title: Illumina miRNA profiles with anatomical study revealed involvement of miR397a in Citrus adaptation to long-term B-toxicity via modulating secondary cell wall biosynthesis

city: Fuzhou

first: Chen

last: Lisong

address: Shangdian street NO.15

institute: Fujian Agriculture and Forestry University

summary: Our previous studies indicated that long-term B-toxicity was mainly limited to leaves of Citrus species; alternations of cell wall structure in vascular bundles were involved in tolerance to B-toxicity. Here, miRNAs and their expression pattern were first identified from B-treated Citrus sinensis (tolerant) and C. grandis (intolerant) leaves with high-throughput sequencing in order to identify miRNAs that might be involved in tolerance to B-toxicity. Results: 51 (23 conserved and 28 novel) miRNAs in C. grandis and 20 (6 conserved and 14 novel) in C. sinensis were differentially expressed after B-toxic treatment, respectively. Illumina sequencing results were validated by stem-loop qRT-PCR, and 82.5% qRT-PCR data coincided with those from direct sequencing. Among the differentially expressed miRNAs, miR395a and miR397a were the most significantly up-regulated in B-toxic C. grandis leaves, yet both were down-regulated in B-toxic C. sinensis ones. With modified 5’-RACE, four auxin response factor genes were confirmed as the real targets of miR160a, and two laccase (LAC) genes as those of miR397a, respectively. Localization of cell wall polysaccharides indicated that up-regulation of LAC4 resulted in secondary deposition of cell wall polysaccharides in regions near the pits of vessel elements in C. sinensis, and that down-regulation of both LAC17 and LAC4, via up-regulating their negative regulator miR397a, led to poorly developed vessel elements in C. grandis.Our findings demonstrated that miR397a played a pivotal role in woody Citrus tolerance to B-toxicity by targeting LAC17 and LAC4, of which both were responsible for secondary cell wall synthesis.

sample_organism:
Citrus sinensis
Citrus maxima

platform_organism:
Citrus sinensis
Citrus maxima

overall_design: Four libaries were constructed from C. grandis and C. sinensis leaves  from seedlings treated with 10 (B-sufficient, control) and 400 (B-toxicity) μM boron acid, and sequenced by illumina sequencing.

first: Jing-hao

last: Huang

first: Li-song

last: Chen


title: A streamline experimental and computational approach for inexpensive, accurate, efficient and high-throughput annotation of 5’ and 3’ ends

status: Public on Feb 13 2017

city: Berkeley

first: Shaked

last: Afik

state: CA

address: Stanley Hall

department: Computational Biology Graduate Group

country: USA

institute: UC Berkeley

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We present a simple and straightforward approach for genome-wide annotation of 5' and 3'-RNA ends. Our approach reliably discerns bona-fide PAS from false PAS that arise due to internal poly(A) tracts, a common problem with current PAS annotation methods. We applied our methodology to study the impact of temperature on the Drosophila melanogaster head transcriptome. We found hundreds of previously unidentified TSS and PAS which revealed two interesting phenomena: First, genes with multiple PASs tend to harbor a motif near the most proximal PAS, which likely represents a new cleavage and polyadenylation signal. Second, motif analysis of promoters of genes affected by temperature suggested that BEAF-32 and DREF mediates a transcriptional program at warm temperatures, a result we validated in a fly line where beaf-32 is downregulated.

overall_design: mRNA-ends extracted from fly head were sequenced using our newly developed sequencing methods (5' was sequenced using Exo-seq, 3' was sequenced using RNaseH-seq and 3' end sequencing without RNase H treatment). This data was used to accurately annotate the mRNA ends and to quantify changes in TSS and PAS between temperatures. ChIP-seq H3K4me3 data was generated to validate our 5' results, and 100bp RNaseH- libraries were used to validate classification of peaks to true PAS or internal tracts. Full length RNA-seq data was used to validate the ability of Exo-seq and RNAseH-seq to quantify transcript expression. 3' RNA-seq was used to validate the involvement of BEAF-32 in the transcriptional response to warm temperature in fly heads.

first: Osnat

last: Bartok

first: Manuel

last: Garber

first: Sebastian

last: Kadener


title: Roles of small RNAs in the effects of nutrition on apoptosis and spermatogenesis in the adult testis

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, we tested whether reduction in spermatozoal quality induced by under-nutrition is associated with an increase in germ cell apoptosis and a reduction in spermatogenesis, and whether these effects are regulated by small RNAs. Groups of 8 male sheep were fed for a 10% increase or 10% decrease in body mass over 65 days. Testicular tissue from underfed males had more apoptotic germ cells (TUNEL assay; P < 0.05) and greater (P < 0.05) levels of expression of apoptosis-related genes than well-fed males. We identified 44 miRNAs and 35 piRNAs that were differentially expressed in well-fed and underfed males (FDR < 0.05) and found that they were predominantly related to development of the reproductive system, apoptosis (miRNAs), or sperm production and quality (piRNAs). Furthermore, experimental validation showed that novel-miR-144, a homologue of miR-98, would target three apoptotic genes (TP53, CASP3, FASL). The proportion of miRNAs as a total of small RNAs was greater in well-fed males than in underfed males (P < 0.05) and was positively correlated with the proportion of piRNAs in well-fed males (r = 0.8, P < 0.05) and underfed males (r = 0.8, P < 0.05). We conclude that the reductions in spermatozoal quality induced by under-nutrition are due, at least partly, to increased germ cell apoptosis and to changes in the expression of miRNAs and piRNAs.

overall_design: Two groups of 8 male sheep were fed for a 10% increase or 10% decrease in body mass over 65 days, and the small RNA expression was profiled.

first: Yongjuan

last: Guan


title: Effect of thermoneutral housing on non-alcoholic fatty liver disease in mice

status: Public on Feb 12 2017

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary:
Purpose: To identify the impact of thermoneutral housing as opposed to standard housing on gene expression profiles in the mouse peripheral blood mononuclear cells (PBMCs), focusing on proinflammatory immune responses and high-fat diet induced non-alcoholic fatty liver disease pathogenesis.

Methods: Expression profiles from PBMCs collected from C57Bl6 mice fed chow or high-fat diet for 8 weeks, following 2 weeks at either standard or thermoneutral housing conditions. Sequencing was performed in duplicate, the Illumina HiSeq 2500.  Transcripts that passed quality filters were analyzed at the gene level, using Strand NGS for accurate alignment and quantification.

Results: We mapped approximately 20million reads per sample to the mm10 genome using annotations produced by Ensembl, which represented 36186 transcripts.  Approximately 14000 genes exhibited reasonable expression in at least one experimental condition. The primary focus was the effect of housing temperature while holding diet consistent (i.e. thermoneutral vs standard, both on high-rat diet), where ~2700 genes exhibited differential regulation.

Conclusions: We present the transcriptomic profile of PBMCs from mice fed chow of high-fat diets, following either standard or thermoneutral housing.  We obseve an augmented proinflammatory immune response.

overall_design: PBMC expression profiles were characterized following eight weeks of chow or high-fat diet, following two weeks of standard or thermoneutral housing.

first: Senad

last: Divanovic

first: Daniel

last: Giles


title: ChIP-Seq data of the Streptomyces venezualae protein Sven6563 (RsrR)

city: Norwich

first: John

middle: Tyson

last: Munnoch

address: Norwich Research Park

department: Schol of Biological Sciences

country: United Kingdom

institute: University of East Anglia

summary: We report the results of ChIP-Seq experiment investigating the Rrf2 family transciptional regulator RsrR (putatively name Redox sensitive response regulator). The experiment utilized an in trans copy of rsrR with an N-terminal 3xFlag tag encoded on the plasmid pMS82 (containing a phiBT1 integration site). The experiment utilized beads associated with anti-flag antibodies, specific for the Flag tagged protein and a WT host strain. We report >600 target binding sites for the RsrR regulon encompassing a broad range of functional targets with specific reference to those associate with NADPH and NADH metabolism and synthesis.

overall_design: WT vs RsrR::apr mutant with an in trans 3xFlag tagged copy of RsrR. Due to the use of strain independent antibodies there is no clean negative control (as would be found with WT using mono/polyclonal antibodies specific to the WT protein.

middle: T


title: Lineage-specific genes are prominent DNA damage hotspots during leukemic transformation of B-cell precursors

city: London

first: Niklas

last: Feldhahn

address: The Commonwealth Building, Hammersmith Hospital, Du Cane Road

department: Department of Medicine

institute: Imperial College London

summary: In human leukemia, lineage-specific genes represent predominant targets of deletion, with lymphoid-specific genes frequently affected in lymphoid leukemia and myeloid-specific genes in myeloid leukemia. To investigate the basis of lineage-specific alterations, we analyzed global DNA damage in primary B-cell precursors expressing leukemia-inducing oncogenes by ChIP-Seq. We identified >1000 sensitive regions, of which B-lineage-specific genes constitute the most prominent targets. Identified hotspots at B-lineage genes relate to DNA-DSBs, affect genes that harbor genomic lesions in human leukemia, and associate with ectopic deletion in successfully transformed cells. We further show that most identified regions overlap with gene bodies of highly expressed genes, and that induction of a myeloid lineage phenotype in transformed B-cell precursors promotes de novo DNA damage at myeloid loci. Hence, we demonstrate that lineage-specific transcription predisposes lineage-specific genes in transformed B-cell precursors to DNA damage, which is likely to promote the frequent alteration of lineage-specific genes in human leukemia.

overall_design: ChIP-seq of serine 139-phosphorylated H2AX (gH2AX) and lysine 27 acetylated H3 (H3K27ac) under BCR-ABL1, C-MYC, and BCR-ABL1 +/-CEBPA (DOX) expressing conditions with input, isotype and empty vector controls. BCR-ABL1 and C-MYC gH2AX ChIPseq data are repeated in duplicate, all others are single replicates. RNA-seq was additionally performed on BCR-ABL1, C-MYC and EV expressing cells in duplicate.

first: Bryant

last: Boulianne

first: Mark

middle: E

last: Robinson

first: Philippa

middle: C

last: May

first: Leandro

last: Castellano

first: Kevin

last: Blighe

first: Jennifer

last: Thomas

first: Alistair

last: Reid

first: Markus

last: Müschen

first: Jane

middle: F

last: Apperley

first: Justin

last: Stebbing


title: ChIP-exo data of the Streptomyces venezualae protein Sven6563 (RsrR)

summary: We report the results of ChIP-Seq experiment investigating the Rrf2 family transciptional regulator RsrR (putativeily name Redox sensitive response regulator).  The experiment utilised an in trans copy of rsrR with an N-terminal 3xFlag tag encoded on the plasmid pMS82 (containing a phiBT1 integration site).  The experiment utilised beads associated with anti-flag antibodies, specific for the Flag tagged protein and a WT host strain.  Exo nuclease treatment was carried prior to immunoprecipitation to improve the resolution of the binding site.  We report >600 target binding sites for the RsrR regulon encompasing a broad range of functional targets with specific refernce to those associate with NADPH and NADH metabolism and synthesis.

overall_design: WT vs RsrR::apr mutant with an in trans 3xFlag tagged copy of RsrR.  Due to the use of strain independent antibodies there is no clean negative control (as would be found with WT using mono/polyclonal antibodies specific to the WT protein.   Exonuclease treatment and processing post lysis and sonication was carrid out by peconicgenomics (http://peconicgenomics.com/science.html) Rhee, H-S., and Pugh, B.F. (2012) Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature, AOP Jan. 18. Rhee, H-S., and Pugh, B.F. (2011) Comprehensive genome-wide protein-DNA interactions detected at single nucleotide resolution. Cell, 147:1408-19.


title: Comparison of cerebellum between High Runner and Control mouse genotypes in Free or Blocked from Wheel running environments

city: Urbana

first: Sandra

last: Rodriguez Zas

state: IL - Illinois

address: 1207 W. Gregory Dr.

institute: University of Illinois at Urbana

summary: The goals of this study were: 1) to compare the cerebellum transcriptome and associated networks of one of the High Runner mouse lines relative to mice from a control line and, 2) to evaluate the modulation of potential transcriptome differences between genotypes by the environmental opportunity for physical activity.

overall_design: At approximately 6 weeks of age, 8 mice from a High Runner line and 8 mice from a Control line were caged individually with free access to wheel for 7 days. On day 7, half of the mice from each genotype were blocked from entering the running wheel.  Samples were profiled using paired-end RNA sequencing


title: Connexin 32-mediated cell-cell communication is essential for hepatic differentiation from human embryonic stem cells

city: Beijing

first: Jinhua

last: Qin

address: Taiping Road

country: China

institute: Beijing Institute of Transfusion

summary: Gap junction-mediated cell-cell interactions are highly conserved and play essential roles in cell survival, proliferation, differentiation and patterning. We report that Connexin 32 (Cx32)-mediated gap junctional intercellular communication (GJIC) is necessary for human embryonic stem cell-derived hepatocytes (hESC-Heps) during step-wise hepatic lineage restriction and maturation. Vitamin K2, previously shown to promote Cx32 expression in mature hepatocytes, up-regulated Cx32 expression and GJIC activation during hepatic differentiation and maturation, resulting in significant increases of hepatic markers expression and hepatocyte functions. In contrast, negative Cx32 regulator 2-aminoethoxydiphenyl borate blocked hESC-to-hepatocyte maturation and muted hepatocyte functions through disruption of GJIC activities. Dynamic gap junction organization and internalization are phosphorylation-dependent and the p38 mitogen-activated protein kinases pathway (MAPK) can negatively regulate Cxs through phosphorylation-dependent degradation of Cxs. We found that p38 MAPK inhibitor SB203580 improved maturation of hESC-Heps correlating with up-regulation of Cx32; by contrast, the p38 MAPK activator, anisomycin, blocked hESC-Heps maturation correlating with down-regulation of Cx32. These results suggested that Cx32 is essential for cell-cell interactions that facilitate driving hESCs through hepatic-lineage maturation. Regulators of both Cx32 and other members of its pathways maybe used as a promising approach on regulating hepatic lineage restriction of pluripotent stem cells and optimizing their functional maturation.

overall_design: Human embryonic stem cells (hESCs) were differentiated to hepatocytes with SB203580(SB) and Vitamin K2 (VK2). Primary human hepatocytes (PHHs)were isolated from adult liver tissues and fetal human hepatocytes (FHHs) were isolated from aborted fetal liver. We used RNA sequencing to detail the global gene expression profile of ESCs-derived hepatocytes with the treatment of SB or VK2, untreated control (Ctrl), PHHs and FHHs to delineate the difference of these cells.

first: Wei

last: Zhu

first: Zhenbo

last: Liu

first: Yunfang

last: Wang

first: Xuetao

last: Pei


title: Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics and 3D genomics

city: Lausanne

first: Marion

last: LELEU

address: Station 15

country: Switzerland

institute: EPFL

summary: Smith-Magenis syndrome (SMS) is a developmental disability/multiple congenital anomaly disorder resulting from haploinsufficiency of RAI1. It is characterized by distinctive facial features, brachydactyly, sleep disturbances and stereotypic behaviors. We investigated a cohort of 15 individuals with a clinical suspicion of SMS, who showed neither deletion in the SMS critical region nor damaging variants in RAI1. Potentially deleterious variants were identified in nine of these subjects using whole-exome sequencing. Eight of these changes affect KMT2D, ZEB2, MAP2K2, GLDC, CASK, MECP2, KDM5C and POGZ, known to be associated with Kabuki syndrome 1, Mowat-Wilson syndrome, cardiofaciocutaneous syndrome, glycine encephalopathy, mental retardation and microcephaly with pontine and cerebellar hypoplasia, X-linked mental retardation 13, X-linked mental retardation Claes-Jensen type and White-Sutton syndrome, respectively. The ninth individual carries a de novo variant in JAKMIP1, a regulator of neuronal translation that was recently found deleted in a patient with autism spectrum disorder. Analyses of coexpression and biomedical text mining suggest that these pathologies and SMS are part of the same disease network. Further support for this hypothesis was obtained from transcriptome profiling that showed that the expression levels of both Zeb2 and Map2k2 are perturbed in Rai1-/- mice. As an orthogonal approach to potentially contributory disease gene variants, we used chromatin conformation capture to reveal chromatin contacts between RAI1 and the loci flanking ZEB2 and GLDC, as well as between RAI1 and human orthologs of the genes that show perturbed expression in our Rai1-/- mouse model. These holistic studies of RAI1 and its interactions allow insights into SMS and other disorders associated with intellectual disability and behavioral abnormalities. Our findings support a pan-genomic approach to the molecular diagnosis of a distinctive disorder.

overall_design: Examination of 4C-seq interaction profile of the gene RAI1 in 2 different cell lines.

first: Maria

middle: N

last: Loviglio

last: Leleu

first: Alexandre

last: Reymond


title: Regulation of Transcription Factor Yin Yang 1 by SET7/9-mediated Lysine Methylation [GRO-Seq]

city: Ganzhou

first: Wenjuan

last: Zhang

state: Jiangxi

address: No. 23, Qingnian Road

department: First Affiliated Hospital

institute: Gannan Medical University

summary: Yin Yang 1 (YY1) is a multifunctional transcription factor shown to be critical in a variety of biological processes. Although it has been reported to be regulated by multiple types of post-translational modifications (PTMs), whether YY1 is methylated, which enzyme methylates YY1, and hence the functional significance of YY1 methylation remain completely unknown. Here we reported the first methyltransferase, SET7/9 (KMT7), capable of methylating YY1 in vitro and in vivo at two highly conserved lysine (K) residues, K173 and K411, located in two distinct domains, one in the central glycine-rich region and the other in the very carboxyl-terminus. Functional study revealed that SET7/9-mediated YY1 methylation regulated YY1 DNA-binding activity both in vitro and at specific genomic loci in cultured cells. Consistently, SET7/9-mediated YY1 methylation was shown to involve in YY1-regulated gene transcription and cell proliferation. Our findings revealed a novel regulatory strategy, methylation by lysine methyltransferase, imposed on YY1 protein, and linked YY1 methylation with its biological functions.

overall_design: The Gro-seq experiment was designed to reveal the transcriptional targets of YY1.

first: Wen

first: Wen-Juan


title: Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells

city: New Haven

first: Xinghua

last: Pan

state: CT

address: 300 Cedar Street, TAC-S320

department: Department of Genetics

institute: Yale University School of Medicine

type: Methylation profiling by high throughput sequencing

summary: This set of data is for assessing and validation of a novel method, CGI-seq, as described in the corresponding paper, for profiling of single cell CpG methylome. We tested 4 different cell lines (K562, GM12878, 551 K1-iPSC, and Fibroblast ATCC-CCL-110) with a low quantity of cells (LQC, here including 100-cell or 10-cell) and with single cells (SC) separately. Briefly, the protocol include these steps. The intact gDNA of the cell(s) was released. This gDNA (i.e. the TEST sample, but this step was omitted for the Methylation Control or MC sample) was cut with the 1st set of  restriction endonucleases, called RE1, which were sensitive to CpG methylation, and distinguished methylated from unmethylated DNA sequences. Then, each sample, including digested TEST DNAs and intact MC DNA, was immediately amplified by MDA method (or REPLIg kit), in which the methylated DNA sequences were highly efficiently amplified, while unmethylated DNA sequences were depleted. The amplicon was then cut with the 2nd set of restriction endonucleases, called RE2, and the appropriate size (between 50-500bp) of fragments were recovered to generate sequencing library, which was to enrich CpG-rich sequences (especially CpG islands) and improve the sequencing efficiency (reduced representation sequencing). Finally, Next Generation Sequencing (NGS) was performed. The outcome sequencing reads were analyzed with a specially designed algorithms. The result shows the high sensitivity, high reliability, high reproduciblity, and high coverage of the method on profiling the genome-wide CpG methylation pattern for single cells. It is a simple, robust and faithful technology for single cell CpG methylation pattern analysis, enabling unsupervised clustering of single cells basing on genome-wide CpG methylation pattern. This method will be valuable to dissect the subpopulation structure for a cellular population heterogeneous in CpG-methylation pattern.

overall_design: We designed 2 protocols (protocol option 1 - BstUI as RE2, and protocol option2 - ABH as RE2, while other steps were the same) for LQC processing (30 samples with 100Cell or 10cell), and the option 2 above was used for SC (8 samples for K562 and GM12878 separately, totally 16 samples). The corresponding Methylation Controls (MCs, for which no RE1 was applied but all other processes were the same as the TEST) were also generated corresponding to each set of TEST samples. The sequencing data was analyzed, and compared with the published ENCODE data generated with RRBS or Infinium HumanMethylation450 BeadChip methods with bulk cells, for CpG islands, promoters and other informative sequencing fragments. These data were also subject to unsupervised clustering analysis of the cells.

first: Hua-Jun

last: Wu


title: smallRNA-Seq analysis comparing p53-null versus ΔNp63Δ/Δ;p53-null thymic lymphoma tumors

city: Tampa

first: Elsa

middle: Renee

last: Flores

state: FL

address: 12902 USF Magnolia Drive

department: Department of Molecular Oncology

institute: Moffit Cancer Center

summary: We performed a smallRNA-Seq analysis comparing thymic lymphoma tissues from the p53-null (n=4) and ΔNp63Δ/Δ;p53-/- (n=3). Mice at 10 weeks of age were injected with either Ad-mCherry or Ad-CRE-mCherry to delete ΔNp63 in the thymic lmyphomas. We aimed to test by deleting the ΔNp63 in these p53-deficient tumors will mediate tumor regression and analyze the expression profile of the small RNAs

overall_design: Examination of thymic lymphoma tissues in 2 different genotypes (p53-/- vs ΔNp63Δ/Δ;p53-/-)

first: Marco

last: Napoli

middle: R


title: Mouse mammary fibroblast gene expression comparison between nulliparous and involution day 6.

status: Public on Feb 11 2017

city: PORTLAND

first: Qiuchen

last: Guo

state: OREGON

address: 3181 SW SAM JACKSON PARK ROAD

department: CDCB

institute: OHSU

summary: We tested the gene expression difference between PDGFRa+ fibroblasts FACS sorted from nulliparous balb/c mouse mammary glands and 6 days post-weaning mammary glands

overall_design: 2 biological replicates of fibroblasts from nulliparous mammary glands and 3 biological replicates of fibroblasts from 6 days post-weaning mammary glands were used for comparison.

first: Pepper

last: Schedin


title: Interaction with ZMYND11 mediates opposing roles of Ras-responsive transcription factors ETS1 and ETS2

city: North Chicago

first: Josh

last: Plotnik

state: IL

address: 1 North Waukegan Rd, AP10/210A

institute: AbbVie Inc.

summary: Aberrant activation of RAS/MAPK signaling is a driver of over one third of all human carcinomas. The homologous transcription factors ETS1 and ETS2 mediate the activation of gene expression programs downstream of RAS/MAPK signaling. ETS1 is important for oncogenesis in many tumor types. However, ETS2 can act as an oncogene in some cellular backgrounds, and as a tumor suppressor in others, and the molecular mechanism responsible for this cell-type specific function remains unknown. Here, we show that ETS1 and ETS2 regulate a cell migration gene expression program in opposite directions, and provide the first comparison of the ETS1 and ETS2 cistromes. This genomic data, and an ETS1 deletion line are used to show that the opposite function of ETS2 is due to binding site competition and a weaker activation function of ETS2 compared to ETS1. This weaker activation was mapped to the ETS2 N-terminus and a specific interaction with the co-repressor BS69 (ZMYND11). Gene expression data from tumor cohorts was then used to show that BS69 expression level in tumors correlates with oncogenic and tumor suppressive roles of ETS2. Therefore, these data indicate a novel and specific mechanism allowing ETS2 to switch between oncogenic and tumor suppressive functions in a cell-type specific manner.

overall_design:
mRNA profiles of ETS2 knockdown DU145 cells were generated using deep sequencing, in triplicate, using Illumina NextSeq. Knockdowns were stable shRNA expression from a lentiviral construct selected with puromycin.

This series includes re-analysis of three luciferase shRNA samples from GSE59020.

first: Joshua

middle: P

first: Peter

last: Hollenhorst


title: RsrR: a novel redox sensitive Rrf2 family transcription factor in Streptomyces venezuelae

first: John

last: Munnoch

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

sample_organism:
Streptomyces venezuelae
Streptomyces venezuelae ATCC 10712

overall_design: Refer to individual Series


title: PRC2 facilitates the regulatory topology required for poised enhancer function during pluripotent stem cell differentiation [RNA-seq EED]

city: Koeln

first: Milos

last: Nikolic

state: Nordrhein-Westfalen

address: Robert Koch Str. 21

country: Germany

institute: Center for Molecular Medicine Cologne

summary: Poised enhancers marked by H3K27me3 in pluripotent cells were previously proposed to facilitate the establishment of somatic expression programs upon embryonic stem cell (ESC) differentiation. However, the functional relevance and mechanism of action of poised enhancers remain unknown. Here, we use genetic deletions to demonstrate that poised enhancers are necessary for the induction of major anterior neural regulators. Mechanistically, poised enhancers enable RNA Polymerase II recruitment to their cognate promoters upon differentiation. Interestingly, poised enhancers already establish physical interactions with their target genes in ESC in a Polycomb repressive complex 2 (PRC2) dependent manner. Loss of PRC2 led to neither the activation of poised enhancers nor the induction of their putative target genes in undifferentiated ESC. In contrast, loss of PRC2 severely and specifically compromised the induction of major anterior neural genes representing poised enhancer targets. Overall, our work illuminates a novel function for polycomb proteins, which we propose facilitate neural induction by providing major anterior neural loci with a permissive regulatory topology.

overall_design: mRNA profiles were generated by RNA-seq from mESC and AntNPC for the following lines: WT mESC, WT AntNPC, EED-/- mESC and EED-/- AntNPC

first: Sara

last: Cruz-Molina

first: Alvaro

last: Rada-Iglesias


title: PRC2 facilitates the regulatory topology required for poised enhancer function during pluripotent stem cell differentiation [ChIP-seq]

overall_design: Genome-wide binding profiles for the co-activator p300 and various histone modifications were investigated in mouse embryonic stem cells (mESC) and AntNPC (anterior neural progenitors).


title: PRC2 facilitates the regulatory topology required for poised enhancer function during pluripotent stem cell differentiation [4C-seq]

overall_design: 4C-seq interaction profiles were generated in WT mESC, WT AntNPC and EED-/- mESC using several selected poised enhancers as viewpoints.


title: The identification of known and novel microRNAs and their targets in peach (Prunus persica) fruit by high-throughput sequencing

city: Nanjing

first: ZHANG

last: chunhua

address: Xuanwu road

institute: Jiangsu Academy of Agricultural Sciences

summary: In this study we performed a comprehensive analysis of miRNAs and their targets from peach fruit tissue using high-throughput sequencing combined with bioinformatics analysis and molecular experiments. A total of 557 known miRNAs and 275 putative novel miRNAs were predicted. 3959 and 1614 target genes for the 349 known and 193 novel miRNAs, respectively, were predicted where a single target gene could be targeted by different miRNAs, and a single miRNA can also have a large number of target genes. Proteins predicted to be targeted by the miRNAs in this study encompass a wide range of transcription factors and are involved in biological processes and pathways ranging from development, metabolism, and stress responses to signal transduction. Thirty conserved miRNAs and 27 novel miRNAs exhibited differential expression profiles in three tissues of peach, with expression patterns of some miRNAs appearing to be tissue or developmental-stage specific. A total of 115 and 101 target genes were identified to be cleaved by 61 known miRNAs and 27 novel miRNAs through degradome sequencing, respectively. These miRNAs induce cleavage of their targets precisely at the position between nucleotides 10 and 11 of the miRNA sequence from 5’ to 3’ end. The findings of this study provide an important basis for the analysis of miRNAs, their targets and the functions of these targets in peach fruit.

overall_design: Equal amounts of total RNA from fruits at each of the different growing stages (35, 55, 75, 90, 105 days after full bloom) were mixed and deep sequenced, one repeat, using the Illumina Solexa platform

first: Chunhua

first: Mingliang

last: Yu


title: PRC2 facilitates the regulatory topology required for poised enhancer function during pluripotent stem cell differentiation


title: dRNA-seq data of the Streptomyces venezualae WT and mutant (sven6563::apr (rsrR::apr)) strains at time point 16 h

summary: We report here the sequence results of S. venezualae WT and the mutant sven6563::apr (rsrR::apr) strains at 16h and the differential expression profile of WT vs. Mutant.  Additionally we report the resulting TSSAR analysis of the transcriptional start site information for the genes expressed at this time point.

overall_design: WT vs RsrR::apr mutant at 16h.  Total RNA was isolated and processed by vertis Biotechnologie AG.  Ribodepletion was carried out to remove ribosomal RNA, the sample split in two, 1 had tex treated to remove processed RNA the other not.  EAch was then converted to cDNA and sequenced.  WT vs Mutant was compared at 16h while the others were used for the purposes of TSS identification.


title: A RUNX2-mediated Epigenetic Regulation of the Survival of p53 Defective Cancer Cells

city: Bethesda

first: Jing

last: Huang

state: MD

institute: National Cancer Institute

summary: The goal is to identify transcripts that are regulated by RUNX2 in SAOS2 cells.

overall_design: SAOS2 cells were transduced with lentiviruses expressing shLuc, shRUNX2_3 and shRUNX2_4 for 4 days followed by 2ug/ul puromycin selection to remove untransduced cells. A no-virus control was included to monitor the transduction efficiency. These control cells died after 2 days of puromycin selection. The lentivirally transduced cells were more than 80% survived, which indicates a high transduction efficiency. After four more days in puromycin, SAOS2 cells were harvested and subjected to total RNA extraction. 1ug total RNA were used to perform RNA-seq.


title: Transcriptome Profile of Near-isogenic Soybean Lines for α-Subunit Deficiency during Seed Maturation

city: Harbin

first: Liu

last: Shanshan

state: Heilongjiang

address: 59 Mucai Street

department: College of Agriculture

institute: Northeast Agricultural University

summary: To identify α-null-related transcriptional changes, the gene expressions of cgy-2-NIL and its recurrent parent DN47 were compared using Illumina high-throughput RNA-sequencing on samples at 25, 35, 50, and 55 days after flowering (DAF). Seeds at 18 DAF served as the control.

overall_design: Compare gene quantity and expression between the cgy-2-NIL and DN47 in five stages of soybean seeds collected at 18, 25, 35, 50, and 55 day after flowering

first: Bo

last: Song


title: Single Cell Transcriptome Conservation in Cryopreserved Cells and Tissues

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

country: Spain

institute: Centro Nacional de Análisis Genómico

summary: Sample preservation method that maintains transcripts in viable single cells and so allows to disconnect time and place of sampling from subsequent processing steps.

sample_organism:
Homo sapiens
Canis lupus familiaris
Mus musculus

overall_design: Single cell transcriptomes from 1,486 fresh and conserved cells from human blood, ovarian and lung tumor xenografts, mouse colon tissue, and human, mouse and canine cell cultures.

last: Rodríguez-Esteban

first: Holger

last: Heyn


title: Comparison of gene expression between MOMT4 transgenic and wild type control poplar

city: Upton

first: Chang-Jun

last: Liu

state: NY

address: 50 Bell Avenue

department: Biology Department

institute: Brookhaven National Lab

summary: Purpose: This experiment was designed to use RNA-seq approach to provide a priliminary examination whether or not overexpression MOMT4 in hybrid aspen disturbes the expression of lignin and other cell wall biosynthetic genes, followed by extensive qRT-PCR analysis. Our study showed that expression of MOMT4 resulted in a little disturbance on the gene expression involved in lignin biosynthesis.

overall_design: The 1st to 15th internodes from the top of 2-month-old hybrid aspen (gray poplar, Populus tremula x Populus alba) stems of MOMT4-0 transgenic and control lines were harvested. After removing their barks, were immediately frozen in liquid nitrogen.  About 100 mg stem samples pooled from 2~3 individual transgenic and control plants, respectively, were grounded to fine powder under liquid nitrogen. Total RNAs were extracted using Qiagen RNeasy Plant Mini Kit. The assessment of purity and concentration of each RNA sample, and the strand-specific RNA-Seq library construction were conducted by using the Polar Genomics (Ithaca, NY) service. Sequencing was done using the Illumina HiSeq2500 platform via 50-bp single-end reads of multiplexed RNA samples.

first: Huijun

last: Yang


title: Comprehensive analysis of ABA effects on ethylene synthesis and signaling during tomato fruit ripening

city: Hangzhou

first: Wangshu

last: Mou

state: Zhejiang

address: Yuhangtang Road 866

department: College of Bio-engineering and Food Science

institute: Zhejiang University

summary:
Purpose: The goals of this study was to provide genome-wide data to investigate the molecular mechanism of the interaction between ABA and ethylene during tomato fruit ripening
Methods: Regarding the fruits sampled at the 9th day as a well-characterized stage, we used RNA-seq to conducted a comparative analysis of exogenous ABA and NDGA effects on all components involved in biosynthesis and signaling of ethylene and ABA.The identified crucial genes in response to ABA were further performed a ripening time-course analysis by RT-PCR. In addition, we also detected how ethylene affected ABA action at the onset of ripening by treating the fruits with 1-MCP immediately after ABA application.
Results: Our study not only illustrated how ABA regulated itself at the transcription level, but also elucidated that ABA can facilitate ethylene production and response by regulating some crucial genes such as LeACS4, LeACO1 and LeETR6 etc. In addition, investigation on the fruits treated with 1-MCP immediately after ABA exposure revealed that ethylene might be essential for the induction of ABA biosynthesis and signaling at the onset of fruit ripening. Furthermore, some specific transcription factors (TFs) known as regulators of ethylene synthesis and sensibility (e.g. MADS-RIN, TAGL1, CNR and NOR etc.) were also observed to be ABA responsive, which implied that ABA influenced ethylene action possibly through the regulation of these TFs expression.
Conclusions: Our data suggested that ABA may act as an upstream regulator to modulate ethylene synthesis and signal transduction, which consequently influenced the ripening process. This comprehensive survey not only demonstrated how ABA regulated itself at the molecular level, but also indicated that ABA had a positive impact on ethylene production and action by regulating key genes such as LeACS2, LeACS4, LeACO1 and LeETR6. Besides, our results also revealed that ethylene might be of great importance to induce ABA accumulation and response at the onset of ripening. Moreover, many ripening related TFs, such as MADS-RIN, TAGL1, CNR and NOR, were observed to be affected by ABA, implying that a TF-mediated manner may be involved in the interaction between ABA and ethylene. This study extends our understanding of the mechanism that how ABA-triggered tomato fruit ripening, and illustrates the complex mechanism of reciprocity between ABA and ethylene at the transcription level.

overall_design: Examination of genome-wide gene expression changes of the 9th day tomato fruits treated with ABA, NDGA and CK, stored at  20 oC,90% RH in the dark.

first: Tiejin

last: Ying


title: Transcriptomic characterization of transcription activator-like effector nucleases-induced XY dmy- sex reversal female medaka (Oryzias latipes)

city: Wuhan

first: Daji

last: Luo

state: Hubei

address: No.185 Donghudong Road, Wuchang distinct

institute: Wuhan University

summary: We assembled transcription activator-like effector nucleases (TALENs) targeting the DMY gene and generated XYdmy- mutants to investigate gonadal dysgenesis in medaka. RNA-seq generated 157 million raw reads from WT male (WT_M_TE), WT female (WT_F_OV) and XYdmy- female medaka (TA_F_OV) gonad libraries. Differential expression analysis identified 144 up- and 293 downregulated genes in TA_F_OV compared to WT_F_OV, 387 up- and 338 downregulated genes in TA_F_OV compared to WT_M_TE.

overall_design: mRNA profiles of 90-day old wild type (WT) and TALENs induced XY dmy- sex reversal female (TA) medaka were generated by deep sequencing, using Illumina HiSeqTM 2000.

first: Wei

last: Hu


title: Comparison of WapCre;Rank;Brca1;p53 and WapCre;Brca1;p53 mouse primary mammary tumors

city: Vienna

first: Verena

last: Sigl

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechnology GmbH

summary: The transcriptional profile of WapCre;Rank;Brca1;p53 and WapCre;Brca1;p53 mouse primary mammary tumor cells was determined by mRNA sequencing and uncovered differences in their molecular signatures including genes involved in oncogenesis, basic metabolism, RNA metabolism, or the regulation of mammary stem cells.

overall_design: Transcriptome comparison of mouse WapCre;Rank;Brca1;p53 and WapCre;Brca1;p53 primary mammary tumors

first: V

first: J

last: Penninger


title: Antisense transcription predicts a distinct chromatin environment at mammalian promoters

city: RTP

first: Christopher

last: Lavender

state: NC

address: 111 T. W. Alexander Drive

institute: NIEHS

summary: Antisense transcription is common at mammalian promoters.  Previous studies have largely focused on characterizing antisense transcription initiating upstream of gene transcription start sites.  Here, we systematically characterize promoter-proximal antisense transcription downstream of gene transcription starts sites in human T-47D cells, investigating the genomic context of downstream antisense transcription. We find that downstream antisense transcription is widespread, with antisense transcription initiation observed within 2 kb of 28% of gene transcription start sites.  Downstream antisense transcription is correlated with many regulatory features at gene promoters despite not being categorically associated with gene activation or repression.  At the downstream antisense transcription start site, DNA is accessible, is enriched for protein-associated sequences motifs, and is bound by a variety of transcription factors.  Downstream antisense transcription initiates between nucleosomes regularly positioned downstream of gene transcription start sites.  Those nucleosomes between gene and downstream antisense transcription start sites carry histone modifications associated with active promoters, such as H3K4me3 and H3K27ac.  Strikingly, this same region is bound by chromatin remodeling complexes such as HDAC and SWI/SNF. The coincidence of transcription initiation with nucleosomes displaying promoter-associated histone marks underlies an apparent connection between antisense transcription and the chromatin environment at gene promoters. The association of chromatin remodelers at sites of downstream antisense transcription initiation suggests that antisense transcription contributes to the deposition and maintenance of these chromatin features at gene promoters.

overall_design: RNA-seq and Start-seq were used to characterize steady-state transcript levels and transcription initation, respectively, in T-47D cells.  MNase-seq and FAIRE-seq were then performed to assess the chromatin environment at identified transcription start sites.

middle: A

first: Kimberly

last: Cannady

first: Jackson

last: Hoffman

first: Kevin

middle: W

last: Trotter

first: Daniel

last: Gilchrist

first: Brian

middle: D

last: Bennett

first: Adam

middle: B

last: Burkholder

first: Craig

middle: J

last: Burd

first: David

last: Fargo

first: Trevor

middle: K

last: Archer


title: CLIP libraries for SUP-26::FLAG

status: Public on Feb 10 2017

first: Katherine

last: McJunkin

address: 50 South Drive, Building 50 Room 3148

institute: National Institutes of Health

summary: Gene expression in early animal embryogenesis is in large part controlled post-transcriptionally. Maternally-contributed microRNAs may therefore play important roles in early development. We have elucidated a major biological role of the nematode mir-35 family of maternally-contributed, essential microRNAs. We show that this microRNA family regulates the sex determination pathway at multiple levels, acting both upstream and downstream of her-1 to prevent aberrantly activated male developmental programs in hermaphrodite embryos. The predicted target genes that act downstream of the mir-35 family in this process, sup-26 and nhl-2, both encode RNA binding proteins, thus delineating a previously unknown post-transcriptional regulatory subnetwork within the well-studied sex determination pathway of C. elegans. Repression of nhl-2 by the mir-35 family is not only required for proper sex determination but also for viability, showing that a single microRNA target site can be essential. Since sex determination in C. elegans requires zygotic gene expression to read the sex chromosome karyotype, early embryos must remain gender-naïve; our findings show that the mir-35 family microRNAs act in the early embryo to function as a developmental timer that preserves naïveté and prevents premature deleterious developmental decisions.

overall_design: The SUP-26::FLAG strain was generated by knocking-in 3 flag tags at the C terminus of the SUP-26 coding sequence in its endogenous genomic locus using CRISPR/Cas-9. CLIP was performed using an anti-FLAG antibody to affinity purify the tagged SUP-26::FLAG.

first: Victor

last: Ambros


title: Global transcriptional profiling using RNA sequencing and DNA methylation patterns in highly enriched mesenchymal cells from young versus elderly women.

city: Rochester

first: Sundeep

last: Khosla

state: MN

address: 200 1st St SW

department: Endocrinology Research

institute: Mayo Clinic

summary:
Purpose:  Identification of relevant genetic pathways that are altered with aging knowing that the precursors for bone-forming osteoblasts reside in the mesenchymal cell population of bone marrow.
Method: harvested and characterized, without in vitro culture, mesenchymal cells form human bone marrow capable of osteogenic differentiation
Results:  Identification of differentially regulated genes with aging in a highly enriched human bone marrow mesenchymal cell population.
Conclusions:  we have for the first time identified age-related differential gene expression and DNA methylation patterns in a highly enriched human bone marrow mesenchymal cell populationprofiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Examination of gene expression and DNA methylation patterns from a highly enriched bone marrow mesenchymal cell population from young (mean age, 28.7 years) versus old (mean age, 73.3 years) women

first: Matthew

last: Roforth


title: Genome-wide RNA-seq analysis during CRE1-mediated carbon catabolite repression in Trichoderma reesei grown in sophorose

city: Campinas

first: Gabriela

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

summary: The mechanism of carbon catabolite repression (CCR) mediated by CRE1 in Trichoderma reesei emerged as a way to adapt to the environment in which the fungus is found. In situations where there is the presence of readily available carbon sources such as glucose, the fungus activates this mechanism and inhibits the production of cellulolytic complex enzymes to avoid unnecessary energy expenditure. CCR has been well described for the growth of T. reesei in cellulose and glucose, however, little is known about this process when the carbon source available to the fungus is sophorose, one of the most potent inducer of cellulase production. Thus, we performed high-throughput RNA sequencing using the Illumina/HiSeq-2000 to contribute to the understanding of CCR during cellulase formation in the presence of sophorose, by comparing the mutant Δcre1 with its parental strain, QM9414. Of the 9129 genes present in the genome of T. reesei, 184 were up- and 344 down-regulated in the mutant strain Δcre1 compared to QM9414. Genes belonging to CAZy, transcription factors and transporters are among the gene classes that were repressed by CRE1 in the presence of sophorose, most of which was regulated by CRE1 in an indirect way. Overall, there was a similarity in the profile of repressed genes when compared with another inducing carbon source, cellulose. These results contribute to a better understanding of CRE1-meadiated CCR in T. reesei when glucose comes from a potent inducer as sophorose, which can be very useful in improving the production of cellulases by the biotechnology sector.

overall_design: T. reesei (QM9414 and Δcre1) was grown in Mandels-Andreotti medium, supplemented with 1 mM of sophorose. The cultures were incubated on an orbital shaker (200 rpm) at 28°C for 2, 4 and 6 hours using sophorose as carbon source. All experiments were performed in three biological replicates. The resultant mycelia were collected by filtration, frozen and stored at -80°C until RNA extraction. After growth, total RNA was isolated from the mycelia using TRIzol® reagent. RNA-seq experiments were performed by LGC Genomics GmbH (Berlin/Germany) using the platform Illumina/HiSeq2000.

first: Amanda

last: Campos Antonieto

first: Renato

last: Graciano de Paula

first: Lílian

last: dos Santos Castro

first: Rafael

last: Silva-Rocha

first: Roberto

last: do Nascimento Silva


title: Next generation sequencing analyses of transcriptomes of 3T3-L1 adipocytes treated with DF, an anti-obesity multi-herbal composition

city: seoul

first: yoosik

last: yoon

address: Heukseok-street 47,Dongjak-gu

country: South Korea

institute: chungang university

summary: Our study provides detailed analysis of DF-induced transcriptomes generated by RNA-Seq technology. RNA-Seq based transcriptome analyzes would elucidate complex molecular mechanisms of multi-herbal composition like DF

overall_design: mRNA profiles of control 3T3-L1 adipocytes and DF-treated 3T3-L1 adipocytes were analyzed by RNA-Seq. Construction of library was performed using SENSE 3’ mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria), and high-throughput sequencing was performed as single-end 75 sequencing using NextSeq 500 (Illumina, Inc. San Diego, CA, USA)

first: Jaewoong

last: Jang

first: Yoosik

last: Yoon


title: Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.

city: Stockholm

first: S Noushin

last: Emami

address: Svante Arrhenius väg 20C

country: Sweden

institute: Stockholm University

summary: Malaria infection renders humans more attractive to Anopheles gambiae sensu lato mosquitoes than uninfected people. The mechanisms remain unknown. Here, we show that an isoprenoid precursor produced by Plasmodium falciparum, (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), affects A. gambiae s.l. blood meal seeking and feeding behaviors, as well as susceptibility to infection. HMBPP acts indirectly by triggering human red blood cells to increase the release of CO2, aldehydes, and monoterpenes, which together enhance vector attraction, and stimulate vector feeding. When offered in a blood meal, HMBPP modulates neural, antimalarial, and oogenic gene transcription without affecting mosquito survival or fecundity, while in a P. falciparum infected blood meal, sporogony is increased.

overall_design: Differential expression was quantified from whole body of mosquitoes in biological triplicates at 1, 3, 6 and 24 hours post treatment with either RBCs or hmbRBCs.

first: S

first: Bo

last: Lindberg


title: NapA Mediates a Redox Regulation of the Antioxidant Response, Carbon Utilization and Development in Aspergillus nidulans

city: Cuernavaca

first: Veronica

last: Jimenez-Jacinto

state: Morelos

address: Av. Universidad 2001. Col. chamilpa

department: Unidad Universitaria de Secuenciación Masiva y Bioinformática

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

summary: Using transcriptomic analysis we show that transcription factor NapA is required for the regulation of at least 214 genes in intact asexual spores, including ethanol utilization genes alcR, alcA and aldA, and large groups of genes encoding proteins involved in transcriptional regulation, drug detoxification, carbohydrate utilization and secondary metabolism, comprising multiple oxidoreductases, membrane transporters and hydrolases.

overall_design: We compare the transcriptomic profiles of WT and ∆napA intact asexual spores (conidia)

first: Ariann

last: Mendoza-Martínez

first: Jesús

last: Aguirre


title: Histone deacetylase inhibitor MS-275 augments expression of a subset of IFN-γ-regulated genes in Toxoplasma gondii-infected macrophages but does not improve parasite control

city: Göttingen

first: Carsten

last: Lueder

address: Kreuzbergring 57

institute: Institut für Medizinische Mikrobiologie

summary: Toxoplasma gondii is a ubiquitous apicomplexan parasite of mammals and birds and an important pathogen of humans. IFN-g is the major mediator of host resistance against T. gondii but intriguingly, parasite-infected host cells including macrophages are severely impaired to respond to IFN-g due to defective transcriptional activation of target genes. Here, we tested the possibility that the impaired responsiveness of T. gondii-infected macrophages to IFN-g can be restored by inhibiting histone deacetylases (HDACs) using the class I-specific inhibitor MS-275. Treatment of RAW264.7 cells with MS-275 indeed increased MHC class II surface expression in infected and non-infected cells and largely abolished the inhibition of IFN-g-regulated MHC class II expression exerted by T. gondii. Genome-wide transcriptome profiling revealed that MS-275 increased mean mRNA levels of IFN-g-regulated genes particularly in non-infected macrophages. Transcript levels of 33% of IFN-g secondary response genes but only those of a few primary response genes were also increased by MS-275 in T. gondii-infected cells. Importantly, the unresponsiveness of parasite-infected cells to IFN-g was however not abolished by MS-275. Furthermore, MS-275 also up-regulated several anti-inflammatory cytokines or signaling molecules in T. gondii-infected macrophages. It additionally regulated expression of more than 2500 genes in non-infected macrophages expression of which was surprisingly counteracted by prior infection with T. gondii. FACS analysis and immunofluorescence microscopy revealed that MS-275 did not considerably diminish the number of parasite-positive cells or the intracellular replication in macrophages stimulated or not with IFN-g. Thus, a supportive therapy using MS-275 appears inappropriate for treatment of toxoplasmosis.

overall_design: High throughput RNA profiles from IFN-g-activated monocytic cells infected with Toxoplasma gondii and treated with MS-275 and control cells were generated by Illumina sequencing. Five experimental conditions with 2 biological replicates each were analysed.

middle: G

last: Lüder

first: Kristina

last: Sumpf

first: Roswitha

last: Nast

last: Salinas

first: Bryan

last: Downie


title: The flowering-related genes responsible for differences in bolting time between two radish lines

city: Deajeon

first: Won Yong

last: Jung

state: N/A = Not Applicable

address: 125 Gwahak-ro, Yuseong-gu

institute: Korea Research Institute Bioscience and Biotechnology(KRIBB)

summary: To elucidate the molecular mechanisms that determine the differences in flowering times between two radish lines, NH-JS1 (late bolting) and NH-JS2 (early bolting) by high-throughput RNA sequencing analysis. In total, 71,188 unigenes were identified by reference-guided assembly, of which 309, 788, and 980 genes were differentially expressed between the two inbred lines after 0, 15, and 35 days of vernalization, respectively.

overall_design: Examination of different flowering time between two radish inbred lines. Leaves mRNA profiles of 0, 15, 35day old NH-JS1 and 2 radish were generated by deep sequencing, in replicate, using Illumina hiseq2000.

first: Hye

middle: S

last: Cho

first: Won

middle: Y

first: Hyun

last: Park

first: Sang

last: Lee

first: Areum

first: Youn-Sung

last: Kim


title: Evaluation of ccpA deletion on global gene expression of three M serotype strains of group A streptococcus

city: Houston

first: Samuel

last: Shelburne

state: TX

address: 1515 Holcombe Blvd

department: Infectious Diseases

institute: MD Anderson Cancer Center

summary: We sought to determine how deletion of ccpA affects the gene expression profile in three M serotype strains of group A streptococcus

overall_design: There were 6 strains analyzed, each in quadruplicate replicates: 1) wild-type MGAS2221 ; 2) MGAS2221 ccpA deletion strain; 3) wild-type MGAS10870; 4) MGAS10870 ccpA deletion strain; 5) wild-type MGAS6180; 6) MGAS6180 ccpA deletion strain

first: Sruti

last: DebRoy

first: Hui

last: Yao

first: Dante

last: Travisany

first: Mauricio

last: Latorre


title: A high-throughput small molecule screen identifies synergism between DNA methylation and Aurora kinase pathways for X-chromosome reactivation

city: Boston

first: Chunyao

last: Wei

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Mass General Hospital

summary: X-chromosome inactivation is a mechanism of dosage compensation in which one of the two X chromosomes in female mammals is transcriptionally silenced. Once established, silencing of the inactive X (Xi) is robust and difficult to reverse pharmacologically. Yet, the Xi is a reservoir of >1000 functional genes that could be potentially tapped to treat X-linked disease. To identify compounds that could reactivate the Xi, here we screened ~367,000 small molecules in an automated high-content screen using an Xi-linked GFP reporter in mouse fibroblasts. Given the robust nature of silencing, we sensitized the screen by “priming” cells with the DNA methyltransferase inhibitor, 5-aza-2’-deoxycytidine (5azadC). Compounds that elicited GFP activity include VX680, MLN8237, and 5azadC,, which are known to target the Aurora kinase and DNA methylation pathways. We demonstrate that the combinations of VX680 and 5azadC, as well as MLN8237 and 5azadC, synergistically upregulated genes on the Xi. Thus, our work identifies a synergism between the DNA methylation and Aurora kinase pathways as being one of interest for possible pharmacological reactivation of the Xi.

sample_organism: Mus musculus musculus x Mus musculus castaneus

overall_design: Examination of transcriptome profiles in mouse tail fibroblasts treated in 4 different conditions

first: Barry

last: Kesner

first: Jeannie

middle: T


title: RUNX2 and CBFB genome-wide binding in osteosarcoma SAOS2 cells

city: Bethesda

first: Jing

last: Huang

institute: National Cancer Institute

summary: The goal is to profile RUNX2 and CBFB binding sites in an osteosarcoma cell line, SAOS2.

overall_design: Fifty million of SAOS2 cells were fixed and subjected to ChIP-seq assay using RUNX2 or CBFB specific antibody.


title: small RNAs produced in the wild-type and mutant Dicer-2 transgenic flies

city: BALTIMORE

first: Ryuya

last: Fukunaga

address: 725 N. Wolfe St. 521A Physiology Bldg

department: Department of Biological Chemistry

institute: Johns Hopkins University School of Medicine

summary: Examine the abundance and length of siRNAs produced by mutant Dicer-2 in vivo and in vitro in order to understand the mechanism by which Dicer-2 produces highly precise 21 nt siRNAs.

sample_organism:
Drosophila melanogaster
synthetic construct


title: Wnt-responsive mesenchymal cells in dorsal back skin and ventral foot skin

city: New York

first: Catherine

middle: Pei-ju

last: Lu

address: 1230 York Ave

institute: Rockefeller University

summary: Canonical WNT-signaling is essential for placode formation irrespective of appendage type. At sites of placode initiation, Although WNT-signaling occurs in both epithelium and mesenchyme, the site of most intense activity as revealed by the WNT reporter Axin2-LacZ was in a zone just below the epithelial-mesenchymal interface. In ventral foot-skin, this WNT activity peaked at E17.5, concomitant with sweat bud fate commitment, while in dorsal back-skin, it began at E14.5, concomitant with HF fate specification.

overall_design: To address whether WNT-signaling within this zone might regionally influence the transcriptional landscape of body-site mesenchymes to support distinct epithelial fates, we transcriptionally profiled the Axin2-positive and Axin2-negative dermal cells following their FACS-purification from E17.5 ventral foot-skin and E14.5 dorsal back-skin

first: Elaine

last: Fuchs


title: CHD1 and H3K4me3 ChIP-seq in prostate cancer cell line PC-3

first: Di

last: Zhao

state: Tx

address: Zayed Building Z7. 4018

summary: Trimethylation of histone H3 at lysine 4 (H3K4me3) is known to be associated with transcriptional activation and CHD1 is known to selectively recognize and bind to H3K4me3 to activate gene transcription. In addition, CHD1 is involved in the maintenance of open chromatin and cooperates with H3K4me3 to control pluripotency of murine embryonic stem cells. To determine the downstream transcriptional targets and pathways of CHD1 and H3K4me3 in PTEN-null PCa cells, ChIP-seq was performed in control versus CHD1 knockdown PC-3 cells.

overall_design: H3K4me3 and CHD1 ChIP-seq was performed in control versus CHD1 knockdown PC-3 cells.

first: Zhengdao

last: Lan

first: Ming

last: Tang


title: Vav proteins are key regulators of Card9 signaling for innate antifungal immunity

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

institute: Max-Planck-Institute for biochemistry

summary: Fungal infections are major causes of morbidity and mortality, especially in immunocompromised individuals. The innate immune system senses fungal pathogens through a family of Syk-coupled C-type lectin receptors (CLRs), which signal through the conserved immune adapter Card9. Although Card9 complexes are essential for antifungal defense in humans and mice, the mechanisms that couple CLR-proximal events to Card9 control are not well defined. Here, using a proteomic approach, we identified Vav proteins as key activators of the Card9 pathway. Vav1, Vav2 and Vav3 cooperate downstream of Dectin-1, Dectin-2 and Mincle to selectively engage Card9 for NF-κB control and proinflammatory gene transcription but are not involved in MAPK activation. Although Vav family members show functional redundancy, Vav1/2/3 triple-deficient cells are severely impaired for NF-κB and cytokine responses upon stimulation with CLR agonists or hyphae, and Vav1/2/3-/- mice phenocopy Card9-/- animals with extreme susceptibility to fungi and rapid mortality upon Candida albicans infection. In this context, Vav3 is the single most important Vav in mice, and a polymorphism in human VAV3 is associated with susceptibility to candidemia in patients. Our results reveal a molecular mechanism for CLR-mediated Card9 regulation that controls innate immunity to fungal infections.

overall_design: RNA profiles of unstimulated or Curdlan-stimulated bone marrow-derived dendritic cells (BMDCs) from wild type (WT) and Vav1/2/3-/- (VAV KO) mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: Jürgen

last: Ruland

first: Susanne

last: Roth


title: Uncover miRNAs in citrus fruit ripening

first: Juxun

last: Wu

address: No.1 of Shizishan street, Hongshan District

institute: Huazhong Agricultral University

summary: Fruit ripening in Citrus is not well understood at the molecular level. Knowledge of the regulatory mechanism of citrus fruit ripening at the post-transcriptional level in particular is lacking. Here, we comparatively analyzed the miRNAs and their targeted genes in a spontaneous late-ripening mutant, ?Fengwan? sweet orange (MT) (Citrus sinensis L. Osbeck), and its wild-type counterpart ('Fengjie 72-1', WT). Using high-throughput sequencing of small RNAs and RNA degradome tags, we identified 107 known and 21 novel miRNAs, as well as 225 target genes. A total of 24 miRNAs (16 known miRNAs and 8 novel miRNAs) were shown to be differentially expressed between MT and WT. The expression pattern of several key miRNAs and their target genes during citrus fruit development and ripening stages was examined. Csi-miR156k, csi-miR159 and csi-miR166d suppressed specific transcription factors (GAMYBs, SPLs and ATHBs) that are supposed to be important regulators involved in citrus fruit development and ripening. In the present study, miRNA-mediated silencing of target genes was found under complicated and sensitive regulation in citrus fruit. The identification of miRNAs and their target genes provide new clues for future investigation of mechanisms that regulate citrus fruit ripening.

overall_design: Small RNA and degradome libraries of a spontaneous late-ripening mutant, ‘Fengwan’ sweet orange (MT) (Citrus sinensis L. Osbeck), and its wild-type counterpart ('Fengjie 72-1', WT) sampled at 170 DAF stage were sequenced by Illumina platform, two biological replicates for small RNA libraries and one biological replicate for degradome library.

first: Hualin

last: Yi


title: Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

institute: IMBA

summary: The post-transcriptional addition of nucleotides to the 3´ end of RNA regulates the maturation, function, and stability of RNA species in all domains of life. Here, we show that, in flies, 3´ terminal RNA uridylation triggers the processive, 3´-to-5´ exoribonucleolytic decay via the RNase II/R enzyme CG16940, a homolog of the human Perlman syndrome exoribonuclease Dis3l2. Together with the TUTase Tailor, dmDis3l2 forms the cytoplasmic, uridylation-triggered RNA processing (TRUMP) complex, that functionally cooperates in the degradation of structured RNA. RNA-immunoprecipitation and high-throughput sequencing reveals a variety of TRUMP complex substrates, including abundant non-coding RNA, such as 5S rRNA, tRNA, snRNA, snoRNA, and the essential RNase MRP, uncovering a key function of the TRUMP complex in the cytoplasmic quality control of RNA polymerase III transcripts. Together with high-throughput biochemical characterization of dmDis3l2 and bacterial RNase R our results imply a conserved molecular function of RNase II/R enzymes as 'readers' of destabilizing post-transcriptional marks - uridylation in eukaryotes and adenylation in prokaryotes - that play important roles in RNA surveillance.

platform_organism:
Drosophila melanogaster
synthetic construct

overall_design: For biochemical high-throughput analysis of dmDis3l2 (Figure 2), input-libraries (15482) served as control and three timepoints after treatment (0.5 min = 15483, 2 min = 15484, 10 min = 15485) have been analyzed as described in detail in the manuscript. The libraries 16546 (Input), 16547 (0.5 min), 16547 (2 min) and 16549 (10 min) serve as replicates and have been used to generate Figure 7. For biochemical high-throughput analysis of ecoRNaseR (Figure 7), input-libraries (16556) served as control and three timepoints after treatment (5 sec = 16557, 10 sec = 16558, 30 sec = 16559) have been analyzed as described in detail in the manuscript. For sample 32613, RNA co-immunoprecipitating with FLAG-dmDis3l2-CM have been subjected to size-selection (10-20 nt) and subjected to small RNA cloning (for details see manuscript, Figure S5). For sample 39892, RNA co-immunoprecipitating with FLAG-dmeDis3l2-CM under optimized conditions (shorter incubation time and addition of EDTA) was subjected to 3  adapter ligation and library preparation using Lexogen FLEX kit (Lexogen, Vienna, Austria). Libraries were subjected to PE50 sequencing but only reverse run was analyzed, since it provided information on post-transcriptional modification status and seuqence identity, by mapping to the Drosophila genome (for details see manuscript, Figure 5). For sample 39894, total RNA was subjected to the same cloning protocol as sample 39892, hence serves as control regarding post-transcriptional modification status and 3  end accumulation in cellular total RNA (Figure 5).

first: Madalena

middle: M

last: Reimão-Pinto

first: Raphael

last: Manzenreither

first: Pawel

last: Sledz

first: Martin

last: Jinek

first: Stefan

middle: L

last: Ameres


title: H3.3 depletion has a mild effect on the global transcriptome

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

country: France

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

summary: Transcriptomic analysis of H3.3 KO/Kd mouse embryonic fibroblasts (MEFs)

overall_design: We isolated total RNA from control shRNA treated or shH3.3A treated H3.3B KO MEFs and carried out Ribozero RNA-seq analysis. RNA-seq analysis was carried out on pooled datasets from biological duplicate experiments.

first: Aysegul

last: Ors

first: Bertrand

last: Favier

first: Yohan

last: Roulland

first: Defne

last: Dalkara

first: Mehmet

last: Ozturk

first: Ali

last: Hamiche

last: Dimitrov

first: Kiran

last: Padmanabhan


title: Host blood trancriptional profiles during Mycobacterium tuberculosis infection.

city: Hannover

first: Aravind

last: Tallam

state: Lower Saxony

address: Feodor-Lynen str. 7

department: BIOM

institute: TWINCORE

summary: We report a pilot investigation for poly-A RNAs differentially expressed during Mycobacterium tuberculosis infection. Participation in this investigation from March 2010 to July 2013 was voluntary, only subjects that were >18 years old and that informed written consent were considered eligible.  The recruitment of tuberculosis (TB) patients was done at public hospitals in Rio de Janeiro, Brazil. The diagnostic criteria for active pulmonary tuberculosis was at least one AFB (acid-fast bacilli) -positive sputum sample for M. tuberculosis and/or positive sputum culture and/or compatible clinical evolution for pulmonary TB and less than 15 days of anti-TB treatment and was in accordance with those of the Brazilian Ministry of Health. Blood was collected from recent close contacts (rCt) and active tuberculosis (TB) index cases (n=6). Latent TB infection (LTBI) was accessed by both tuberculin skin test (TST, cut-off = 5mm) and in house interferon-gamma release assays (IGRA, cut-off = 100 pg/ml), therefore, 12 rCt were classified as uninfected controls and 16 with LTBI.  Subsequently, the sequencing was performed following the standard protocols on Illumina HiSeq® 2500 Sequencing System (Illumina, San Diego, CA) running 100 bp paired-end reads (PE100) and generating approximately 30 million reads passing filter for each sample to produce the mRNA reads. Mining these RNAseq data, highly prominent modulation of DOCK9, EPHA4, and NPC2 mRNA expression was observed in the TB samples, indicating that they might have a role in TB pathogenesis. These differential modulations upon M. Tuberculosis infection were further validated by additional evidences in larger cohorts from different geographical areas.

overall_design: We collected blood samples from the recent close contacts (rCt) at the recruitment and monitored them for 1-year. All TB participants were treatment-naïve. An infection mRNA signature was derived from whole blood RNA sequencing data by comparing TB and uninfected rCt. We selected the 3 most prominent genes, by area under the ROC curve analysis, for additional validations. Some of the LTBI participants also showed the mRNA infection profile.

first: L

last: de Araujo

last: Vaas

first: R

last: Geffers

first: F

middle: C

last: Mello

first: M

middle: H

last: Saad

last: Pessler


title: Gene expression data of mRNA from liver of pig breed German Landrace

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

institute: FBN

summary: 47,880 probe-sets were screened, in the first part of this study, they were analysed for correlation of transcripts levels with body composition traits

overall_design:
RNAs of liver at adult stage were hybridized to Affymetrix Porcine Snowball Array.
correlations and association

first: Klaus

last: Wimmers


title: CD19 CAR immune pressure on B cell acute lymphoblastic leukemia induces myeloid lineage switch exposing inherent leukemic plasticity (RNA-Seq)

city: bethesda

first: Jack

last: Shern

address: 10 Center drive

institute: NCI

summary: This study establishs lineage switch as a mechanism of CAR resistance exposing inherent plasticity in genetic subtypes of pre-B cell ALL

overall_design: Examination of genome wide H3K27ac peaks associate with CAR T cell resistance

first: Elad

last: Jacoby


title: CD19 CAR immune pressure on B cell acute lymphoblastic leukemia induces myeloid lineage switch exposing inherent leukemic plasticity (ChIP-Seq)


title: CD19 CAR immune pressure on B cell acute lymphoblastic leukemia induces myeloid lineage switch exposing inherent leukemic plasticity

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

overall_design: Refer to individual Series


title: An RNA-seq dataset for studies of gene expression variation in the MAGIC line resource of Arabidopsis thaliana

city: Salt Lake City

first: Richard

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

summary: To understand the population genetics of structural variants (SVs), and their effects on phenotypes, we developed an approach to mapping SVs, particularly transpositions, segregating in a sequenced population, and which avoids calling SVs directly. The evidence for a potential SV at a locus is indicated by variation in the counts of short-reads that map anomalously to the locus. These SV traits are treated as quantitative traits and mapped genetically, analogously to a gene expression study. Association between an SV trait at one locus and genotypes at a distant locus indicate the origin and target of a transposition. Using ultra-low-coverage (0.3x) population sequence data from 488 recombinant inbred Arabidopsis genomes, we identified 6,502 segregating SVs. Remarkably, 25% of these were transpositions. Whilst many SVs cannot be delineated precisely, PCR validated 83% of 44 predicted transposition breakpoints. We show that specific SVs may be causative for quantitative trait loci for germination, fungal disease resistance and other phenotypes. Further we show that the phenotypic heritability attributable to sequence anomalies differs from, and in the case of time to germination and bolting, exceeds that due to standard genetic variation. Gene expression within SVs is also more likely to be silenced or dysregulated, as inferred from RNA-seq data collected from a subset of just over 200 of the MAGIC lines. This approach is generally applicable to large populations sequenced at low-coverage, and complements the prevalent strategy of SV discovery in fewer individuals sequenced at high coverage.

overall_design: 209 samples consisting of different inbred lines from the Multiparent Advance Generation InterCross (MAGIC) population in the reference plant, Arabidopsis thaliana. For each sample, RNA was collected from the aerial shoot at the 4th true leaf stage, and Illumina mRNA-seq libraries were constructed (a single library was constructed with each line; that is, each MAGIC line is represented by one biological replicate). Using these libraries, which were non-stranded, paired-end 100 bp RNA-seq Illumina reads were generated for each sample, and used to quantify gene expresison in each MAGIC line. The resulting expression phenotypes are suitable for describing the impacts of genetic variation in the MAGIC line founders on the control of gene expression.

last: Mott

first: Gunnar

last: Raetsch

first: Andre

last: Kahles

first: Josh

last: Steffen

first: Edward

last: Osborne

first: Robert

last: Greenhalgh


title: RNA-Seq Revealed Differences in Transcriptomes between 3ADON and 15ADON Populations of Fusarium graminearum

city: Fargo

first: Shaobin

last: Zhong

state: ND

address: 306 Walster Hall

department: Plant Pathology

institute: North Dakota State University

summary: Fusarium graminearum is the major causal agent of Fusarium head blight (FHB) in North America and other regions of the world. The pathogen causes direct yield losses and produces various types of trichothecenes mycotoxins [Deoxynivalenol (DON) and its acetylated forms (3-acetyl-4-deoxynivalenol=3ADON and 15-acetyl-4-deoxvevalenol=15ADON), nivalenol (NIV). Recent studies indicated that 3ADON-type isolates were significantly increased in North America and China in recent years and appears to be more aggressive based on growth rate, disease severity on different cultivars, and DON production in vitro. Thus the overall objective of this this study was to understand the molecular mechanisms that make 3ADON- and 15ADON-type populations different during infection using a susceptible cultivar, and to compare the transcriptomes of the 3ADON- and 15ADON-type populations in vitro and in planta using the RNA-seq approach as well as to identify the expression differences of candidate genes related to aggressiveness and DON production.

overall_design: Experimental samples were collected from in-vitro and in-planta inoculations with Fusarium graminearum isolates producing different mycotoxin derivatives. In in-vitro, Mung Bean Media was inoculated with a mix of 10 isolates of either 3ADON or 15ADON isolate population, incubated for five days and harvested to extract RNA. While for in planta, a susceptible spring wheat cultivar- Briggs was point inoculated at the flowering stage by both populations separately. The samples were collected at 48, 96 and 144 hours after plant inoculation. In both cases, samples were flash frozen in liquid nitrogen and ground to power for RNA extraction using Promega SV total RNA isolation kit. Extracted RNA was converted dscDNA and used for library preparation and sequencing using TruSeq RNA sample preparation kit from Illumina.

first: Krishna

last: Puri


title: CTCF-mediated topological boundaries during development foster appropriate gene regulation

city: New York City

first: Danny

last: Reinberg

state: New York

address: 522 First Avenue, 2nd floor Rm 211

institute: NYU School of Medicine / HHMI

summary: In this experiment, we performed 5C across a 4Mb region surrounding the HoxA region in WT and Δ5|6:7|9 ESCs and MNs

first: Varun

last: Narendra

first: Milica

last: Bulajic

first: Job

last: Dekker

first: Esteban

last: Mazzoni


title: HDAC inhibitor panobinostat engages host immune defenses to promote the tumoricidal effects of trastuzumab in HER2+ tumors

city: Melbourne

first: Nicole

middle: Margaret

last: Haynes

state: Victoria

address: 305 Grattan Street

department: Sir Peter MacCallum Department of Oncology

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Characterisation of the tumor extrinsic (immune-mediated) mechanisms by which panobinostat and trastuzumab can collaboratively promote tumor-associated NK cell infiltration to eradicate trastuzumab-refractory HER2+ tumors

overall_design: RNA sequencing was performed on established whole AU565(pv) HER2+ human breast tumors, harvested from SCID mice 2-days post treatment initiation with vehicle (PBS/D5W), panobinostat (15mg/kg/day), trastuzumab (10mg/kg day 1) or both drugs in combination. Each treatment group comprised of 4 mice.

first: Mikolaj

last: Medon

first: Eva

last: Vidacs

first: Jason

last: Li

first: Misty

middle: R

last: Jenkins

first: Kelly

last: Ramsbottom

first: Mark

last: Smyth

first: Peter

last: Atadja

first: Michael

last: Henderson

first: Ricky

last: Johnstone

first: Stephin

last: Vervoort

first: Joseph

last: Trapani

first: Phillip

last: Darcy


title: Cyclin Y-mediated changes in RNA-sequencing based transcriptome profiling in hippocampal neurons

city: Daejeon

first: Jong Hwan

last: Kim

department: Genome structure research center

institute: Korea Research Institute of Bioscience and Biotechnology

summary: We report the transcriptome changes mediated by Cyclin Y in rat hippocampal neurons.

overall_design: Cultured hippocampal neurons were infected with lentivirus expressing EGFP (as control), CCNY-WT-EGFP (for CCNY overexpression) or CCNY-shRNA-EGFP (for CCNY knockdown) at DIV5-6 and the neuronal cell lysates were harvested at DIV14 for total RNA isolation and subsequent RNA-seq.  Total 3 conditioned samples with duplicates each were performed.

first: I-Seul

last: Joe

first: Hanna

first: Mirang

first: Mikyoung

last: Park


title: Gene expression analysis of C4-2 cells treated with ACLY inhibitor and Enzalutamide

city: Philadelphia

first: Kathryn

last: Wellen

state: PA

address: 421 Curie Blvd, BRB 653

department: Cancer Biology

institute: University of Pennsylvania

summary: This study examined the gene expression effects of treating androgen-deprived C4-2 prostate cancer cells with the ACLY inhibitor BMS-303141 and the AR antagonist enzalutamide.

overall_design: Cells were treated with vehicle control, ACLY inhibitor alone, Enzalutamide alone, and ACLY-inhibitor and Enzalutamide combined together for 24 hours under androgen-depleted conditions (RPMI + 5% charcoal stripped serum). Biological triplicate samples were prepared.

first: Supriya

last: Shah


title: RNA-sequencing of non-senescent and senescent mouse skin fibroblast

city: St. Louis

first: John

middle: R.

last: Edwards

state: MO

address: 660 S. Euclid Ave, Campus Box 8220

department: Center for Pharmacogenomics

institute: Washington University School of Medicine

summary: Mouse skin fibroblasts (MSFs) were obtained from a FASST (Fibroblasts Accelerate Stromal-Supported Tumorigenesis) mouse.  This mouse model allows for spatial and temporal control for senescence induction by using a stromal specific Cre-recombinase driven by the pro-collagen-alpha II promoter.  The stromal specific Cre activates expression of the p27IRESGFP transgene that is expressed from the ROSA locus.  We cultured the MSFs in vitro, induced senescence using 10uM tamoxifen added to the media.  Non-senescent cells were treated with equal volume of vehicle alone (ethanol).  Upon tamoxifen treatment, cells were moved to a modular incubation chamber and maintained at 3% oxygen at 37 degrees celcius for 12 days total before collection.  At the time of collection, cells were trypsynized and pelleted by centrifugation.  The cells were lysed using Trysol reagent and RNA was isolated using a RiboPure RNA isolation kit (Ambion).

overall_design: For this study, 2 treatment groups were analyzed (non-senescent, EtOH samples and senescent, TAM samples).  Each treatment group was performed 3 times for a total of 6 samples for analysis.  The gene expression analysis is a comparison of expression in senescent (TAM) vs non-senescent (EtOH) mouse skin fibroblasts.

first: Sheila

middle: A

last: Stewart

first: Megan

last: Ruhland


title: Histone variant H3.3 demarcates GC-rich coding and subtelomeric sequences and serves as a potential memory mark for virulence gene expression in P. falciparum

city: Nijmegen

first: Sabine

last: Fraschka

address: Geert Grooteplein 28

country: Netherlands

institute: Radboud University Nijmegen

summary: ChIP-seq experiments were performed to profile PfH3.3 (PF3D7_0617900) in the malaria parasite Plasmodium falciparum. Sequencing of ChIP samples showed enrichment of PfH3.3 at GC-rich coding sequences and subtelomeric repetitive regions throughout the intraerythrocytic life cycle and additionally in intergenic regions during trophozoite stages. Also the promoter and the coding sequence of the active and poised var2CSA gene were marked (reference genome Plasmodium falciparum 3D7 from PlasmoDB version 6.1)

overall_design: DCJ P. falciparum parasites (Dzikowski et al., 2006) were transfected with a pHH1-plasmid (Reed et al., 2000) encoding a C-terminally Ty1-tagged version of PfH3.3 that contained a CTG instead of the start codon ATG and resulted in endogenous expression of PfH3.3-Ty1. These endogenously PfH3.3-Ty1 expressing DCJ P. falciparum parasites were selected for var2CSA expression by affinity purification as in (Noviyanti et al., 2001). Afterwards, parasite cultures were used to isolate nuclei from formaldehyde cross-linked early ring (10hpi) stages, late ring stages (20hpi), trophozoite stages (30hpi) or schizont stages (40hpi). Subsequently chromatin was prepared and used for chromatin immunoprecipitations using monoclonal anti-Ty1 antibody (BB2) (Brookman et al., 1995) or  anti-histone H3 (recognizes PfH3 and PfH3.3, Abcam Ab1791). Total RNA was isolated from the same starting material (10hpi, 20hpi, 30hpi or 40hpi), PolyA-selected and fragmented. Subsequent cDNA synthesis was modified to maintain directional information for strand-specific RNA-Seq as described  in (Kensche et al., 2015). ChIP-seq and directional RNA-seq libraries were prepared according to a Plasmodium-optimized library preparation procedure including KAPA polymerase-mediated PCR amplification. Obtained data were normalized to the amount of mapped reads per million (RPM). For log2 ratio tracks PfH3.3 values were divided through the respective PfH3core values and log2 was calculated.

first: Richárd

last: Bártfai


title: Optimized Approaches for Generation of Integration-free iPSCs from Human Urine-derived Cells with Small Molecules and Autologous Feeder

city: Guangzhou

first: qianyu

last: chen

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

summary: We generated iPSCs from human urine cells (hUCs) with the aid of small molecules and autologous hUC feeders. A compound cocktail including Cyclic Pifithrin-a, a p53 inhibitor and other compounds known for benefiting reprogramming like A-83-01, CHIR99021, Thiazovivin, NaB and PD0325901 was used to aid hUC reprogramming (Plan B). Aided by this cocktail, we achieved significantly improved efficiency (170 folds more) for hUC reprogramming and iPSC generation. In addition, to enable iPSC generation in some cases that massive cell death occurred during delivering reprogramming factors, we replaced Matrigel with autologous hUCs as feeder for reprogramming and iPSC generation (Plan C). Replacing Matrigel with autologous feeder not only enhanced reprograming, but also avoided concern using animal components for human iPSC generation. These were efficient approaches to enable iPSC generation from hUCs that were otherwise difficult for reprogramming, which would be valuable for banking patient’s specific iPSCs.

overall_design: We compared the transcriptome of hESCs, hiPSC, hUC by RNA-Seq. hiPSCs were generated from Plan B and Plan C. Plan B: RM at day 0~1, RM+5M at day 2~9, mTeSR1+6M at day10~17. UCs were seeded on Matrigel. Plan C: Medium was the same with Plan B, but seeded on autologous UCs as feeders before nucleofection.

first: Di

last: Li

first: Qianyu

last: Chen

first: Zhongzhou

last: Yang

first: Andrew

last: Hutchins

first: Guangjin

last: Pan

first: Juan

last: Du


title: RNA-seq analysis of transcriptomes in cae2-1, CA1-1 and cae2-1 CA1-1 Arabidopsis genotypes

city: Beibei

first: Zhi-Liang

last: Zheng

state: Chongqing

address: 15 Ganjuchun

department: Citrus Research Institute

institute: Southwest University

summary: Transcriptome comparison was used to determine the genes that are affected by the mutations in cae2-1, CA1-1 and the cae2-1 CA1-1 enhancer.

overall_design: mRNA profiles of young shoots from four genotypes showing various cotyledon cell shape phenotypes, each with two biological replicates.


title: Trancriptome study of zebrafish mutant fn10a

city: Beijing

first: Shouyu

last: Yan

address: 5#, Yiheyuan Road

department: Institution of Molecular Medicine

institute: Peking University

summary: We  conducted functional analysis on zebrafish mutant fn10a by polyA+, 100bp paired end, strand-specific RNA-seq. By comparing the transcriptome of fn10a mutants and their wildtype siblings or wildtype controls, we revealed a transcriptome-wide RNA splicing deficiency and a large amount of intron-retaining transcripts, which resulted in compromised nonsense-mediated RNA decay and activation of the p53 pathway in fn10a mutants. 2 biological replicates were performed to consolidate the findings. We also conducted subcellular RNA-seq between fn10a mutants and wildtype siblings, to investigate the localization of intron retaining transcripts.

overall_design: The wild-type control group (WT-control group) of 36-hpf embryos was generated from mating crosses between wild-type TL zebrafish, while fn10a mutants (mutant group) and siblings (WT-sibling group) were generated from mating crosses of fn10a heterozygote zebrafish. RNA-seq of 36hpf embryos for fn10a mutants, their wildtype siblings and wildtype TL. RNA-seq of cytoplasm RNA and nuclear RNA from 36hpf embryos for fn10a mutants and their wildtype siblings.

first: Chuan-Yun

first: Jing-Wei

last: Xiong


title: Characterization of Staphylococcus epidermidis biofilm-released cells (BRC) transcriptome upon interaction with whole human blood and its cellular and soluble components

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

summary: The release of cells from S. epidermidis biofilms formed on medical devices has been associated with the onset of bloodstream infections resulting in increased morbidity and mortality among infected patients. In order to better understand the role of BRC in the pathogenesis of S. epidermidis biofilm-related infections, the transcriptome of these cells was evaluated upon exposure to human blood components. The major alterations observed were involved in the biosynthesis and metabolism of amino acids and import and export of substances through ABC transporters. In addition, the transcription of genes involved in biotin metabolism was found significantly up-regulated suggesting this pathway as a possible target for future therapeutic strategies.

overall_design: S. epidermidis BRC transcriptomic profile before and after 2 hours of interaction with whole human blood, PMN or MN cells, plasma and TSB

first: Angela

last: Franca

first: Gerald

middle: B

last: Pier

first: Manuel

last: Vilanova

first: Nuno

last: Cerca


title: The transcriptional activator GaaR of Aspergillus niger is required for release and utilization of D-galacturonic acid from pectin

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

institute: Centre of fungal biodiversity

summary: We identified the D-galacturonic acid (GA) responsive transcriptional activator GaaR of the saprotrophic fungus Aspergillus niger, which was found to be essential for growth on GA and polygalacturonic acid (PGA). Growth of the ΔgaaR strain was reduced on complex pectins. Genome-wide expression analysis showed that GaaR is required for the expression of genes necessary to release GA from PGA and more complex pectins, to transport GA into the cell and to induce the GA-catabolic pathway. Residual growth of ΔgaaR on complex pectins is likely due to expression of pectinases acting on rhamnogalacturonan and subsequent metabolism of the monosaccharides other than GA.

overall_design: The GA-responsive transcriptional activator GaaR of A. niger was identified by in-silico homology search. Deletion analysis and transcriptomic profiling studies performed in this study showed that the A. niger GaaR ortholog is required for growth on GA and PGA and for the induction of the GA-regulon when grown on sugar beet pectin.

first: Ebru

last: Alazi

first: Jing

last: Niu

first: Joanna

middle: E

last: Kowalczyk

first: Mao

last: Peng

first: Maria

middle: V

last: Aguilar-Pontes

first: Jan

last: van Kan

first: Jaap

last: Visser

middle: P

first: Arthur

middle: F

last: Ram


title: The absence of quorum sensing signals triggers the expression of the symbiotic genes in broad host range rhizobia

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: Plant-released flavonoids induce the transcription of symbiotic genes in rhizobia and one of the first bacterial responses is the synthesis of so called Nod factors. They are responsible for the initial root hair curling during onset of root nodule development. This signal exchange is believed to be essential for initiating the plant symbiosis with rhizobia affiliated with the alphaproteobacteria. Here, we provide evidence that in broad host range rhizobia the complete lack of quorum sensing molecules results in an elevated copy number of its symbiotic plasmid (pNGR234a). This in turn triggers the expression of symbiotic genes and the production of Nod factors in the absence of plant signals. Therefore, increasing the copy number of specific plasmids could be a widespread mechanism of specialized bacterial populations bridging gaps in signalling cascades and providing a competitive advantage.

overall_design: To study the influence of flavonids as well as the complete absence of quorum sensing signals on gene expression in Sinorhizobium fredii NGR234, we analyzed in total 12 samples: Thereby we compared the NGR234 wild type to NGR234 wild type treated with 1 µM apigenin as a flavoniod. Furthermore, we compared the gene expression in NGR234 quorum sensing double mutant strain to the NGR234 double mutant supplemented with 1 µM apigenin.

first: Jessica

last: Grote

first: Dagmar

last: Krysciak

first: Katrin

last: Petersen

first: Simon

last: Güllert

first: Christel

last: Schmeisser

middle: U

first: Hari

last: Krishnan

first: Wolfgang

last: Streit


title: Ecdysone signaling induces two phases of cell cycle exit in Drosophila cells

city: Chapel Hill

first: Daniel

last: McKay

state: NC

address: 250 Bell Tower Drive

department: Biology and Genetics

institute: University of North Carolina, Chapel Hill

summary: Pulsed ecdysone signaling remodels cell cycle dynamics, causing distinct primary and secondary cell cycle arrests, similar to those observed in the wing during metamorphosis.

overall_design: This was a timecourse transcriptome analysis of the Drosophila pupal wing during metamorphosis by RNAseq. Timepoints include the proliferative wandering L3 larval stage (-10h APF), the temporary G2 arrest (6h APF) the final cell cycle (18h APF) the permanent cell cycle arrest (24h APF), and stages of terminal differentiation including vein differentiation, wing hair formation and cuticle protein production (36 and 44h APF)

first: Yongfeng

last: Guo

first: Kerry

last: Flegel

first: Kaitlyn

last: Norman

first: Jayashree

last: Kumar

middle: J

first: Laura

last: Buttitta


title: Testosterone deficiency induces changes of the transcriptomes of visceral adipose tissue in miniature pigs fed a high-fat and high-cholesterol diet

city: Nanjing

first: lifan

last: zhang

state: Jiangsu

address: No.6 Tongwei road

department: College of Animal Science and Technology

institute: Nanjing agricultural university

summary: Testosterone deficiency causes fat deposit, particularly in the visceral region, and its replacement might reverse fat accumulation, but the underlying mechanisms of such processes are largely unclear. To gain insights into the genome-wide role of testosterone on visceral adipose tissue (VAT), RNA-Seq was used to investigate testosterone deficiency induced changes of VAT in miniature pigs fed a high-fat and high-cholesterol (HFC) diet among intact male pigs (IM), castrated male pigs (CM), and castrated male pigs with testosterone replacement (CMT) treatments. The results showed that testosterone deficiency induced VAT deposit and increased serum leptin level. Moreover, a total of 1,732 differentially expressed genes (DEGs) were identified between different two groups. Compared with gene expression profiles in IM and CMT pigs, upregulated genes in CM pigs, i.e., LOC100520753 (CD68), LCN2, EMR1, NCF1 (p47phox), and NOX2 (GP91-PHOX), were mainly enriched in inflammatory response, oxidation-reduction process, and response to oxidative stress, while downregulated genes in CM pigs, i.e., DIO3, PCK1, and ABHD5, mainly focused on small molecule metabolic process. Taken together, our study provides a novel genome-wide view on the role of testosterone on VAT deposit under HFC diet, thus improving our understanding of the molecular mechanisms involved in VAT changes induced by testosterone deficiency.

overall_design: mRNA profiles of intact male pigs fed a HFC diet (IM+HFC), castrated male pigs fed a HFC diet (CM+HFC) ,and castrated male pigs treated with testosterone (CM+HFC+T) in visceral adipose tissue were generated by RNA sequencing using Ion Torren Proton

first: Lifan

last: Zhang

first: Zhaowei

last: Cai


title: DNA methylation profile of triple negative breast cancer-specific genes (MBD-Seq)

city: New Lambton Heights

first: Kelly

last: Avery-Kiejda

state: NSW

address: Kookaburra Circuit

department: Medical Genetics

institute: Hunter Medical Research Institute

summary: This part of the study was used to validate our findings comparing the DNA methylation in lymph node metastasis to that in normal tissue. We compared our findings (comparing LN versus NAT) with MBDcap sequencing data provided by Dr. Clare Stirzaker and Prof. Susan Clark from the Garvan Institute Sydney. This analysis provides regional DNA methylation information therefore a strict validation with our CpG-specific analysis was not possible. The regions that were analysed using the MBDcap data included our genes of interest (83 genes that are associated with LN metastasis, identified in 16) starting 2kb upstream of the first transcription start site (TSS) to the 3’ end of the genes. These regions are broken up into 1kb tiles. Methylation differences between LN and NAT samples were assessed using a Student’s t-test (using the R base package) (p<0.05).

overall_design: Genome wide profiling of 7 Lymph node metastatic triple negative breast tumours was performed using MBDCap-seq. Methylation in these samples was compared to normal breast samples that can be found at GSE58020 (GSM1399530,GSM1399522,GSM1399520,GSM1399524). To account for inter patient and inter-region variation, read counts were normalised to total library size and then divided by read counts in a 100% methylated control sample (see GSE58020 sample GSM1399545).

first: Warwick

last: Locke