing targets and demonstrated nuclear but not cytoplasmic editing of novel exonic sites in intestinal (but not hepatic) apoB RNA.  RNA editing was validated using cell-free extracts from wild-type but not Apobec-1 deficient mice. These studies define selective, tissue-specific targets of Apobec-1 dependent RNA editing and show the functional consequences of editing are both transcript- and tissue-specific.

overall_design: Examination of C-to-U RNA editing in mouse liver and intestine

first: Valerie

last: Blanc

first: Sabine

last: Schaefer

first: Melanie

last: Miller

first: Yiing

last: Lin

first: Susan

last: Kennedy

first: Anja

middle: M

last: Billing

first: Hisham

last: Hamidane

first: Johannes

last: Graumann

last: Mortazavi

first: Joseph

last: Nadeau

first: Nicholas

middle: O

last: Davidson


title: RNAseq transcriptome data from reprogramming human CD34+ cells to iPS

status: Public on May 24 2014

first: Julien

last: Duc

address: Station 19 CH-1015 Lausanne

institute: EPFL

summary: We reprogrammed human CD34+ cells from cord blood using a lentiviral vector encoding OCT4, SOX2 and KLF4.We collected RNA from parental CD34+ cells (3samples), reprogramming timepoints (9 timepoints), iPS clones derived from this experiment (6 clones), and human ES cell lines (9 samples). All samples were sequenced at 100bp reads.

overall_design: Endogenous retroelement expression during reprogramming

first: Marc

last: Friedli

first: Didier

last: Trono


title: Stage-specific regulation of translation revealed by ribosome profiling of Trypanosoma brucei

city: SEATTLE

first: Gowthaman

last: Ramasamy

state: WASHINGTON

address: 307 WESTLAKE AVE N

department: GHBC

institute: SEATTLE BIOMEDICAL RESEARCH INSTITUTE

summary: Trypanosoma brucei subspecies infect humans and animals in sub-Saharan Africa.  This early diverging eukaryote shows many novel features in basic biological processes, including the use of polycistronic transcription to generate all protein-coding mRNAs.  Therefore we hypothesized that translational control provides a means to tune gene expression during parasite development in mammalian and fly hosts. We used ribosome profiling to examine genome-wide protein production in animal-derived slender bloodstream forms and cultured procyclic (insect midgut) forms.  About one-third of all CDSs showed statistically significant regulation of protein production between the two stages.  Of these, more than two-thirds showed a change in translation efficiency, but few were controlled by this parameter alone.  Ribosomal proteins were translated poorly, especially in animal-derived parasites.  A disproportionate number of metabolic enzymes were up-regulated at the mRNA level in procyclic forms, as were variant surface glycoproteins in bloodstream forms.   Comparison with cultured bloodstream forms from another strain identified stage-specific changes in protein production that transcend strain and growth conditions.  Genes with upstream ORFs had a lower mean translation efficiency but no evidence was seen for involvement of these ORFs in stage-regulation. Ribosome profiling revealed that differences in the production of specific proteins in T. brucei slender bloodstream and procyclic forms are more common than anticipated from analysis of mRNA abundance.  While in vivo and in vitro derived slender bloodstream forms of different strains are more similar to one another than to procyclic forms, they showed numerous differences at both the mRNA and protein production level.

overall_design: Ribosome profiling and mRNA libraries were constructed in triplicate from in vitro  PCF and in vivo  BF lifestages of theT. brucei Treu927 and in vitro T. brucei  Lister427, to evaluate role of translational gene regulation

first: Bryan

middle: C

last: Jensen

first: Elton

last: Vasconcelos

last: Ingolia

first: Peter

last: Myler

first: Marilyn

last: Parsons


title: Transcriptome analysis of Th9 CD4+ T cells differentiated with or without Il-1beta

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

institute: CGFL

summary: We report that the Th9 differenciation program is boosted in presence of Il-1beta

overall_design: Examination of the expression profile of Th9 CD4+ T cells after 1 hour and 3 days of differentiation and after in vivo injection

first: F

last: Vegran

first: H

last: Berger

first: R

first: L

last: Apetoh

last: Ghiringhelli


title: Genome-Wide Small RNA Profiling of a Soybean Seed Compartment-Early Maturation Stage

first: John

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California

summary: We performed small-RNA profiling of soybean seed regions and sub-regions, to gain new insights into the regulatory processes required for seed differentiation.

overall_design: Seventeen subregions of the Early Maturation stage of the soybean seeds were analyzed. Two biological replicates were collected for each subregions.

first: Robert

last: Goldberg

first: Ryan

last: Kirkbride

first: Julie

last: Pelletier

first: Tina

middle: Y

last: Wang

first: Ssu-Wei

last: Hsu

first: Shu-Heng

last: Chang

first: Russell

middle: W

last: Baden

first: Rie

last: Uzawa

first: Alexander

last: Olson

first: Lourenz

last: Balayan

first: Erik

last: Garber

first: Meryl

last: Hashimoto

first: Uranus

last: Chau


title: Hepatosplenic T cell lymphoma

first: Julio

last: Finalet

address: Herestraat 49

institute: KULeuven


title: Genome-Wide Small RNA Profiling of a Soybean Seed Compartment-Heart Stage

status: Public on May 22 2014

overall_design: Eight subregions of the Heart stage of the soybean seeds were analyzed. Two biological replicates were collected for each subregions.


title: Identification of activity-induced Npas4-regulated genes in cortical inhibitory and excitatory neurons

first: Ivo

last: Spiegel

address: 220 Longwood Ave

department: Department of Neurobiology

institute: Harvard Medical School


title: Discovery of the p53 targetome in MCF7 cells from RNA-seq and ChIP-seq data

first: Rekin's

last: Janky

first: Annelien

last: Verfaillie

first: Stein

last: Aerts


title: Identification of activity-induced genes in cortical inhibitory neurons (RNA-Seq)

summary: To identify the activity-induced gene expression programs in inhibitory neurons, we analyzed RNA extracted from cultured E14 mouse MGE-derived neurons (DIV 10) after these cultures were membrane-depolarized for 0, 1 and 6 hrs with 55mM extracellular KCl.

overall_design: Mouse E14 MGE-derived neurons were cultured for 9 days, quieted overnight with TTX and AP-5 and then membrane-depolarized for 0, 1 or 6 hours by raising the extracellular KCl-concentration to 55mM. RNA was then extracted and WT RNA-Seq was performed on ABi SOLiD

first: I

first: A

middle: R

last: Mardinly

first: M

last: Greenberg


title: Genome-Wide Small RNA Profiling of a Soybean Seed Compartment-Cotyledon Stage

first: John

last: Harada

overall_design: Eight subregions of the Cotyledon stage of the soybean seeds were analyzed. Two biological replicates were collected for each subregions.

middle: J

first: Robert

last: Goldberg

first: Ryan

last: Kirkbride

first: Julie

last: Pelletier

first: Tina

last: Wang

first: Ssu-Wei


title: Unambiguous Identification of miRNA:target site Interactions by Different Types of Ligation Reactions

city: Berlin

first: Nikolaus

last: Rajewsky

state: Berlin

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

summary: To exert regulatory function, miRNAs guide Argonaute (AGO) proteins to partially complementary sites on target RNAs. Crosslinking and immunoprecipitation (“re state-of-the-art to map AGO binding sites, but assigning the targeting miRNA to these sites relies on bioinformatics predictions and is therefore indirect. To directly and unambiguously identify miRNA:target site interactions, we modified our CLIP methodology in C. elegans to experimentally ligate miRNAs to their target sites. Unexpectedly, ligation reactions also occurred in absence of the exogenous ligase. Our in vivo dataset and re-analysis of published mammalian AGO-CLIP data for miRNA-chimeras yielded >17,000 miRNA:target site interactions. Analysis of interactions and extensive experimental validation of chimera-discovered targets of viral miRNAs suggest that our strategy identifies canonical, non-canonical, and non-conserved miRNA interactions. Our data suggest that ~80% of miRNA:targets have perfect or partial seed complementarity. In summary, analysis of miRNA:target chimeras enables the systematic, context-specific, in vivo discovery of miRNA interactions.

overall_design: In vivo PAR-CLIP basically as described previously (Jungkamp et al. 2011) using GFP-tagged ALG-1 expressing worms in L3 stage. Worm lysate was treated with RNase T1. Following immunoprecipitation and a second RNase T1 digest, it was proceeded as described in Hafner et al. 2010. For the modified iPAR-CLIP ligation samples and its control samples immuno-purified complexes were treated with PNK phospathase minus, subjected to ligation with T4 RNA ligase/no ligase added and subsequently phosphorylated with PNK. Protein purification and RNA library preparation essentially as described in Hafner et al., but with the selection of longer RNA products.

first: Stefanie

last: Grosswendt

first: Andrei

last: Filipchyk

first: Mark

last: Manzano

first: Filippos

last: Klironomos

first: Marcel

last: Schilling

first: Margareta

last: Herzog

first: Eva

last: Gottwein


title: Early B-cell Factor 1 Regulates Adipocyte Morphology and Lipolysis in White Adipose Tissue [ChIP-seq]

city: Huddinge

first: hui

last: Gao

address: Novum

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

summary: Examination of EBf1 binding by ChIP-seq in  differentiated human adipose stromal cell (hASC) pre-adipocyte

overall_design: Pre-Adipocytes differentiated in-vitro were fixed in 1% formaldehyde for 15 min at room temperature and quenched for 5 min by adding glycine to a final concentration of 0.125 M. ChIP assays were then performed with custom-made EBF1 antibody or rabbit IgG . ChIP-sequencing libraries were prepared using NEBnext chip-seq library Prep master mix set  from 5 ng of anti-EBF1 and anti-IgG ChIP DNA, respectively. Sequence data were generated with Illumina HiSeq 2000 single-read sequencing and aligned against the human genome (hg19, NCBI).

first: Hui

first: Niklas

last: Mejhert

first: Mikael

last: Rydén

first: Peter

last: Arner


title: Early B-cell Factor 1 Regulates Adipocyte Morphology and Lipolysis in White Adipose Tissue

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

overall_design: Refer to individual Series


title: The p53-regulated long noncoding RNA, lincRNA-p21 promotes the expression of Polycomb target genes and enforces the G1/S checkpoint by activating p21 in cis [RNA-seq]

city: LOS ANGELES

first: Jesse

last: Zamudio

address: 610 CHARLES E. YOUNG DRIVE EAST BOX 957239

department: MCDB

institute: University of California, Los Angeles

summary: The p53-regulated long non-coding RNA, lincRNA-p21, has been proposed to promote apoptosis and to repress in trans the expression of genes in the p53 transcriptional network. Here, we report the generation of a conditional knockout mouse model developed to further examine lincRNA-p21 function. Using this genetic approach, we find that the primary function of lincRNA-p21 is to activate in cis the expression of its neighboring gene, the cyclin-dependent kinase inhibitor p21. Mechanistically, we show that lincRNA-p21 acts in concert with hnRNP-K as a co-activator for p53-dependent transcription of p21. Additional phenotypes of lincRNA-p21 deficiency, including deregulated expression and altered chromatin state of a set of Polycomb target genes, defective G1/S checkpoint, increased proliferation rates, and enhanced reprogramming efficiency could be attributed to diminished p21 levels. This study reveals a novel paradigm, whereby the long non-coding RNA lincRNA-p21 affects global gene expression and influences events in the p53 tumor suppressor pathway by acting in cis as a locus-restricted transcriptional co-activator for p53-mediated expression of p21.

overall_design: mRNAseq in 2  cell types (WT and lincRNA-p21 KO) in the presence and absence of Doxorubicin performed in biological  triplicate.


title: Transcriptome sequencing of Brassica oleracea tissues

city: Shenzhen

first: Zhangyan

last: Wu

address: Yantian district, Shenzhen

institute: Beijing Genomics Institute

summary: Deep sequencing of mRNA from seven different tissues of Brassica oleracea

overall_design: Analysis of ploy(A)+ RNA of multiple different tissues of Brassica oleracea containing Bud, Callus, Root, Stem, Leaf, Flower and Silique.

first: Yumei

last: Liu

first: Zhiyuan

last: Fang

first: Wanxing

first: Xinhua

last: Yang

first: Wanshun

last: Li

first: Chaobo

last: Tong

first: Shengyi


title: The p53-regulated long noncoding RNA, lincRNA-p21 promotes the expression of Polycomb target genes and enforces the G1/S checkpoint by activating p21 in cis [ChIP-seq]

overall_design: Examination of 2 different histone modifications (H3K4me3 and H3K27me3)  in 2 cell types (WT and lincRNA-p21 KO) in the presence and absence of Doxorubicin.


title: The p53-regulated long noncoding RNA, lincRNA-p21 promotes the expression of Polycomb target genes and enforces the G1/S checkpoint by activating p21 in cis


title: Genome-Wide Small RNA Profiling of a Soybean Seed Compartment-Globular Stage

status: Public on May 21 2014

first: John

last: Harada

overall_design: Six subregions of the Globular stage of the soybean seeds were analyzed. Two biological replicates were collected for each subregions.

first: Robert

last: Goldberg

first: Ryan

last: Kirkbride

first: Julie

last: Pelletier

first: Tina

last: Wang

first: Ssu-Wei

last: Hsu

first: Shu-Heng

last: Chang

first: Russell

last: Baden

first: Rie

last: Uzawa

first: Alexander

last: Olson

first: Lourenz

last: Balayan

first: Erik

last: Garber

first: Meryl

last: Hashimoto

first: Uranus

last: Chau


title: Modeling Fanconi Anemia pathogenesis and therapeutics using   integration-free patient iPSCs [ChIP-seq]

city: Barcelona

first: Nuria

last: Montserrat

address: Baldiri Reixac, 10-12

country: Spain

institute: Institute for Bioengineering of Catalonia (IBEC)

summary: We compared the epigenetic status of the mutant and disease-free iPSCs at the whole genome level. Whole epigenome profiling based on trimethylated H3K4 (H3K4me3) showed concordant epigenetic remodeling in the two corrected clones when compared with two mutant iPSC clones.

overall_design: Examination of the trimethylated H3K4 histone modification in Fanconi anemia patient iPSCs before and after gene correction

first: Luca

last: Cozzuto


title: Modeling Fanconi Anemia pathogenesis and therapeutics using integration-free patient iPSCs


title: Modeling Fanconi Anemia pathogenesis and therapeutics  using integration-free patient iPSCs [RNA-seq]

overall_design: Examination of genome-wide gene expression in Fanconi anemia patient iPSCs before and after gene correction


title: Global expression profiles of the wild-type and overexpression of OsNMD3ΔNLS transgenic plants

city: Beijing

first: Baocai

last: Zhang

state: Beijng

address: Beichen west road

department: Center for Genome Biology

institute: Institute of Genetics and Developmental Biology, CAS

summary: Plants have mechanisms that coordinate protein synthesis and gene transcription, although they operate at different cellular sites. The altered translational efficiency may have a feedback effect on gene expression. To determine the global changes in ribosome biogenesis, we used an Illumina RNA sequencing approach to investigate the global expression profiles of the wild-type,OsNMD3ΔNLSL1,and OsNMD3ΔNLSL2 plants.These expression profiles suggested that overexpression of OsNMD3ΔNLS affected ribosome biogenesis and certain basic pathways, leading to pleotropic abnormalities in plant growth.

overall_design: The mRNA profiles of the 2nd internodes of development-matched wild-type and overexpression of OsNMD3ΔNLS transgenic plants.

first: Yanyun

last: Shi

first: Yihua

last: Zhou


title: Regulation of FAS Exon Definition and Apoptosis by the Ewing Sarcoma Protein

city: Budapest

first: Endre

last: Sebestyén

address: Üllői út 26.

department: 1st Department of Pathology and Experimental Cancer Research

country: Hungary

institute: Semmelweis University

summary: The Ewing’s sarcoma protein EWS belongs to the TET family (FUS/TLS, EWS, TAF15) of RNA and DNA binding proteins, implicated in DNA transcription, pre-mRNA splicing and maintenance of genomic integrity. Translocations of these genes are characteristic of particular neoplasias, including Ewing’s sarcoma. To identify physiological RNA targets of EWS, we performed in vivo cross-linking and immunoprecipitation followed by high-throughput RNA sequencing (HITS-CLIP/CLIP-Seq) in HeLa cells. Sequencing identified EWS binding sites characterized by guanosine-rich motifs in nearly 9000 genes, with particular enrichment in exonic regions near 5’ splice sites. Exon 6 of the Fas/CD95 receptor, which is alternatively spliced to generate isoforms with opposing activities in programmed cell death, was found as a prominent EWS CLIP target, as well as by chromatin-immunoprecipitation (ChIP) and functional analysis. Manipulation of EWS levels and mutation of EWS binding sites led to changes in alternative splicing consistent with EWS promoting exon 6 inclusion and leading to the synthesis of the pro-apoptotic Fas/CD95 isoform. Biochemical characterization of factors associated with FAS exon 6 are consistent with the notion that EWS binds to exonic sequences near the 5’ splice site and promotes the recruitment of U1snRNP, favoring also recognition of the upstream 3' splice site by U2AF and thus exon definition.  Consistent with a role for EWS in the regulation of programmed cell death, cells depleted of EWS show decreased sensitivity to Fas-induced apoptosis. We discuss the potential implications of this novel function of EWS in Ewing’s sarcoma.

overall_design: CLIP-Seq analysis of EWS, with 2 biological replicates of EWS and one non-specific control

first: Maria

last: Paronetto

first: Isabella

last: Bernardis

first: Elisabetta

last: Volpe

first: Elias

last: Bechara

first: Eduardo

last: Eyras

first: Juan

last: Valcárcel


title: Myelodysplastic syndromes are propagated by rare and distinct human cancer stem cells in vivo

city: Oxford

first: Petter

last: Woll

address: Weatherall Institute of Mol Med

institute: University of Oxford

summary: Gene expression analysis of purified hematopoietic stem and progenitor cells isolated from low to intermediate risk MDS patients and age-matched normal healthy controls.

overall_design: Analysis of lineage associated genes and PCA clustering of populations

first: P

first: M

last: Ngara

first: S

last: Thongjuea

first: Sten

last: Jacobsen


title: IVT-seq reveals extreme bias in RNA-sequencing

city: Philadelphia

first: Nicholas

last: Lahens

state: PA

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

department: ITMAT

institute: University of Pennsylvania

summary:
Background:
RNA-seq is a powerful technique for identifying and quantifying transcription and splicing events, both known and novel. However, given its recent development and the proliferation of library construction methods, understanding the bias it introduces is incomplete but critical to realizing its value.

Results:
We present a method, in vitro transcription sequencing (IVT-seq), for identifying and assessing the technical biases in RNA-seq library generation and sequencing at scale. We created a pool of over 1,000 in vitro transcribed RNAs from a full-length human cDNA library and sequenced them with polyA and total RNA-seq, the most common protocols. Because each cDNA is full length, and we show in vitro transcription is incredibly processive, each base in each transcript should be equivalently represented. However, with common RNA-seq applications and platforms, we find 50% of transcripts have more than two-fold and 10% have more than 10-fold differences in within-transcript sequence coverage. We also find greater than 6% of transcripts have regions of dramatically unpredictable sequencing coverage between samples, confounding accurate determination of their expression. We use a combination of experimental and computational approaches to show rRNA depletion is responsible for the most significant variability in coverage, and several sequence determinants also strongly influence representation.

Conclusions:
These results show the utility of IVT-seq for promoting better understanding of bias introduced by RNA-seq. We find rRNA depletion is responsible for substantial, unappreciated biases in coverage introduced during library preparation. These biases suggest exon-level expression analysis may be inadvisable, and we recommend caution when interpreting RNA-seq results.

sample_organism:
Homo sapiens
Mus musculus
mixed libraries

overall_design: 5 rRNA-depleted samples with duplicates, 1 polyA selected, 1 total RNA, and 1 plasmid library all without replicates.

middle: F

first: Ibrahim

last: Kavakli

first: Ray

first: Katharina

last: Hayer

first: Michael

last: Black

first: Hannah

last: Dueck

first: Angel

last: Pizarro

first: Junhyong

last: Kim

first: Rafael

last: Irizarry

first: Russel

last: Thomas

first: Gregory

last: Grant

first: John

last: Hogenesch


title: The ETS family member GABPa mediates the development of castrate-resistant prostate cancer (ChIP-Seq)

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: In prostate cancer, the androgen receptor (AR) is a key transcription factor at all disease stages. We recently showed that during progression to castrate-resistant prostate cancer the AR acquires the ability to bind to a distinct set of genomic sites in tissue samples and that some of the genes that are regulated by the AR in these conditions correlate with poor prognosis. Based on this work we hypothesised that the AR is reprogrammed through interactions with other transcription factors. In the present study we show that GABPá, an ETS transcription factor which is upregulated in CRPC, is an AR-interacting transcription factor. Ectopic expression of GABPA in prostate cancer cell-lines enables them to acquire some of the molecular and cellular characteristics of CRPC tissues as well as more aggressive growth phenotypes.

overall_design: VCaP prostate cancer cells and Jurkat lymphoma cells were studied for the ETS factors ERG and GABPa binding sites. Each sample was compared to its input.

first: Naomi

last: Sharma

first: Suraj

last: Menon


title: Discovery of ethanol responsive small RNAs in Zymomonas mobilis

status: Public on May 20 2014

city: Austin

first: Seung Hee

last: Cho

state: Texas

address: 200 E Dean Keeton St. Stop C0400

department: iCMB

institute: University of Texas at Austin

summary: This study is aimed for the identification of novel small RNAs under different ethanol producing conditions. We have applied transcriptome analysis to facilitate identification and validation of 15 novel sRNAs in Zymomonas mobilis. We furthermore characterize their expression in the context of high and low levels of intracellular ethanol. Here, we report that 3 of the sRNAs (Zms2, Zms4 and Zms6) are differentially expressed under aerobic and anaerobic conditions, when low and high ethanol productions are observed respectively. These data suggests that in this organism regulatory RNAs can be associated with metabolic functions involved in ethanol stress responses.

sample_organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

overall_design: Z. mobilis was grown under aerobic and anaerobic conditions which showed low and high ethanol production, respectively. Each samples were sequenced for identification of small RNA candidates and differentially expressed candidates between two conditions.

first: Seung

first: Lydia

last: Contreras


title: The ETS family member GABPa mediates the development of castrate-resistant prostate cancer


title: Translational profiling of hypothalamic and midbrain neurons that project to the nucleus accumbens.

city: New York

first: Jeffrey

last: Friedman

state: NY

address: 1230 York Avenue

department: Molecular Genetics

institute: The Rockefeller University

summary: Neuroanatomical methods enable high-resolution mapping of neural circuitry, but do not allow systematic molecular profiling of neurons based on their connectivity. Here, we report the development of a novel approach for molecularly profiling projective neurons. We show that ribosomes can be labeled with a camelid nanobody raised against GFP and that this system can be engineered to selectively capture translating mRNAs from cells expressing GFP. We generated a transgenic mouse encoding a nanobody-ribosomal protein fusion (Syn-NBL10) and used a retrograde virus (CAV) encoding GFP to immunoprecipitate ribosomes from projection neurons. This enabled us to profile neurons projecting to the nucleus accumbens. The current method provides a new means for profiling neurons based on their projections.

overall_design: Translating mRNAs immunoprecipitated from neurons projecting to the nucleus accumbens. Each Input and IP sample corrspond to a pooled group of 6 mice.

first: Mats

middle: I

last: Ekstrand

first: Alexander

last: Nectow


title: A Large-Scale RNAi-Based Mouse Tumorigenesis Screen Identifies    New Lung Cancer Tumor Suppressors that Repress FGFR Signaling

city: Worcester

first: Michael

middle: R.

last: Green

state: MA

address: 364 Plantation Street

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

summary: We sequenced mRNA from SA cells with SFRS9 knocking down or    non-silencing control.

overall_design: Examination of alternative splicing between SFRS9 KD    and NS.

first: Ling

last: Lin


title: Large-scale multi-species survey of metabolome and lipidome

city: Leuven

first: Jieyi

last: Xiong

address: Herestraat 49, box 912

institute: VIB-KULeuven Center for Cancer Biology

summary: This dataset was generated with the goal of comparative study of gene expression in three brain regions and two non-neural tissues of humans, chimpanzees, macaque monkeys and mice. Using this dataset, we performed studies of gene expression and gene splicing evolution across species and search of tissue-specific gene expression and splicing patterns. We also used the gene expression information of genes encoding metabolic enzymes in this dataset to support a larger comparative study of metabolome evolution in the same set of tissues and species.

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens
Mus musculus

overall_design:
120 tissue samples of prefrontal cortex (PFC), primary visual cortex (VC), cerebellar cortex (CBC), kidney and skeletal muscle of humans, chimpanzees, macaques and mice.
The data accompanies a large set of metabolite measurements of the same tissue samples. Enzyme expression was used to validate metabolite measurement variation among species.

first: Xiong

last: Jieyi

first: Jiang

last: Xi

first: Kasia

last: Bozek

first: Philipp

last: Khaitovich


title: Characterization and parental contribution of piRNAs and endo-siRNAs to mouse zygotes.

city: Madrid

first: Jesus

last: Garcia Lopez

address: C/Ramiro de Maeztu 9

department: Cellular and Molecular Biology

institute: Cib (CSIC)

summary: Transposable elements (TEs) are widely represented in eukaryotic genomes. Recently, a set of small RNAs known as rasRNAs (repeat-associated small RNAs) have been related to the down-regulation of TEs conferring a means to safeguard genome integrity. Two key members of the rasRNAs group are piRNAs and endo-siRNAs. In this study, we have performed a comparative analysis of piRNAs and endo-siRNAs present in mouse oocytes, spermatozoa and zygotes, identified by deep sequencing and bioinformatic analysis. Both piRNAs and endo-siRNAs regulate TEs in addition to other repetitive elements such as tRNAs and rRNAs, suggesting an alternative role of rasRNAs with regard to translation regulation. The detection of piRNAs and endo-siRNAs in sperm cells and revealed also in zygotes, hints to their potential delivery to oocytes during fertilization. However, a comparative assessment of the three cell types indicates that both piRNAs and endo-siRNAs are mainly maternally inherited. Finally, we have assessed the role of the different rasRNA molecules in connection with amplification processes by way of the “ping-pong cycle”. Our results suggest that the ping-pong cycle can act on other rasRNAs, such as tRNA- and rRNA-derived fragments, thus not only being restricted to TEs during gametogenesis, as was evidenced in spermatozoa, oocytes and zygotes.

overall_design: Comparative analysis from deep sequencing of piRNAs and endo-siRNAs in mouse oocytes, spermatozoa and zygotes

first: J

last: Garcia-Lopez

last: Hourcade

first: L

last: Alonso

first: D

middle: B

last: Cárdenas

last: del Mazo


title: Genome wide effects of maternal undernutrition

city: London

first: Gioia

last: Altobelli

address: 5 University Street

institute: UCL

summary: DNA methylation profiles of the livers of 1 day old rats from mothers fed with three different diets during gestation. The first animal group was fed with a normal diet (c=control); second group received much less protein than normal and slighlty more carbs (p=low protein, or programmed); third group diet was same as low protein but with extra folic acid (f=low protein+folate). All diets were matched for energy.

overall_design: Genomic DNA from rat livers was subjected to selection according to the methyl-CpG binding domain-based (MBD) protein protocol (DNA pooled from 6 individuals per group) and the resulting fragments sequenced in high throughput. Methylated DNA was captured with MethylCap kit (Diagenode). Approximately 10 ng of captured DNA was used for library preparation (ChIP-seq DNA sample Prep Kit, Illumina).

first: Irina

last: Bogdarina


title: H3K27me3 in four squamous cell carcinoma cell lines

city: Ann Arbor

first: Maureen

middle: A

last: Sartor

state: MI

address: 2017 Palmer Commons Bldg., 100 Washtenaw Ave

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan

summary: ChIP-Seq for H3K27 trimethylation was performed for two HPV-positive and two HPV-negative squamous cell carcinoma cell lines. The data served two purposes. First, the data were used as an example implementation of our novel ChIP-Seq Peak Prioritization pipeline, PePr.  We have developed the PePr pipeline, a ChIP-Seq Peak Prioritization pipeline that accounts for the variation among replicates and peak location relative to a gene. We show, using a transcription factor dataset (which exhibited small variation among samples), that PePr performs favorably compared to commonly used peak callers and that it achieves balanced sensitivity and specificity. We also show, using histone modification data (which exhibited larger variation among samples), that PePr can improve the detection of differential H3K27me3 regions compared with a common current approach. Using data from ChIP-Seq and gene expression experiments performed in parallel on the same samples, we show that the incorporation of functional annotations can improve the prioritization of functional sites. Secondly, the data were used to assess real differences in the genome-wide H3K27me3 profiles between HPV-positive and HPV-negative carcinoma cell lines.  Careful analysis and integration of the data with DNA methylation and gene expression data performed on the same cell lines demonstrated striking differences exist.

overall_design: ChIP-Seq for H3K27 trimethylation was performed for two HPV-positive and two HPV-negative squamous cell carcinoma (SCC) cell lines. Input DNA was also sequenced for each sample to serve as a control. The goal was to determine overall differences in H3K27me3 patterns observed between the HPV-positive and HPV-negative SCC cell lines.

first: Yu-Hsuan

first: Yanxiao

last: Zhang

first: Laura

last: Rozek


title: The transcription factor GATA6 allows self-renewal of colon adenoma stem cells by repressing BMP gene expression

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

overall_design: Refer to individual Series


title: Analysis of the Epigenomic and Transcriptional Landscapes during mammalian spermatogenesis [sperm; RNA-seq]

status: Public on May 19 2014

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: Adult germline stem cells (AGSCs) are multifunctional - they must self renew, maintain genome pluripotency, and prepare for gametogenesis – which involves meiotic and chromatin repackaging phases. To better understand AGSCs and gametogenesis, we derived high-resolution profiles of transcription, DNA methylation, 5hmC, and multiple histone modifications at key stages. First, AGSCs display chromatin ‘poising’ of enhancers and promoters of genes utilized in embryo development. Second, the pluripotency network in AGSCs is remarkably distinct from ESCs - lacking Nanog, Sox2, or Prdm14 expression.  Third, spermatogenesis involves stage-specific transcription and distinctive chromatin dynamics, but virtually no changes in DNAme.  Surprisingly, we observe co-incidence of RNA polymerase II, high H3K4me3, and DNA methylation at 20-35% of genes transcribed during gametogenesis - including piRNA clusters - but often observe attendant promoter 5hmC.  Our work reveals key differences between AGSCs and other germ/stem cells, and reveals both logical and unexpected chromatin-transcription relationships accompanying germline developmental transitions.

overall_design: mRNA and small RNA profiles of human sperm generated by deep sequencing using Illumina HiSeq 2000 and Illumina Genome Analyzer II.

first: Sue

last: Hammoud


title: Analysis of the Epigenomic and Transcriptional Landscapes during mammalian spermatogenesis [sperm; ChIP-seq]

overall_design: Examination of 3 different histone modifications in human sperm


title: A global non coding RNA system modulates fission yeast protein levels in response to stress

city: Manchester

first: Hui Sun

last: Leong

address: Wilmslow Road

department: The University of Manchester

institute: Cancer Research UK Manchester Institute

summary: Mitogen Activated Protein Kinase (MAPK) signaling cascades transduce information arising from events external to the cell, such as environmental stresses, to a variety of downstream effectors and transcription factors. The fission yeast stress activated MAP kinase (SAPK) pathway is conserved with the p38 and JNK pathways in humans, and comprises the MAPKKKs Win1, Wis4, the MAPKK Wis1, and the MAPK, Sty1. Sty1 and its main downstream effector Atf1 regulate a large set of core environmental stress response genes. The fission yeast genome encodes three other ATF proteins: Atf21, Atf31 and Pcr1. Among these, atf21 is specifically induced under conditions of high osmolarity. We have therefore instigated a programme to investigate the role played by non coding RNAs (ncRNAs) in response to osmotic stress challenge in wild type and atf21Δ cells. By integrating global proteomics and RNA sequencing data, we identified a systematic program in which elevated antisense RNAs arising both from ncRNAs and from 3'-overlapping convergent gene-pairs is directly associated with substantial reductions in protein levels throughout the fission yeast genome. We also found an extensive array of ncRNAs with trans associations that have the potential to influence different biological processes and stress responses in fission yeast, suggesting ncRNAs comprise additional components of the SAPK regulatory system.

overall_design: Global transcription profiles of fission yeast wild type (WT) and atf21Δ (atf21del) strains over an osmotic stress time course following treatment with 1M sorbitol at 0, 15, 30, 60, 120 and 180 mins. Strand-specific single end sequencing of total RNA was performed in biological triplicates on the Applied Biosystems SOLiD 5500xl Genetic Analyzer System.

first: Hui-Sun

first: Keren

last: Dawson

first: Chris

last: Wirth

first: Yaoyong

last: Li

first: Yvonne

last: Connolly

first: Duncan

middle: L

last: Smith

first: Caroline

last: Wilkinson

first: Crispin

last: Miller


title: Impact of nuclear Piwi elimination on chromatin state in Drosophila melanogaster ovaries

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

institute: University of Geneva

summary: The piRNA-interacting Piwi protein is involved in transcriptional silencing of transposable elements in ovaries of D. melanogaster. Here we characterized the genome-wide effect of nuclear Piwi elimination on the presence of the heterochromatic H3K9me3 mark and HP1a, as well as on the transcription-associated mark H3K4me2. Our results demonstrate that a significant increase in the H3K4me2 level upon nuclear Piwi loss is not accompanied by the alterations in H3K9me3 and HP1a levels for several germline-expressed transposons, suggesting that in this case Piwi prevents transcription by a mechanism distinct from H3K9 methylation. We found that the targets of Piwi-dependent chromatin repression are mainly related to the elements that display a higher level of H3K4me2 modification in the absence of silencing, i.e. most actively transcribed elements. We also show that Piwi-guided silencing does not significantly influence the chromatin state of dual-strand piRNA-producing clusters. In addition, host protein-coding gene expression is essentially not affected due to the nuclear Piwi elimination, but we noted an increase in small nuclear spliceosomal RNAs abundance and propose Piwi involvement in their posttranscriptional regulation. Our work reveals new aspects of transposon silencing in Drosophila, indicating that transcription of transposons can underpin their Piwi dependent silencing, while canonical heterochromatin marks are not obligatory for their repression.

overall_design: Examination of histone modifications in ovaries from two different fly lines- piwiNt/piwi2 (mutant) and piwi/+ (wildtype)

first: Mikhail

middle: S

last: Klenov

first: Sergey

last: Lavrov

first: Alina

middle: P

last: Korbut

first: Anastasia

middle: D

last: Stolyarenko

first: Evgeny

last: Yakushev

first: Michael

last: Reuter

first: Vladimir

last: Gvozdev


title: TET1-mediated hydroxymethylation facilitates hypoxic gene induction in neuroblastoma

city: Chicago

first: Christopher

last: Mariani

state: IL

institute: University of Chicago

summary: Analysis of 5-hydroxymethylcytosine changes in hypoxia in neuroblastoma cells

overall_design:
5-hmC distribution was analyzed from cells exposed to hypoxia (1% O2) or normoxia (20% O2); mRNA was sequenced in parallel for expression analysis.
RNA-seq was done using NBL-WN cells, hMe-SEAL experiment was done using NBL-WN cells and SK-N-BE(2) cells

first: Lucy

last: Godley


title: Eic1 links Mis18 with the CCAN/Mis6/Ctf19 complex to promote CENP-A assembly

city: Edinburgh

first: Nicholas

last: Toda

state: Midlothian

address: 6.34 Michael Swann Building

department: Institute of Cell Biology

institute: University of Edinburgh

summary: CENP-A chromatin  the foundation for kinetochore assembly in all eukaryotes. CENP-A is incorporated outside of S phase and depends on its chaperone HJURPScm3, and Mis18 in vertebrates and fission yeast. The recruitment of Mis18 and HJURPScm3 to centromeres is cell cycle regulated. Vertebrate Mis18 associates with Mis18BP1KNL2 and RbAp46/48Mis16/Hat2.  Mis18BP1KNL2 is critical for the recruitment of Mis18 and HJURPScm3 to vertebrate centromeres. However, no ortholog of Mis18BP1KNL2 has been identified in fission yeast, consequently it remains unknown how the key Cnp1CENP-A loading factor Mis18 is recruited. We identify two novel Mis18-interacting proteins (Eic1 and Eic2) in fission yeast.  Our analyses show that Eic1 and Eic2 are components of a Mis18 complex. Eic1 is essential to maintain normal Cnp1CENP-A levels at centromeres and therefore is crucial for kinetochore integrity whereas Eic2 is dispensable. Eic1 also associates with components of the large constitutive CCAN/Sim4/Ctf19 complex. Our findings suggest that Eic1 is the functional counterpart of Mis18BP1KNL2 and acts as a link with constitutive kinetochore components to allow the temporally regulated recruitment of the Mis18 Cnp1CENP-A loader.

overall_design: 100bp paired end ChIP-Seq analysis of GFP tagged Eic1, Eic2, Scm3, and Mis18 with sonicated whole cell extract input DNA in asynchornous Schizosaccharomyces pombe cells.

first: Lakxmi

last: Subramanian

first: Juri

last: Rappsilber

first: Robin

last: Allshire


title: Analysis of the Epigenomic and Transcriptional Landscapes during mammalian spermatogenesis [ChIP-seq]

first: Diana

last: Low

overall_design: Examination of 7 different histone modifications and 5hMC in 4 different cell types

middle: H

first: Sue

last: Hammoud


title: Analysis of the Epigenomic and Transcriptional Landscapes during mammalian spermatogenesis [RNA-seq]

overall_design: mRNA profiles of 8-week old wild type (WT) mice were generated by deep sequencing, in quadruplicate, using Illumina HiSeq 2000 and Illumina Genome Analyzer II.


title: Analysis of the Epigenomic and Transcriptional Landscapes during mammalian spermatogenesis [sperm; Bisulfite-Seq]

overall_design: Methylation profiles of human sperm were generated by bisulfite sequencing using Illumina HiSeq 2000.


title: Chromatin and Transcription Transitions of Mammalian Adult Germline Stem Cells and Spermatogenesis

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

relation:
SuperSeries of: GSE49621
SuperSeries of: GSE49622
SuperSeries of: GSE49623
SuperSeries of: GSE57095
SuperSeries of: GSE57096
SuperSeries of: GSE57097

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Large numbers of putative miRNAs originate from DNA transposons and are coincident with a large species radiation in bats.

city: Mississippi State

first: neal

last: platt

address: 32 Creelman St.

institute: Mississippi State Univeristy

summary: Vesper bats (family Vespertilionidae) experienced a rapid adaptive radiation beginning around 36 mya that resulted in the second most species rich mammalian family.  Coincident with that radiation was an initial burst of DNA transposon activity that has continued into the present.  Deep sequencing of small RNAs from the vespertilionid, Eptesicus fuscus, as well as dog and horse revealed that substantial numbers of novel bat miRNAs are derived from DNA transposons unique to vespertilionids.  In fact, 35.9% of Eptesicus-specific miRNAs derive from DNA transposons compared to 2.2 and 5.9% of dog- and horse-specific miRNAs, respectively and targets of several miRNAs are identifiable.  Timing of the DNA transposon expansion and the introduction of novel miRNAs coincides remarkably well with the rapid diversification of the family Vespertilionidae. We suggest that the rapid and repeated perturbation of regulatory networks by the introduction of many novel miRNA loci was a factor in the rapid radiation.

sample_organism:
Canis lupus familiaris
Equus caballus
Eptesicus fuscus

overall_design: A testicular tissue sample from dog, horse, and two different Eptesicus fuscus individuals. Four samples total.

first: Roy

middle: N

last: Platt

last: Vandewege

first: Colin

last: Kern

first: Carl

last: Schmidt

first: Federico

middle: G

last: Hoffmann

first: David

last: Ray


title: MicroRNAs Shape Circadian Hepatic Gene Expression on a Transcriptome-Wide Scale

city: Lasuanne

last: Gatfield

address: UNIL CIG

department: CIG

institute: University of Lausanne

summary:
Introduction: A considerable proportion of mammalian gene expression undergoes circadian oscillations. Post-transcriptional mechanisms likely make important contributions to mRNA abundance rhythms.
Aim: We have investigated how microRNAs contribute to core clock and clock-controlled gene expression using mice in which microRNA biogenesis can be inactivated in the liver.
Results: While the hepatic core clock was surprisingly resilient to microRNA loss, whole transcriptome sequencing uncovered widespread effects on clock ouput gene expression. Cyclic transcription paired with microRNA-mediated regulation was thus identified as a widespread phenomenon that affected up to 30% of the rhythmic transcriptome and served to post-transcriptionally adjust the phases and amplitudes of rhythmic mRNA accumulation. However, only a few mRNA rhythms were actually generated by microRNAs. Finally, we pinpoint several microRNAs predicted to act as modulators of rhythmic transcripts, and identify rhythmic pathways particularly prone to microRNA regulation.
Conclusion: Our study provides a comprehensive analysis of miRNA activity in shaping hepatic circadian gene expression and can serve as a valuable resource for further investigations into the regulatory roles that miRNAs play in liver gene expression and physiology.

overall_design: RNA-Seq of rRNA-depleted total RNAs from two independent full time series around-the-clock of Dicer knockout and control mouse livers

first: Ngoc

last: Du

first: Alaaddin

last: Arpat

first: Mara

last: De Matos