title: Integration of kinase and calcium signaling at the level of chromatin underlines inducible gene activation in T cells

city: Coventry

first: Nigel

middle: Paul

last: Dyer

address: Gibbet Hill Road

institute: University of Warwick

summary:
Aim: to perform a genome-wide investigation of chromatin landscape and gene expression patterns downstream of calcium and kinase signaling in Jurkat T cells.
Methods: PMA and ionomycin were used to activate the calcium and kinase signalling networks involved in T cell activation. Global gene expression was measured using RNA-seq, whilst ATAC-seq was used to probe chromatin landscape following 3 hours of stimulation with PMA, ionomycin or both. All experiments were performed in triplicate. For RNA-seq all sequencing was performed using paired-end sequencing on an Illumina HiSeq2500 instrument. For ATAC-seq sequencing was performed using a HiSeq 1500.
Results: we mapped approximately 60 million reads per sample for ATAC-seq, and 22 million reads per library for RNA-seq. Overall we identified 57,825 transcripts and 19,763 ATAC-seq peaks. We identifiead 1648 genes whose expression was increased by 2-fold or more by at least one treatment in comparison to untreated cells. Similarly, we identified 3972 ATAC peaks that were induced by at least 2-fold by treatment in comparison to untreated cells.
Conclusions: we found that chromatin landscape was associated with gene expression downstream of calcium and kinase signaling in Jurkat cells. Further to this we found that activation of the full complement of TCR-responsive genes is dependent upon both PMA and ionomycin, and amounts to more than just the sum of both.

overall_design: RNA-sequencing and ATAC-sequencing were performed after 3 hours of treatment with either PMA, ionomycin or co-treatment with PMA and ionomycin.

first: Ruth

last: Brignall


title: DMS-seq for in vivo genome-wide mapping of protein–DNA interactions and nucleosome centers

status: Public on Sep 18 2017

city: Fukuoka

first: Taichi

last: Umeyama

state: Fukuoka

address: Maidashi 3-1-1, Higashi-ku

department: School of Medicine

country: Japan

institute: Kyushu University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Dimethyl sulfate (DMS) is a methylating reagent that has long been used to detect footprints of DNA-bound proteins in vitro as well as in vivo. Here we describe DMS-seq for in vivo genome-wide mapping of protein-DNA interactions. DMS-seq exploits the cell-permeable nature of DMS to obviate the need for nuclear isolation, thereby simplifying the process to detect binding sites of transcription factors. Furthermore, we found that DMS preferentially attacks nucleosome centers in vivo, evidencing for DMS-seq as a first method that locates them without using genetically-modified histones and is hence applicable to any eukaryote. DMS-seq should be a simple and unique method in epigenomics.

overall_design: DDBJ Bioproject:PRJDB5048, DRA submission:DRA004939

first: Takashi

last: Ito


title: Sensory neurons co-opt classical immune signaling pathways to mediate chronic itch

city: St. Louis

first: Landon

middle: Kyle

last: Oetjen

state: MO

address: 660 S Euclid Avd

country: USA

institute: Washington University

type: Expression profiling by high throughput sequencing

summary: Mammals have evolved neurophysiologic reflexes such as coughing and scratching to expel invading pathogens and noxious environmental factors. It is well established that these responses are also associated with chronic inflammatory diseases such as asthma and atopic dermatitis. However, the mechanisms by which inflammatory pathways promote sensations such as itch remain poorly understood. Here, we show that the type 2 cytokines IL-4 and IL-13 directly stimulate sensory neurons and that chronic itch is dependent on neuronal IL-4Rα and JAK1 signaling. In proof-of-concept clinical studies, we further show that patients with recalcitrant chronic itch markedly improve when treated with JAK inhibitors. Thus, signaling mechanisms previously ascribed to the immune system may represent novel therapeutic targets within the nervous system. Collectively, these studies reveal an evolutionarily conserved paradigm in which the sensory nervous system employs classical immune signaling pathways to influence mammalian behavior.

overall_design: RNA-sequencing of bulk ear skin from 4 adult C57Bl/6 mice treated with vehicle control (ethanol, EtOH) compared to bulk ear skin from 4 adult C57Bl/6 mice treated with 1 nmol topical calcipotriol (MC903) daily for 12 days.

middle: K

first: Brian

middle: S

last: Kim


title: Comprenhensive lncRNA expression analysis through normal hematopoiesis and AML

city: London

first: M Joaquina

last: Delas

address: 1 Midland Road

department: Briscoe Lab

country: United Kingdom

institute: The Francis Crick Institute

summary: It is well understood how proteins regulate cell fate, both in normal development and disease. However, a substantial fraction of the genome is transcribed in a cell type- specific manner, producing long non-coding RNAs (lncRNA) rather than protein- coding transcripts. Here we systematically characterize transcriptional dynamics (both mRNA and lncRNA) during hematopoiesis and in hematological malignancies. We present de novo assembled transcriptome models and expression values for hematopoietic lncRNAs. We found lncRNAs to be regulated during differentiation and misregulated in disease. We assessed lncRNA function via an in vivo RNAi screen in a model of acute myeloid leukemia. With this approach, we identified several lncRNAs essential for leukemia maintenance, and found that a number act by promoting leukemia stem cell signatures. Leukemia blasts show a myeloid differentiation phenotype when these lncRNAs were depleted, and our data indicates that this effect is mediated via effects on the c-MYC oncogene.

overall_design: Low input RNAseq libraries were prepared from biological duplicates for 9 normal hematopoietic cell types, cultured AML and AML isolated from transplanted mice.

first: M

middle: J

first: G

last: Hannon


title: The splicing co-factor Barricade/Tat-SF1, is required for cell cycle and lineage progression in Drosophila neural stem cells.

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

summary: Stem cells need to balance self-renewal and differentiation for correct tissue development and homeostasis. Defects in this balance can lead to developmental defects or tumor formation. In recent years, mRNA splicing has emerged as one important mechanism regulating cell fate decisions. Here we address the role of the evolutionary conserved splicing co-factor Barricade (Barc)/CUS2/Tat-SF1 in Drosophila neural stem cell (neuroblast) lineage formation. We show that Barc is required for the generation of neurons during Drosophila brain development by ensuring correct neural progenitor proliferation and differentiation. Barc associates with components of the U2 small nuclear ribonucleic proteins (snRNP), and its depletion causes alternative splicing in form of intron retention in a subset of genes. Using bioinformatics analysis and a cell culture based splicing assay, we found that Barc dependent introns share three major traits: they are short, GC rich and have weak 3’ splice sites. Our results show that Barc, t...

overall_design: Comparison of transcriptomes of Drosophila melanogaster wild-type and barc RNAi neural stem cells (type I) and S2 cells.

first: Monika

last: Abramczuk

middle: R

first: Juergen

middle: A

last: Knoblich


title: lncRNA dependencies in acute myeloid leukemia

type: Non-coding RNA profiling by high throughput sequencing

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

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: shRNA screen identifies lncRNAs required for acute myeloid leukemia progresion

overall_design: High throughput sequencing was performed to identify the shRNA representation at the intitial (input) or final (mouse) timepoints, with 3-5 biological replicates per pool. Each pool consists of 50 shRNAs.


title: RNAseq analysis of AML cells upon lncRNA knockdown

overall_design: Transcriptome analysis was performed on cells expressing inducible shRNAs against the candidate lncRNAs. 9 different lncRNAs were knocked down with two different hairpins, in biological duplicates (clonar line A and B). Renilla lucifearase knockdown and Myc knocdown were also included as controls (3 biological replicates each).


title: BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

type: Methylation profiling by high throughput sequencing


title: BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment [ChIP-seq]

summary: Cancer arises from the malignant interplay between oncogenic signaling and cell specification.  Transcriptionally activated stem, growth and survival programs reshape an epigenomic identity defined by a transcriptional core regulatory circuitry.  To study and disrupt oncogenic transcription, we first created inhibitors of BET bromodomains.  Selective antagonism of oncogenic transcriptional signaling arises from bromodomain-specific activity.  Recently, we innovated a strategy to induce selective and pronounced degradation of BET coactivator proteins via phthalimide conjugation for E3 ubiquitin ligase recruitment.  Degraders of BET bromdomains (dBETs) exhibited superior efficacy to bromodomain inhibitors in cultivated leukemia cells, through unknown mechanisms.  Here, we use chemically optimized small-molecule degronimids and kinetic measures of chromatin structure and function to unveil an unrecognized, essential role for BRD4 in the control of global productive transcriptional elongation.  Rapid loss of BRD4 attenuates phosphorylation of the carboxy-terminal domain of RNA polymerase II, independent of genomewide recruitment of CDK9 to promoters, leading to a collapse of the transcriptional core regulatory circuitry.  These mechanistic studies are performed in translational models of T-cell acute lymphoblastic leukemia, a disease emblematic for transcriptional addiction, to establish a rationale for human clinical investigation.

overall_design: ChIP-Seq for BRD4, CDK9, and RNA Pol II in MOLT4 T-ALL cells treated with JQ1, dBET6, or DMSO.

first: Georg

middle: E

last: Winter

first: Dennis

middle: L

last: Buckley

first: Michael

last: Erb


title: Epigenetic restriction of embryonic and extraembryonic lineages mirrors the somatic transition to cancer (ATAC-seq)

first: Jiantao

last: Shi

address: 3 Blackfan Circle

institute: dana farber cancer institute

summary: Concerted efforts over past decades have established a thorough understanding of the canonical somatic DNA methylation landscape as well as its systematic misregulation across most human cancers.  However, the underlying mechanism that directs this genome-scale transformation remains elusive, with no clear model for its acquisition or understanding of its potential developmental utility. Here we present base pair resolution analysis of global remethylation from the hypomethylated state of the preimplantation embryo into the early epiblast and extraembryonic ectoderm. We show that these two states acquire highly divergent genomic distributions: while the proximal epiblast establishes a canonical CpG-density dependent pattern found in somatic cells, the extraembryonic epigenome becomes substantially more mosaic.  Moreover, this alternate pattern includes specific de novo methylation of hundreds of CpG island promoter containing genes that function in early embryonic development and are orthologously methylated across an extensive cohort of human cancers.  From these data, we propose a model where the evolutionary innovation of extraembryonic tissues in eutherian mammals required cooption of DNA methylation-based suppression as an alternate pathway to the embryonically utilized Polycomb group proteins, which otherwise coordinate germ layer formation in response to extraembryonic cues at the onset of gastrulation.  Moreover, we establish that this decision is made deterministically downstream of the promiscuously utilized, and frequently oncogenic, FGF signaling pathway and utilizes a novel combination of epigenetic cofactors.  Recruitment of this silencing mechanism to developmental genes during cancer therefore reflects the misappropriation of an innate regulatory pathway that may be spontaneously sampled as an alternate epigenetic landscape within somatic cells.

overall_design: Comparison of chromatin accessibility patterns in Extraembryonic Ectoderm and cancer

first: Zachary

middle: D

last: Smith

first: Julie

last: Dongahey

first: Davide

last: Cacciarelli

first: Franziska

last: Michor

first: Alexander

last: Meissner


title: Episomal S/MAR-based replicons do not alter expression profile of host genome

city: Witten

first: Claudia

last: Hagedorn

address: Stockumer Strasse 10

department: Chair for Biochemistry and Molecular Medicine

country: Germany

institute: Witten/ Herdecke University

summary:
Methods: mRNA profiles of untransfected HeLa cells (wild-type; wt) were compared with mRNA profiles of HeLa cells stably maintaining an S/MAR-based episome.
Results: We here report for the first time that episomally maintained S/MAR-based vectors do not alter gene expression profile of the host cell's genome. No global changes in gene expression in episome maintaining cells, compared to non-transfected cells could be observed. To identify differentially expressed genes, false discovery rate (FDR; q-value) cut off was set to 0.01. Significantly differentially expressed genes with q<0.01 and an absolute fold-change of 2 were not detected. For verification, we chose five genes with high fold-change and low q-values (q<0.05) and compared expression levels between untransfected HeLa and HeLa stably maintaining an S/MAR-based within three replicates in qPCR.
Conclusions: S/MAR-based replicons used in this study do not code for viral proteins but tend to co-localise with promoter sequences and transcription start sites. Recent observations that cooperatively transcribed promoters can influence each other raise concerns that S/MAR-based replicons have the potential to alter endogenous gene expression. Therefore, we compared the transcriptome of untransfected HeLa cells with HeLa cells stably maintaining an S/MAR-based episome. Setting the FDR to <0.01, we found no significantly differentially expressed genes. This finding is of utmost importance for potential gene therapeutic application of S/MAR-based replicons.

overall_design: Examination of mRNA profiles in two different HeLa populations.

first: Hans

last: Lipps


title: Microprocessor recruitment to elongating RNA Polymerase II is required for differential expression of microRNAs

status: Public on Sep 15 2017

city: Evanston

first: Richard

last: Carthew

state: IL

address: 2205 Tech Drive

institute: Northwestern University

summary: The cellular abundance of mature microRNAs (miRNAs) is dictated by the efficiency of nuclear processing of primary miRNA transcripts (pri-miRNAs) into pre-miRNA intermediates. The Microprocessor complex of Drosha and DGCR8 carries this out, but it has been unclear what controls Microprocessor's differential processing of various pri-miRNAs. Here, we show that Drosophila DGCR8 (Pasha) directly associates with the C terminal domain of the RNA polymerase II elongation complex when it is phosphorylated by the Cdk9 kinase (pTEFb). When association is blocked by loss of Cdk9 activity, a global change in pri-miRNA processing is detected. Processing of pri-miRNAs with a UGU sequence motif in their apical junction domain increases, while processing of pri-miRNAs lacking this motif decreases. Therefore, phosphorylation of RNA polymerase II recruits Microprocessor for co-transcriptional processing of non-UGU pri-miRNAs that would otherwise be poorly processed. In contrast, UGU-positive pri-miRNAs are robustly processed by Microprocessor independent of RNA polymerase association.

overall_design: There are 2 samples, one control and one experimental

first: Victoria

last: Church

middle: W


title: Therapeutic utility of natural estrogen receptor beta agonists on ovarian cancer

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: We examined the transcriptional changes modulated by ESR2 agonist liquiritigenin by perfroming global transcriptome analysis. ES2 cells were treated with either vehicle or liquiritigenin for 24 h and the isolated RNA was utilized for RNA-seq analysis. Our results demonstrated that liquiritigenin modulated several genes that are involved in NF-kB signaling, inflammation, NRF2 mediated oxidative stress response, and MMP signaling.

overall_design: Total RNA was isolated from the ES2 cells that were treated with vehicle or liquiritigenin for 24 hours. Illumina TruSeq RNA Sample Preparation was performed following manufacturer's protocol. Samples were run on an Illumina HiSeq 3000 in duplicate. The combined raw reads were aligned to UCSC hg19 and genes were annotated by Tophat. Genes were annotated and quantified by HTSeq-DESeq pipeline.

first: Gangadhara

last: Sareddy

first: Ratna

last: Vadlamudi


title: Succinate transport is not essential for symbiotic nitrogen fixation by Sinorhizobium meliloti nor Rhizobium leguminosarum

status: Public on Sep 16 2017

city: Hamilton

first: Turlough

middle: M

last: Finan

state: Ontario

address: 1280 Main St. W.

department: Department of Biology

country: Canada

institute: McMaster University

summary: Symbiotic nitrogen fixation (SNF) is an energetically expensive process performed by bacteria known as rhizobia during endosymbiotic relationships with leguminous plants.  The bacteria require the plant to provide a carbon source for generation of the reductant to power SNF.  Although it is well known that C4-dicarboxylates (succinate, fumarate, malate) function as the primary, if not sole, carbon source provided to the rhizobia, the relative contribution of each C4-dicarboxylate is not known.  Here, we employ genetic and systems-level analyses to address this issue.  Expression of a malate specific transporter (MaeP) in Sinorhizobium meliloti Rm1021 dct mutants unable to transport C4-dicarboxylates resulted in malate import rates up to ~ 30% that of wild type S. meliloti.  This was sufficient to support SNF with Medicago sativa, with acetylene reduction rates up to ~ 50% those of plants inoculated with wild type S. meliloti.  Rhizobium leguminosarum bv. viciae 3841 dct mutants unable to transport C4-dicarboxylates but expressing the maeP transporter had strong symbiotic properties, with Pisum sativum plants inoculated with these strains appearing similar to plants inoculated with wild type R. leguminosarum.  This was despite malate transport rates by the mutant bacteroids being < 10% those of the wild type.  A transcriptomics analysis of the combined plant/bacterium nodule transcriptome was performed using RNA-sequencing to identify any systems-level adaptations in response to the inability of the bacteria to import succinate or fumarate.  Few transcriptional changes, with no obvious pattern, were revealed by this analysis.  Overall, these data illustrated that succinate and fumarate are not essential for SNF, and that at least in specific symbioses, L-malate is likely to naturally serve as the primary C4-dicarboxylate provided to the bacterium.

overall_design: There were a total of 6 samples for the RNA-sequencing analysis: two conditions performed in biological triplicates.  Total plant and bacterial RNA was isolated from Pisum sativum cv. Homesteader nodule tissue containing one of two bacterial strains.  The first was wild type Rhizobium leguminosarum bv. viciae 3841.  The second was a R. leguminosarum bv. viciae 3841 dctA mutant expressing the maeP gene of Streptococcus gallolyticus in trans.  All plants were grown in nitrogen free sand-vermiculate set-ups.  Sequencing was performed using Illumina HiSeq 1500 with 51 nt single reads.

last: Mitsch

first: George

middle: C

last: diCenzo

first: Alison

last: Cowie


title: AmpliSeq analysis of human iPSC-derived cardiomyocytes

city: Fujisawa

first: Yoshiyuki

last: Tsujihata

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-chome

institute: Takeda Pharmaceutical Company Limited

summary: Analysis of human iPSC-derived cardiomyocytes unstimulated or stimulated with endothelin-1 in the presence of either vehicle (DMSO), Ivermectin, Importazole, IPA-3, or verapamil. Results provide insight into the pathways regulated by the treatments.

overall_design: AmpliSeq of human iPSC-derived cardiomyocytes untreated or treated with endothelin-1 in the presence of either vehicle (DMSO), Ivermectin, Importazole, IPA-3, or verapamil for 18 hours, in quadruplicate, using Ion Proton System.

first: Tomoko

last: Satomi

first: Hiroaki

last: Nagai

first: Kuniko

last: Kikuchi

first: Hirokazu

last: Tozaki


title: RNA sequencing analysis of HL-1 cardiomyocytes

summary: Analysis of murine cardiomyocyte cell line HL-1 treated with Ivermectin or Importazole. Results provide insight into the pathways regulated by the treatments.

overall_design: RNA-seq of mouse HL-1 cardiomyocytes treated with vehicle (DMSO), Ivermectin, or Importazole for 24 hours, in triplicate, using Ion Proton System.


title: Gene expression in control and DOCK8 CRISPR KHYG1 NK cells

city: Melbourne

first: Conor

last: Kearney

address: Grattan Street

country: Australia

institute: Peter MacCallum cancer Centre

summary: Mutations in the DOCK8 gene cause an autosomal recessive form of hyper-immunoglobulin E syndrome, characterised by chronic immunodeficiency with persistent microbial infection and increased incidence of malignancy. These manifestations suggest a defect in cytotoxic lymphocyte function and immune surveillance. However, how DOCK8 regulates NK cell-driven immune responses remains unclear. Here, we demonstrate that DOCK8 regulates NK cell cytotoxicity and cytokine production in response to target cell engagement or receptor ligation. Genetic ablation of DOCK8 in human NK cells attenuated cytokine transcription and secretion through inhibition of Src family kinase activation, particularly Lck, downstream of target cell engagement or NKp30 ligation. PMA/Ionomycin treatment of DOCK8 deficient NK cells rescued cytokine production, indicating a defect proximal to receptor ligation. Importantly, NK cells from DOCK8 deficient patients had attenuated production of IFNγ and TNFα upon NKp30 stimulation. Taken together, we reveal a novel molecular mechanism by which DOCK8 regulates NK cell driven immunity.

overall_design: KHYG1 cells were cultured as indicated prior to stimulation with anti-Nkp30 (duplicate samples). After 90 minutes, cell pellets were collected and total RNA was extracted using the Nucleospin® RNA extraction kit (Macherey-Nagel). RNA quality was checked on the Agilent 4200 Tapestation and RNA with RIN values > 9 were used for the subsequent analysis. Sequencing libraries were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen) according to the manufacturers instructions using 200ng total RNA input. Single-end 75bp RNA-sequencing was performed on the NextSeq 500 (Illumina).


title: RNA sequencing analysis of cardiomyocytes

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Arabidopsis CLE peptide hormones contribute to pollen development through precisely regulated transcriptomic and proteomic networks

city: Shanghai

first: Shuangshuang

last: Wang

state: Shanghai / 上海

address: 2005 Songhu Road

country: China

institute: Fudan University

summary: The CLAVATA3/ESR-RELATED (CLE) peptide hormones are required for numerous plant growth and developmental processes. However, little is known regarding the function and working mechanism of the CLEs in the anther. Here, using RNA in situ hybridization analyses, we identified 7 CLE genes that are specifically expressed in the tapetum and microsporocytes in the anther, and the dominant-negative mutant plants of each of these genes exhibited significantly reduced anther size, pollen number, and abnormal pollen wall formation. Further transcriptomic and proteomic studies on cle19, DN-CLE19, and CLE19-OX mutant lines revealed that CLE19 affected the expression of more than 1,000 genes at the RNA level and 595 at the protein level, including genes involved in pollen coat and pollen exine formation, lipid metabolism, pollen germination, and hormone metabolism processes. Phenotypic analyses of mutants of the CLE19 downstream genes GRP20, ACOS5 and MEE48 revealed that the formation of pollen exine was affected in these mutants, confirming that these genes function downstream of CLE19 in the regulation of pollen wall formation. These findings demonstrate the function and downstream genes of CLE19 and redundant genes, providing insights into working pathways of the peptide hormones in pollen development.

overall_design: mRNA-seq data of wild type (WT and C24), CLE19::DNCLE19 and 35S::CLE19 transgenic plants stage 4-10 anther were generated by deep sequencing by the Illumina™ Hi-seq 2000 system

first: Fang

last: Chang


title: Identification of imprinted gene Grb10 to associate with the pluripotency state in nuclear transfer embryonic stem cells using high throughput sequencing technology

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

summary: We compared the exactly syngeneic ntESCs and iPSCs with same genomic insertion generated from adipocyte progenitor cells (APCs) isolated from the all-iPSC mice through the primary TF mediated reprogramming by performing the high-throughput sequencing. There were 84 genes significantly upregulated in fully reprogrammed ntESCs compared with partially reprogrammed ntESCs and 391 genes upregulated in fully reprogrammed iPSCs compared with partially reprogrammed iPSCs. An overlapping gene, Grb10, was identified to associate with the pluripotency state of ntESCs.

overall_design: Examination of the mRNA expression in different cell types.

first: Hui

last: Li

first: Zhiming

last: Han

first: Shaorong

last: Gao


title: Accumulation of small RNA populations in response to allopolyploidy: analysis of small RNA sequencing data from resynthesized Brassica napus allotetraploid in comparison to their diploid progenitors

city: Gif-sur-Yvette

first: Karine

last: Alix

address: Chemin du Moulon

country: France

institute: GQE - Le Moulon

summary: Evolution and adaptation of living organisms are results of permanent fights against diverse threats, which imply specific responses from the genome itself. Allopolyploidy, combining interspecific hybridization with whole genome duplication, is recognised as an important evolutionary force in plants. Its evolutionary success can be related to the rapid and profound genome reorganizations generated in response to the “Genome Shock” that allow the neo-allopolyploid to adapt efficiently to new environments. While work has focused on the structural and functional consequences of allopolyploidy, studies dedicated to the response of the neo-allopolyploid genome at the level of the functional regulation of genome expression have been rarely conducted. Recently, the hypothesis of a major role for small non coding RNAs (sRNAs) in mediating the immediate functional response of neo-allopolyploid genomes has progressively emerged. Here, we characterize the global response of sRNAs to allopolyploidy in Brassica, using three independent resynthesized B. napus allotetraploids surveyed at two different generations in comparison with their diploid progenitors, by high-throughput sequencing of sRNAs. Our evidence suggests an immediate but transient response of specific sRNA populations, targeting non-coding components of the genome. We identify the early accumulation of both 21- and 24-nt sRNAs involved in the regulation of the same targets, supporting a PTGS-to-TGS shift at the first stages of the neo-allopolyploid formation. We propose that sRNAs are early mobilized in response to allopolyploidy to control the unexpected transcriptional reactivation of various non-coding elements thus, playing the role of guardians of genome integrity during the first steps of neo-allopolyploid formation.

sample_organism:
Brassica napus
Brassica rapa
Brassica oleracea
Brassica oleracea var. botrytis
Brassica rapa subsp. oleifera

overall_design: A total of 11 small RNA libraries were constructed and sequenced: 5 small RNA libraries for the parental generation, with 2 libraries for each diploid progenitor (i.e. 2 technical replicates for each progenitor) and 1 library for a 1:1 parental RNA mix (i.e. technical replicate representing the additive reference); 3 libraries for 3 independent resynthesized B. napus allotetraploids (corresponding to 3 biological replicates) from early generation of the neo-polyploid formation (S1) and 3 others for the same resynthesized B. napus allotetraploids but from more advanced generation (S5).

first: Paulina

last: Martinez Palacios

first: Marie-Pierre

last: Jacquemot

first: Marion

last: Tapie

first: Agnès

last: Rousselet

first: Matthieu

last: Falque

first: Andrew

last: Lloyd

first: Eric

last: Jenczewski

first: Gilles

last: Lassalle

first: Anne-Marie

last: Chèvre

first: Christine

last: Lelandais

first: Martin

last: Crespi

first: Philippe

last: Brabant

first: Johann

last: Joets


title: Gene expression during conidia germination in Neurospora crassa on different media

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary: Conidia germination is critical for fungi to colonize various habitats. We sampled RNA expression at four stages of conidia germination, including fresh conidia (15min), polar growth (120min), doubling of long axis (240min), and first hyphal branching (360min) in Neurospora crassa. Cultures were made on two different media, including Bird medium supporting only asexual development and maple sap medium supporting both asexual and sexual development, and two biological replicates were collected for all data points. The growth was under a labratory condition of 25C and constant light.

overall_design: mRNA were sampled and compared from four time points across conida germination in Neurpsora crassa on different media

last: Lopez-Giraldez

first: Jeffrey

middle: P

last: Townsend


title: Epigenetic restriction of embryonic and extraembryonic lineages mirrors the somatic transition to cancer (RNA-seq)

first: Jiantao

last: Shi

overall_design: Comparison of gene expression patterns in Extraembryonic Ectoderm and cancer

first: Zachary

last: Smith

first: Julie

last: Dongahey

first: Davide

last: Cacciarelli

first: Franziska

last: Michor

first: Alexander

last: Meissner


title: Transcriptional repression in hypoxia is mediated by the Sin3A histone deacetylase complex [RNA-seq]

city: Madrid

first: Luis

last: del Peso

state: Madrid

address: Arzobispo Morcillo

department: Biochemistry

country: Spain

institute: Universidad Autonoma de Madrid

summary: Cells adapt to environmental changes, including fluctuations in oxygen levels, through the induction of specific gene expression programs. To identify genes regulated by hypoxia at the transcriptional level, we pulse-labeled HUVEC cells with 4-thiouridine and sequenced nascent transcripts. Then, we searched genome-wide binding profiles from the ENCODE project for factors that correlated with changes in transcription and identified binding of several components of the Sin3A co-repressor complex, including SIN3A, SAP30 and HDAC1/2, proximal to genes repressed by hypoxia. SIN3A interference revealed that it participates in the downregulation of 75% of the hypoxia-repressed genes in endothelial cells. Unexpectedly, it also blunted the induction of 47% of the upregulated genes, suggesting a role for this corepressor in gene induction. In agreement, ChIP-seq experiments showed that SIN3A preferentially localizes to the promoter region of actively transcribed genes and that SIN3A signal was enriched in hypoxia-repressed genes, prior exposure to the stimulus. Importantly, SINA3 occupancy was not altered by hypoxia in spite of changes in H3K27ac signal. In summary, our results reveal a prominent role for SIN3A in the transcriptional response to hypoxia and suggest a model where modulation of the associated histone deacetylase activity, rather than its recruitment, determines the transcriptional output.

overall_design: Exponentially growing non-synchronized HUVEC were transduced with lentiviral particles encoding for shRNA targeting SIN3A or control shRNA. 72h after infections cells were exposed to normoxia or hypoxia (21% or 1%  oxygen respectively) for 16 hours. RNA was extracted from samples and analyzed by high-throughput sequencing. Data include 8 samples corresponding to 2 independent biological replicates.

first: María

last: Tiana


title: Identification of qkia/c target genes

status: Public on Sep 17 2017

city: PARIS

first: sophie

last: lemoine

address: 46 rue d'Ulm

department: Biologie

institute: Ecole Normale Supérieure

summary:
Quaking are RNA binding proteins, which are known to regulate the expression of different genes at the post-transcriptional level. Genetic interference with quaking a (qkia) and quaking c (qkic) leads to major myofibril defects during zebrafish development, without affecting early muscle differentiation.
In order to understand how qkia and qkic jointly regulate myofibril formation, we performed a comparative analysis of the transcriptome of qkia/qkic (qkia mutant injected with qkic morpholino) versus control embryos. We show that Quaking activity is required for accumulation of the muscle-specific tropomyosin 3 transcript, tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation, reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus, we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking.

overall_design: Transcriptome of control versus qkia/qkic embryos at 24-26hpf. Biological triplicate were prepared for both condition (3x2 samples).

first: Aline

last: Bonnet

first: Guillaume

last: Lambert

first: François-Xavier

last: Dutrieux

first: Sylvain

last: Ernest

first: Fanny

last: Coulpier

first: Sophie

last: Lemoine

first: Riadh

last: Lobbardi

first: Frédéric

last: Rosa


title: BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment [NET-seq]

first: James

last: Bradner

overall_design: NET-Seq for DMSO, dBET6, or JQ1 treated MOLT4 cells

first: Georg

last: Winter

first: Dennis

last: Buckley


title: BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment [RNA-seq]

overall_design: RNA-Seq for DMSO, dBET6, or JQ1 treated MOLT4 cells and RNA-seq of primary T cells and PDX T-ALL cells with JQ1 and dBET6 treatment

first: Michael

last: Erb


title: Hypoxic regulation of gene expression in HUVEC is dominated by EPAS1

overall_design: Exponentially growing non-synchronized HUVEC were transduced with lentiviral particles encoding for shRNA targeting HIF1A or EPAS1 or a control shRNA. 72h after infection cells were exposed to normoxia or hypoxia (21% or 1%  oxygen respectively) for 16 hours. RNA was extracted from samples and analyzed by high-throughput sequencing. Data includes 6 samples from a single biological replicate.


title: Hypoxic regulation of transcription in HUVEC is mediated by EPAS1

overall_design: Exponentially growing non-synchronized HUVEC were transduced with lentiviral particles encoding for shRNA targeting EPAS1 or control shRNA. 72h after infection, cells were exposed to normoxia or hypoxia (21% or 1%  oxygen respectively) for 8 hours and pulse-labelled with 4‐thiouridine during the last two hours of treatment. RNA was extracted from samples in each condition (total RNA) and an aliquot subjected to affinity chromatography to purify the 4‐thiouridine-labelled RNA fraction (newly transcribed RNA, Newly Tr). Both RNA fractions from each condition were analyzed by high-throughput sequencing. Data includes 8 samples from a single biological replicate.


title: Genome-wide mapping of HIF binding sites by ChIP-seq in HUVEC cells exposed to hypoxia

overall_design: ChIP-Seq analysis of HIF1A, EPAS1, and ARNT binding in hypoxia in HUVEC cells compared with the preimmune control. The data is from a single biological replicate.


title: RNA-seq analysis of the effects of BCL6-inhibiting and BCL6-degrading compounds in lymphoma cell lines

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

institute: Boehringer Ingelheim RCV GmbH & Co KG

summary: The goal of this experiment is to measure the changes in gene expression induced by small molecules that either inhibit the interaction of the transcription factor BCL6 with co-repressor proteins, or that induce degradation of BCL6, in lymphoma cell lines.

overall_design: Treatment of various cell lines with saturating amounts of BCL6-inhibitors/degraders for 24 and 168 hours.

first: Tilman

last: Voss

first: Norbert

last: Schweifer

first: Manfed

last: Koegl


title: Changes in relative transcript amounts caused by ∆ftsH in Staphylococcus aureus USA300

city: Gary

first: Taeok

last: Bae

state: IN

address: 3400 Broadway

department: Microbiology & Immunology

institute: IU School of Medicine

summary: Staphylococcus aureus is an important human pathogen causing skin infection and many serious diseases such as pneumonia, sepsis, and toxic shock syndrome. In the bacterium, the membrane-bound protease FtsH plays important roles in the bacterial resistance to various stresses. This study was initiated to explain the strain-specific aggregation of the ftsH-deletion mutant of the Newman strain. To understand the molecular basis of the phenotype, we identified FtsH substrate proteins by comparing the protein contents of two different strains, Newman and USA300, and found that, in the strain Newman, a single nucleotide change in the sensor histidine kinase saeS gene placed the SaeRS two-component system under the control of FtsH, leading to the strain-specific cell-aggregation phenotype. Not only does our study provide a new methodology for protease-substrate determination but it also demonstrates that even a single nucleotide polymorphism can rewire bacterial regulatory network, resulting in a strain-specific phenotype. Our study shows the pitfall of making sweeping conclusion based on experimental results from a single bacterial strain.

sample_organism: Staphylococcus aureus subsp. aureus USA300

overall_design: RNA was prepared from cultures of strains USA300_P23 and USA300_P23_∆ftsH grown late-exponential phage cells in TSB media at 37°C. Three independent biological replicates of RNA were prepared for each strain or condition. cDNA libraries were sequenced and the sequencing results were used as the data base for differential expression analysis.

first: Bae

last: Taeok

first: Douglas

middle: B

last: Rusch

last: Ford


title: Metabolic Labeling of Newly Transcribed RNA for High Resolution Gene Expression Profiling of RNA Synthesis and Decay in response to hypoxia in HUVEC cells

first: Luis

last: del Peso

overall_design: Exponentially growing non-synchronized HUVEC were exposed to normoxia or hypoxia (21% or 1%  oxygen respectively) for 8 hours and pulse-labelled with 4‐thiouridine during the last two hours of treatment. RNA was extracted from samples in each condition (total RNA) and an aliquot was subjected to affinity chromatography to purify the 4‐thiouridine-labelled (newly transcribed RNA, Newly Tr) and non-labelled (Pre-existent) RNA fractions. All  three RNA fractions (total, newly transcribed and pre-existent) from each sample were analyzed by high-throughput sequencing. Submission includes 12 samples corresponding to 3 independent biological replicates.

first: María

last: Tiana


title: Impaired DNA replication derepresses chromatin and generates a transgenerationally inherited epigenetic memory

city: Boulder

first: Eduard

last: Casas

state: Colorado

address: Porter Biosciences, CU Campus

department: MCDB

institute: CU Boulder

summary: Impaired DNA replication is a hallmark of cancer and a cause of genomic instability. We report that, in addition to causing genetic change, impaired DNA replication during embryonic development can have major epigenetic consequences for a genome. In a genome-wide screen, we identified impaired DNA replication as causing increased expression from a repressed transgene in Caenorhabditis elegans. The acquired expression state behaved as an “epiallele,” being inherited for multiple generations before fully resetting. Derepression was not restricted to the transgene but was caused by a global reduction in heterochromatin-associated histone modifications due to the impaired retention of modified histones on DNA during replication in the early embryo. Impaired DNA replication during development can therefore globally derepress chromatin, creating new intergenerationally inherited epigenetic expression states.

overall_design: 3 replicates of div-1 mutant worms and N2 wild type worms

first: Adam

last: Klosin

first: Kadri

last: Reis

first: Cristina

last: Hidalgo-Carcedo

first: Tanya

last: Vavouri

first: Ben

last: Lehner


title: Integrated Transcriptomic and Proteomic Dynamics of Rituximab Treatment in B Lymphoblastoid Cells

city: East Lansing

first: George

last: Mias

address: 775 Woodlot Drive, Rm1319

department: Biochemistry and Molecular Biology

institute: Michigan State University

summary: The investigation aims to profile the molecular dynamics of Rituximab treatment in cells.  Specifically, a B-lymphoblast cells line was treated with Rituximab, and sampled every hour over a 24hour period. Treated and untreated cells were processed to extract RNA and protein that were subsequently used in high-throughput analysis of the transcriptome (RNA-Sequencing) and proteome (mass spectrometry). We expect our approach not only to provide a unique reference dataset to the scientific community but to also act as a paradigm as an approach to identify novel transcriptome-proteome molecular markers utilized in mapping drug action pathways. We have identified specific expression at both the gene and protein levels and are inferring associations between the omics through the use of temporal pattern identification, thus defining time-varying networks. This study will provide the next steps in the development of reference dynamic omics data that may be used in creating integration models, with further applications in dynamic monitoring of samples in precision medicine implementation.

overall_design: Examination of dynamics in a treated cell line and a parallel untreated control line, both sampled over 24hrs every hour. Validation using a new repeated experiment, with treated and untreated tracks, sampled over 6 selected time points.

middle: I

first: Hogune

last: Im

first: Lihua

last: Jiang

last: Snyder


title: Identification and expression profiling of Helicoverpa armigera microRNAs and their possible role in the regulation of digestive protease genes

city: Pune

first: Ashok

last: Giri

address: Pashan road, pune

country: India

institute: NCL

summary: Using Illumina platform, deep sequencing of 12 small RNA libraries was performed from Helicoverpa armigera larvae fed on artificial diet (AD) or recombinant Capsicum annuum PI-7 (rCanPI-7) incorporated diet at various time intervals (0.5, 2, 6, 12, 24, and 48h). Several candidate miRNAs (conserved and novel) were differentially expressed in rCanPI-7 fed larvae as compared to the larvae fed on AD. The investigation revealed potential roles of miRNAs in H. armigera protease gene regulation.

overall_design: miRNA expression analysed in H. armigera larvae in response to PI ingestion

first: Purushottam

last: Lomate

first: Neha

last: Mahajan

first: Sandip

last: Kale

first: Vidya

last: Gupta


title: Treatment Paradigms for Retinal and Macular Diseases Using 3-D Retina Cultures Derived From Human Reporter Pluripotent Stem Cell Lines

status: Public on Sep 14 2017

city: Bethesda

first: Matthew

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: We discuss the use of pluripotent stem cell lines carrying fluorescent reporters driven by retinal promoters to derive three-dimensional (3-D) retina in culture and how this system can be exploited for elucidating human retinal biology, creating disease models in a dish, and designing targeted drug screens for retinal and macular degeneration. Furthermore, we realize that stem cell investigations are labor-intensive and require extensive resources. To expedite scientific discovery by sharing of resources and to avoid duplication of efforts, we propose the formation of a Retinal Stem Cell Consortium. In the field of vision, such collaborative approaches have been enormously successful in elucidating genetic susceptibility associated with age-related macular degeneration.

overall_design: CRX+ flow sorted cells from human retina derived organoids were collected at 6 time points during differentiation (day (D) 37, 48, 67, 90, 134, 220).

first: Rossukon

last: Kaewkhaw

first: Manju

last: Swaroop

first: Kohei

last: Homma

first: Jutaro

last: Nakamura

first: Koray

last: Kaya

first: Vijender

last: Chaitankar

first: Sam

last: Michael

first: Gregory

last: Tawa

first: Jizhong

last: Zou

first: Mahendra

last: Rao

first: Wei

last: Zheng

first: Tiziana

last: Cogliati

first: Anand


title: RORɣt and RORα Signature Genes in Human Th17 Cells

city: San Diego

first: Xuejun

last: Liu

state: CA

address: 3210 Merryfield Row

department: Immunology

institute: Janssen Research & Development, LLC

summary: In an effort to study gene expression modulated by RORɣt and RORα in human Th17 cells, global gene expression of human CD4 T cells activated under Th17 skewing conditions was profiled by RNA sequencing. RORɣt and RORα signature genes were identified in these Th17 cells treated with specific siRNAs to knock down RORɣt or RORα expression. In addition, selective small molecule RORɣt modulators were also utilized as pharmacological tools in RORɣt signature gene identification.

overall_design:
Human CD4 T cells from 2 healthy donors were used in studies. 5.0 × 106 human CD4 T cells were used per sample and cell samples were collected at 0, 24 and 48 hours of Th17 differentiation for gene expression studies with RNA-Seq.
For compound treatment, CD4 T cells were pre-treated with compounds or DMSO vehicle control at 37°C for 1 hour before T cell activation. RORγt inverse agonists compound A, B and C were tested at two concentrations and DMSO treatments were used as controls in human Th17 differentiation assays.
For siRNA treatment, three RORγt siRNAs, two RORα siRNAs, two control siRNAs were tested at 1 μM, and mock transfected samples were included as controls. siRNA treatment was performed by Amaxa electroporation of human CD4 T cells with siRNAs..
T cells after compound or siRNA treatments were stimulated with anti-CD3/anti-CD28 coated beads (Miltenyi Biotech) at 2:1 bead to cell ratio in culture medium containing 10 ng/ml IL1β (R&D), 10 ng/ml IL23 (R&D), 30 ng/ml TGFβ1 (R&D), 10 μg/ml of anti-IL4 and anti-IFNγ (eBioscience). T cell cultures were collected at different time points for RNA extraction and gene expression studies

first: Wai-Ping

last: Fung-Leung


title: Goose Mx and OASL play vital roles in the antiviral effects of type I, II, and III interferon against newly emerging avian flavivirus

city: Chengdu

last: Zhang

state: WenJiang

address: Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu City, Sichuan Province, 611130, China.

institute: Sichuan Agricultural University

summary:
Purpose：Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. PBMCs are important immune cells and effectively respond to IFN treatment. Therefore, the goals of this study are to compare the transcriptional profile of the goose IFN (goIFNα, goIFNγ and goIFNλ)-mediated immune response in PBMCs.

Methods：Peripheral blood mononuclear cells (PBMCs) were stimulated with recombinant goIFN-α, γ and λ for 3 h, and those treated with cell lysates from pcDNA3.1 (+)-transfected BHK-21 cells were considered as control group. Cells were harvested with 1 mL RNAiso Plus reagent for RNA extraction. Obtained RNA quantity and quality were evaluated using NanoDrop, Qubit and Agilent 2100 Bioanalyzer. After qualification and quantification using an Agilent 2100 Bioanalyzer and ABI Step One Plus Real Time PCR System, the libraries were sequenced with Illumina HiSeqTM 2000.

Results：Comparisons between IFN treatment groups and the control group were performed, and DEGs were analysed using the DESeq R package, a model based on the negative binomial distribution. For the statistical analysis, all read counts were normalized by calculating the FPKM value, and further, the FPKM + 1 values were log2 transformed and the means of expression (in log2 FPKMs) were used for further analysis. An P value < 0.05, which was adjusted by the false discovery rate (FDR), was defined as the threshold of DEGs, and log2-fold change ＞ 0 (or < 0) was defined as up-regulated (down-regulated genes). According to the results of DEG analysis, we selected 17 IFN‑responsive genes from the RNA-seq data for validation by RT-qPCR.

Conclusion：Our study represents the first detailed analysis of the transcriptional profile of the goose IFN (goIFNα, goIFNγ and goIFNλ) immune response in PBMCs. The stimulation of goIFNs initiated a series of signalling cascades at early stages, leading to the transcriptional regulation of hundreds of DEGs, and each IFN induced a unique and partially overlapping set of ISGs. Most importantly, we identified approximately 101 immune-related genes, which were mainly involved in the toll-like receptor signalling pathway, JAK-STAT signalling pathway and antiviral pathway. Moreover, these results were verified by RT-qPCR, and the correlation analysis of RNA-Seq data and qRT-PCR results showed that some relevant relationships between candidate genes may be related to the balance of the host immune response, which remains to be further studied in the future.

overall_design: Deep RNA sequencing (RNA-seq) was carried out to generate a high-resolution transcriptome map for goIFNα, goIFNγ and goIFNλ-treated PBMCs, and subsequently, some ISGs that might be involved in the IFN-dependent antiviral response were identified.

first: Shun

last: Chen

first: Anchun

last: Cheng


title: Comprehensive transcriptome profiling of Salvia miltiorrhiza for discovery of downstream and regulatory genes involved in tanshinone and phenolic acid biosynthesis

city: Hangzhou

last: Zhou

state: Zhejiang

address: 548 Binwen Road, Binjiang district

department: college of pharmacy

institute: zhejiang chinese medical university

summary: Tanshinones and phenolic acids are crucial bioactive compounds biosynthesized in Salvia miltiorrhiza. Methyl jasmonate (MeJA) is an effective elicitor to enhance the production of phenolic acids and tanshinones simultaneously, while yeast extract (YE) is used as a biotic elicitor that only induce tanshinones accumulation. However, little was known about the different molecular mechanism. To identify the downstream and regulatory genes involved in tanshinone and phenolic acid biosynthesis, we conducted comparative transcriptome profiling of S. miltiorrhiza hairy roots treated with either MeJA or YE.Total 55588 unigenes were assembled from about 1.72 billion clean reads, of which 42458 unigenes (76.4%) were successfully annotated. The expression patterns of 19 selected genes in the significantly upregulated unigenes were verified by quantitative real-time PCR. The candidate downstream genes and other cytochrome P450s involved in the late steps of tanshinone and phenolic acid biosynthesis pathways were screened from the RNA-seq dataset based on co-expression pattern analysis with specific biosynthetic genes. Additionally, 375 transcription factors were identified to exhibit a significant up-regulated expression pattern in response to induction. This study can provide us a valuable gene resource for elucidating the molecular mechanism of tanshinones and phenolic acids biosynthesis in hairy roots of S.miltiorrhiza.

overall_design: Examination of  2 different elictors at two different induced time points and the control

first: Guoyin

last: Kai


title: ME31B/DDX6 globally represses maternal mRNAs by two distinct mechanisms during the Drosophila maternal-to-zygotic transition

city: Toronto

first: Olivia

last: Rissland

address: 686 Bay Street

institute: The Hospital for Sick Children

summary: Using RNA immunoprecipitation sequencing, we found that ME31B binding represses expression of thousands of genes in the Drosophila early embryo, but the mechanism by which ME31B acts changes: before the maternal-to-zygotic transition, ME31B represses translation, while afterwards, it stimulates mRNA decay.

overall_design: RNA immunoprecipitation sequencing was performed for PABP and ME31B in S2 cells, and in the early embryo (0-5 hours for w1118, eGFP-me31B; 0-1 and 2-3 hours for png50; 0-1 hours for eGFP-me31B;png50 flies )

first: Miranda

last: Wang

first: Michael

last: Ly

first: Andrew

last: Lugowski


title: Intrinsic Plasma Cell Differentiation Defects in BENTA Patient B cells

last: Snow

state: Maryland

address: 4301 Jones Bridge Road, C-2013

department: Pharmacology & Molecular Therapeutics

institute: Uniformed Services University of the Health Sciences

summary: From purified naïve B cells from a BENTA patient cohort, we performed differential expression analysis by RNA-seq to show that BENTA B cells exhibit intrinsic defects in B cell differentiation with poor induction of specific genes required for plasma cell commitment.

overall_design: Transcriptome profiling of one cell type in technical duplicate for 4 individuals per group

first: Clifton

last: Dalgard


title: Altered Hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways [ATAC-seq]

city: Bronx

first: Amit

last: Verma

state: NY

address: 1300 Morris Park Ave

department: Medicine

institute: Albert Einstein College of Medicine

summary: Transcriptional deregulation of oncogenic pathways is a hallmark of cancer, and can be due to epigenetic alterations. 5-hydroxymethylcytosine is a recently discovered epigenetic modification that has not been studied in pancreatic cancer. Genome-wide analysis of 5-hmC enriched loci with hmC-seal was conducted in low-passage pancreatic cancer cell lines and primary patient-derived xenografts and revealed strikingly altered patterns in neoplastic tissues. Differentially hydroxymethylated regions preferentially affected regulatory regions of the genome, specifically overlapping with known H3K4me1 enhancers. Furthermore, base pair resolution analysis of methylation and hydroxymethylation with oxidative bisulfite sequencing was conducted and correlated with chromatin accessibility by ATAC-seq in pancreatic cancer and control samples. 5hmC was specifically enriched at open regions of chromatin and gain of 5-hmC was correlated with upregulation of the cognate transcripts, including many oncogenic pathways implicated in pancreatic neoplasia, such as myc, KRAS, VEGF and BRD4. Specifically, BRD4 was overexpressed and acquired 5hmC at enhancer regions in majority of neoplastic samples. Functionally, acquisition of 5hmC at BRD4 promoter regulated increase in transcript expression. Furthermore, blockade of BRD4 inhibited pancreatic cancer growth in vivo. In summary, redistribution of 5-hmC and preferential enrichment at oncogenic enhancers is a novel regulatory mechanism in human cancer.

overall_design: Atac-seq analysis to obtain chromatin accessibility patterns for pancreatic control and cancer cells was performed

first: Kith

last: Pradhan


title: Altered Hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways

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

overall_design: Refer to individual Series


title: Altered Hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways [RNA-seq]

overall_design: Gene expression profiling using RNAseq was performed to assess transcriptomic profiles of pancreatic controls and pancreatic cancer cells


title: Identification of anti-salt genes in rice culture

city: Los angeles

first: Xiangming

last: Ding

address: 650 Charles E Young Dr S, Los Angeles, CA 90095

institute: UCLA

summary: Salt-water Rice has stronger resistance than common rice under high salt environment. We aim to find anti-salt genes by comparing  the gene expression, which can provide target genes for further function research

overall_design: Compare the gene exprerssion in rice cultured in sea water and in fresh water

first: Risheng


title: Targeted sequencing of potential CRISRP/Cas9 off-target editing sites in modified human CD34+ Haematopoietic Stem Cells

city: Oxford

first: Jelena

last: Telenius

address: MRC Weatherall Institute of Molecular Medicine University of Oxford John Radcliffe Hospital Headington

department: Weatherall Institute of Molecular Medicine (WIMM)

institute: Oxford University

summary: We report the use of short biotinylated oligonucleotides for the targeted pulldown of potential CRISPR/Cas9 off-target loci in condition and control to measure the frequency of off target editing

overall_design: NG Capture-C was used to investigate the Potential off-target CRISPR/Cas9 loci. NG Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. Potential off-target CRISPR/Cas9 loci were identified using the Sanger tool (http://www.sanger.ac.uk/htgt/wge/find_off_targets_by_seq) and 70bp oligonucleotides designed for target-pulldown. Whole genome amplified (WGA) DNA from edited clones from two editing strategies was pooled and indexed. Indexed WGA DNA was then pulled down in two rounds of hybridization with biotinylated oligonucleotides and streptavadin beads to enrich for putative off-target editing loci.

first: Damien

last: Downes

first: Mohsin

last: Badat

first: Chris

last: Fisher

first: Sachith

last: Mettananda

first: Jim

last: Hughes


title: RNA sequencing data for 30 bladder cancer cell lines

city: Houston

first: Woonyoung

last: Choi

state: TX

address: 1515 Holcombe

institute: Md Anderson Cancer center

summary: RNA-sequencing of a panel of urothelial cancer cells. The goal of the study is to examine the genome-wide expression profile in each of the 30 urothelial cancer cells tested in our laboratory.

overall_design: Each of the 30 cell lines was DNA fingerprinted to confirm its real identity. Total RNA was obtained from each cell line and subjected to Illumina RNA sequencing.

first: I-ling

last: Lee

first: David

last: McConkey

first: Xiaoping

last: Su


title: Open chromatin profile of primary and lymph node oral cancer cells

city: Singapore

first: Ankur

last: Sharma

state: Singapore

address: 60 Biopolis St, #02-01,

department: CTSO

country: Singapore

institute: Genome Institute Singapore

summary: We employed FAIRE-seq to identify open chromatin in head and neck squamous cell carcinoma (HNSCC) patient-derived primary and lymph node cell lines. We further analysed this data to identify differential open chromatin between primary and metastatic cells.

overall_design: Examination of open chromatin in primary vs. lymph node metastatic cells from a patient (HS137) with HNSCC.

first: Ramanuj

last: DasGupta


title: Altered Hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways [MeDIP-seq]

overall_design: hmC-seal assay was used to obtain genome wide 5hmC patterns for pancreatic control and cancer cells was performed


title: Integration of lncRNA-miRNA-mRNA reveals novel insights into reproductive regulation in honey bees

city: Beijing

first: Xiao

last: Chen

state: Beijing

address: Haidian Xiangshan Beigou No.1

institute: Institute of Apicultural Research, Chinese Academy of Agricultural Sciences

summary: The present study is the first study to identify the involvement of mRNA, lncRNAs and miRNA in the ovary activation and oviposition regulation processes in honey-bee queens. mRNA, lncRNA and miRNA expresion profiles were examined in ovaries of virgin queens, egg-laying queens, egg-laying inhibited queens and egg-laying recovery queens.

overall_design: To identify the involvement of mRNAs, lncRNAs and miRNAs in the ovary activation and oviposition regulation processes in honey-bee queens, a total of four different ovaries samples were used in this study: (1) ovaries of virgin queens (n=3); (2) ovaries of egg-laying queens (n=3); (3) ovaries of egg-laying inhibited queens (n=3) (4) ovaries of egg-laying recovered queens (n=3). To sample the caged queens' ovaries, the queens were caged and placed in the original colony respectively for seven days. And at the end of the seventh day, ovaries samples were collected. To sample the recovered queens' ovaries, the queen was released after caged for seven days. And then, on the eighth day, the queen recovered to normal condition and laid eggs, and ovaries samples were collected. All the samples were collected immediately, snap frozen in liquid nitrogen and stored at -80C.


title: Alteration In Auxin Homeostasis By Overexpression Of PINOID Kinase Causes Leaf Growth Defects In Arabidopsis thaliana

city: Antwerp

first: Kris

last: Vissenberg

state: Antwerp

address: Groenenborgerlaan 171 U636

department: Biology

country: Belgium

institute: University of Antwerp

summary: We studied two growth phases- proliferation, and expansion in first pair of leaves in Arabidosis using two different overexpression lines of PID gene. Ectopic expression of PID lead to small rosette and leaf phenotype.

overall_design: We used first pair of leaves from proliferation ( 9 DAS-days after stratification) and expansion (16 DAS) stage from wild type Col-0 ecotype, 35S::PID10, 35S::PID21. Three genotype, three biological replicates, two time points (=18 sample). Experiment repeated twice generating two reads in two lanes i.e. L001 & L002 for each sample. Results calculated after combining reads from both lanes (=18x2=36 raw files; 2 for each sample)

first: Kumud

last: Saini

first: Malgorzata

last: Zdanio

first: Daria

last: Balcerowicz

first: Marios

last: Nektarios Markakis

first: Tom

last: Beeckman

first: Lieven

last: De Veylder

first: Els

last: Prinsen

first: Gerrit

middle: T

last: Beemster


title: Transcriptome sequencing in the tammar wallaby unveils conserved gene expression networks underlying reproduction in therian mammals

city: Stanford

first: Michael

middle: Warren

last: Guernsey

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University School of Medicine

summary: We characterized the transcriptome of the wallaby placenta and lactating mammary gland over the course of reproduction

overall_design: Expression profiling of three time points in two tissue types of the wallaby placenta and three time points of lactating mammary gland tissue

first: Julie

last: Baker


title: Mycobacterium bovis Bacillus Calmette-Guerin (BCG) reprograms melanoma microenvironment to promote antitumor T cell responses

city: Torrance

first: Delphine

last: Lee

address: 1124 W Carson St

department: Dermatology/Immunology

institute: Los Angeles Biomedical Institute

summary: Intralesional therapy using Mycobacterium bovis Bacillus Calmette-Guérin (BCG) for cutaneous metastatic melanoma induces regression of injected, but also non-injected lesions. Tumor-associated macrophages (also known as M2) infiltrate solid tumors and impair antitumor immunity. Since macrophages play a pivotal role in both tumors and mycobacterial infections, we hypothesized BCG alters M2 to promote antitumor immunity. BCG-treated, in vitro-polarized M2 (M2-BCG) show dramatic transcriptional changes involving inflammation, immune cell recruitment, cross-talk and activation pathways. Mechanistic network analysis indicates potential for M2-BCG to improve IFN-γ responses, frequently used as a marker for successful antitumor immunity. Accordingly, we found an increased frequency of IFN-γ-producing CD4+ T cells responding to M2-BCG vs mock-treated M2 (p<0.05). Moreover, supernatant from M2-BCG increased the frequency of granzyme B-producing CD8+ tumor-infiltrating lymphocytes (TIL) responding to autologous melanoma cell lines (p<0.01). Comparing the transcriptome of injected vs uninjected lesions biopsied from IL-BCG patients showed immune function prevailing in injected lesions, with the most enriched pathways representing T cell activation mechanisms. In vitro BCG-infected tumor cells also stimulated IFN-γ production from HLA-A2-restricted syngeneic TIL from the same melanoma patient (p<0.05). Together, our data indicates BCG can promote an antitumor microenvironment in cutaneous metastatic melanoma.

overall_design: 15 samples in total. 3 groups: M1 with media, M2 with media, M2 with BCG (5 replicates for each group with patient pairing)

first: Ricardo

last: Lardone


title: Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 reveals vib1 to be essential for cellulase induction

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

summary: The ascomycete Trichoderma reesei is an industrial producer of cellulolytic and hemicellulolytic enzymes and also serves as a model for investigations on these enzymes and their genes. The strain QM9978 has a cellulase negative phenotype and therefore presents a valuable tool for understanding the mechanisms underlying cellulase regulation. A transcriptomic analyses of the cellulase negative strain QM9978 and the original strain QM6a have been performed to identify the genetic differences between QM6a and QM9978 leading to the cellulase-negative phenotype

overall_design: Two strains were used: T. reesei QM6a (ATCC13631) and QM9978 (Torigoi, E. et al. Mutants of Trichoderma reesei are defective in cellulose induction, but not basal expression of cellulase-encoding genes. Gene 173, 199-203 (1996)) with two time points for each strain T0h (glucose starvation), T24h and T48h (after lactose pulse). All samples are in duplicate.

first: C

last: Ivanova

first: F

last: Bidard

first: S

last: Lemoine

last: Blugeon


title: Expression profiling analyses of ECF sigma factor PG0162-PG1660 mutant of Porphyromonas gingivalis W83 [RNA-Seq]

city: Loma Linda

first: Yuetan

last: Dou

address: 11021 Campus Street AH114

department: Microbiology and Molecular Genetics

institute: Loma Linda University

summary: The role of ECF sigma factors PG0162, PG01660 were involved in virulence regulationin Porphyromonas gingivalis was published Yuetan Dou, Devon Osbourne, Rachelle McKenzie, Hansel M Fletcher. (2010) Involvement of extracytoplasmic function sigma factors in virulence regulation in Porphyromonas gingivalis W83. FEMS Microbiology Letter, 312(1):24-32.

overall_design: To study the expression profile of ECF sigma factor PG0162-PG1660 mutant under hydrogen peroxide stress conditions compared to the wild-type W83 by using RNA-Seq.

first: Xin

last: Chen

first: Charles

last: Wang

first: Hansel

last: Fletcher


title: Transcriptional regulatory networks of psoriasis

city: Moscow

first: Evgeny

last: Chekalin

address: Gubkina, 3

country: Russia

institute: Vavilov Institute of General Genetics

summary: Psoriasis is a common inflammatory skin disease with complex etiology and chronic progression. To provide novel insights into the molecular mechanisms of regulation of the disease we performed RNA sequencing (RNA-Seq) analysis of fourteen pairs of skin samples collected from psoriatic patients with consequent pathway analysis and identification of the main transcriptional regulators of psoriasis-associated pathways. In order to identify the most important regulators of the disease, we combined the results obtained with MetaCore Interactome enrichment tool and cisExpress algorithm and compared them to regulatory psoriasis response elements found in literature. Comparative approach allowed us to identify 42 core transcriptional regulators of the disease associated with inflammation (NFkB, IRF9, JUN, FOS, SRF), activity of T-cells in the psoriatic lesions (STAT6, FOXP3, NFATC2, GATA3, TCF7, RUNX1, etc.), hyper-proliferation and migration of keratinocytes (JUN, FOS, NFIB, TFAP2A, TFAP2C), and with lipid metabolism (TFAP2, RARA, VDR). We also identified 66 transcription factors not previously associated with psoriasis. Using MetaCore pathway maps we illustrated and described the molecular basis of psoriatic skin lesions.

overall_design: Skin mRNA profiles for samples pairs taken from 14 psoriasis patients, LS- sample from psoriatic lesional skin, NL- sample from psoriatic nonlesional skin

first: A

last: Zolotarenko

first: E

last: Mesentsev

first: L

last: Kiseleva

last: Gribanova

first: R

last: Mehta

last: Baranova

first: T

middle: V

last: Tatarinova

last: Pirusian

last: Bruskin


title: ATRX is necessary for cellular senescence and represses HRAS to drive cells from quiescence into senescence [ChIP-Seq]

city: New York

first: Willey

last: Liao

address: 101 Avenue of the Americas

department: Bioinformatics

institute: New York Genome Center

summary: Senescence is a state of stable cell cycle exit that has important implications for development, physiology and disease.  It is distinct from quiescence in which cells can be induced to re-enter the cell cycle. Although it is well known that there are massive changes in the heterochromatin of senescent cells, the molecular mechanisms underpinning the transition from reversible quiescence into irreversible senescence have remained elusive. Here, we demonstrate that the chromatin-remodeling enzyme ATRX is required for senescence. ATRX accumulates in nuclear foci during both replicative and cellular senescence. Using ChIP-seq and RNA-seq we identified HRAS as part of an ATRX regulated gene expression program associated with senescence. Repression of HRAS is sufficient to promote the transition of quiescent cells into senescence. Thus we conclude that the repression of HRAS is likely a direct consequence of ATRX binding and critical to how it mediates its role in senescence.

overall_design: ATRX binding was analyzed in dedifferentiated liposarcoma cell lines under cycling, quiescent and senescent (using two unique inducers) conditions via ChIP-seq

first: Marta

last: Kovatcheva

first: Will

first: Mary

last: Klein

first: Nicolas

last: Robine

first: Heather

last: Geigher

first: Aimee

last: Crago

first: Mark

last: Dickson

first: William

last: Tap

first: Samuel

last: Singer

first: Andrew

last: Koff


title: ATRX is necessary for cellular senescence and represses HRAS to drive cells from quiescence into senescence [RNA-Seq]

overall_design: mRNA expression profiles were analyzed in dedifferentiated liposarcoma cell lines under cycling, quiescent and senescent (using two unique inducers) conditions via RNA-seq


title: Analysis of age-associated transcriptome changes in  uterus and decidua

city: Cambridge

first: Laura

last: Woods

address: Babraham Hall

institute: The Babraham Institute

summary: We use RNA-sequencing to measure global transcription in uteri of young and aged (~1yr old) C57BL/6 females at day 3.5 (E3.5) of pregnancy, and of the decidual part of E11.5 placentas developed in young and aged (~1yr old) females. We report dys-regulation of gene expression in the E3.5 uteri and E11.5 deciduae of aged mice. We compare the transcriptome of young and aged E11.5 deciduae with that of young deciduae from E9.5-E12.5 of pregnancy, and report that aged E11.5 deciduae are developmentally retarded in comparison to young deciduae.

overall_design: For E3.5 uterus RNA-seq data, we generated biological replicates from 3 young (8-20 week old) and 3 aged (47-49 week old) mice. Data for each biological replicate was generated by constructing RNA-seq libraries from 2 equivalent portions of each uterus, data from both libraries was treated as technical replicates and pooled at the analysis stage, after confirming there was no significant difference between the replicates from a single uterus. For E11.5 data, we generated biological replicates of 6 deciduae from 3 litters (2 from each litter) from young mothers (9-10 weeks, n=6) and 10 deciduae from 5 litters of aged mothers (43-47 weeks, 2 deciduae from each litter). Aged E11.5 samples were split into 2 groups: those accompanying embryos that appeared normal (An, n=5) and those with morphologically abnormal embryos (Aa, n=5). One An and one Aa decidua was taken from each litter. For decidua timecourse data, 3 biological replicates each were generated from 3 separate litters from young 9-10 week old mothers at E9.5, E10.5, E11.5, and E12.5 of pregnancy.

first: Vicen

last: Perez-Garcia

first: Jens

last: Kieckbusch

first: Xiaoqui

last: Wang

first: Francesco

last: DeMayo

last: Colucci

first: Myriam

last: Hembrger


title: Salt-responsive differential gene expression analysis by RNA sequencing in the roots of a mangrove Avicennia officinalis

first: Prakash

last: Kumar

address: 14 Science Drive 4,

department: Department of Biological Sciences

institute: National University of Singapore

summary: The roots of halophytes such as mangroves provide the first line of defense against the constant salt stress they experience. Such adaptation should include major reprogramming of the gene expression profiles. Using RNA-sequencing approach we identified 101,446 ‘all-unigenes’ from the seedling roots of the mangrove tree Avicennia officinalis. From the data 6618 genes were identified to be differentially regulated by salt when two-month-old greenhouse-grown seedlings without prior exposure to sea water were subjected to 24 h of 500 mM NaCl treatment. About 1,404 genes were significantly up-regulated, while 5214 genes were down-regulated. Based on Gene Ontology analysis, they could be classified under various categories, including metabolic processes, stress and defense response, signal transduction, transcription-related and transporters. Our analysis provides the baseline information towards understanding salt balance in mangroves and hence mechanism of salt tolerance in plants.

overall_design: Differential gene expression was studied upon salt treatment using two controls and two salt treated (24h with 500 mM NaCl) samples.

first: Pannaga

last: Krishnamurthy

first: Bijayalaxmi

last: Mohanthy

first: Edward

last: Wijaya

first: Dong-Yup

last: Lee

first: Tit-Meng

last: Lim

first: Qingsong

last: Lin

first: Xu

last: Jian

first: Chiang-Shiong

last: Loh


title: Transcriptional profile of brown adipose tissue (BAT) and white vastus lateralis (WV) from BATI4KO mice

status: Public on Sep 13 2017

city: Boston

first: Evan

last: Rosen

state: MA

address: 3 Blackfan Cir

department: Endocrinology

institute: Beth Israel Deconess Medical Center

summary: We report RNA-seq data from the brown fat and vastus muscles of mice lacking IRF4 in brown fat (BATI4KO) vs floxed littermate controls

overall_design: Whole tissue (BAT and white vastus) was harvested from BATI4KO mice or floxed littermate controls

first: Xingxing

last: Kong

first: Brian

last: Dawes


title: Genome-wide analysis of herpes simplex virus type 1 (HSV-1) infected cells

city: Kunming

first: Jiandong

last: Shi

state: Yunnan

address: 935# Jiaoling Road

department: Department of Vaccine Research

institute: Institute of Medical Biology

summary: The goal of this study was to compare the whole transcriptional profile (RNA-seq) of herpes simplex virus type 1 (HSV-1) infected and mock infected human fibroblast KMB17 strain at 48 hours post infection.There is increasing evidence that circular RNAs (circRNAs) are involved in diverse pathogenesis processes; however, their roles in virus infection remain unclear. Here, we profiled global changes of circRNAs, genes and microRNA (miRNAs) under herpes simplex virus type 1 (HSV-1) infection by RNA-seq. Numerous dysregulated transcripts comprised of 536 circRNAs, 3,885 genes and 207 miRNAs were found during viral infection. The dysregulated genes were enriched to NOD-like receptor signaling pathway, Jak-STAT signaling pathway and pathways of apoptosis, cell cycle progression and cell death, all of which may be implicated in viral pathogenesis and cellular immunity. Further integration analysis of circRNAs, genes and miRNAs reveals putative involvement of circRNAs in viral pathogenesis and antiviral immunity by circRNA-miRNA-gene regulatory axis. This work provides a comprehensive view for dysregulated circRNAs induced by HSV-1 and their interplay with miRNAs and genes, thus offering new insights into the mechanisms of interactions between HSV-1 and its host.

overall_design: Whole transcriptome profiles of  herpes simplex virus type 1 (HSV-1) infected and mock infected human fibroblast KMB17 strain at 48 hours post infection were generated by deep sequencing, in triplicate, using Illumina Hiseq 4000 platform.

first: Yunzhang

last: Hu


title: Distinct cell cycle control in naïve and primed mouse pluripotency [gDNA-seq]

city: Nijmegen

first: Menno

last: ter Huurne

address: Geert Grooteplein 26

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen

summary: The cell cycle of primed pluripotent mouse serum ESCs is characterised by a shortened G1-phase. Here we assessed the differences in cell cycle between serum ESCs and naive 2i ESCs.

overall_design: Mouse ESCs were cultured either in serum conditions and genomic DNA was extracted.

first: Henk

last: Stunnenberg


title: Distinct cell cycle control in naïve and primed mouse pluripotency [RNA-seq]

overall_design: Mouse ESCs were cultured either in serum conditions or 2i conditions. Cells were sorted and RNA was extracted from cells in early G1-phase.  Biological replicate included.


title: Regulation of mRNA translation and subcellular location controls protein synthesis of key modulators of the DNA damage response during B cell activation

first: Felix

last: Krueger

address: Granta Park

institute: Altos Labs

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

overall_design: Refer to individual Series


title: Regulation of mRNA translation and subcellular location controls protein synthesis of key modulators of the DNA damage response during B cell activation [PolyRiboSeq]

summary: Post-transcriptional regulation of cellular mRNA is essential for protein synthesis. Here we describe the importance of mRNA translational repression and mRNA subcellular location for protein expression during B lymphocyte activation and the DNA damage response. Cytoplasmic RNA granules are formed upon cell activation with mitogens, including stress granules that contain the RNA binding protein Tia1. Tia1 binds to a subset of transcripts involved in cell stress, including p53 mRNA, and controls translational silencing and RNA granule localization. DNA damage promotes mRNA relocation and translation in part due to dissociation of Tia1 from its mRNA targets. Upon DNA damage, p53 mRNA is released from stress granules and associates with polyribosomes to increase protein synthesis. Global analysis of cellular mRNA abundance and translation indicates that this is an extended ATM-dependent mechanism to increase protein expression of key modulators of the DNA damage response.

overall_design: Splenic B cells from C57BL/6Babr mice were isolated and activated with LPS for 48 hours prior induction or not of DNA damage with etoposide. After 4 hours, cells were treated with cycloheximide (100 microgrames per ml) for 3 minutes. Then, cytoplasmic extracts were collected. Polysome fractionation in sucrose gradients (10-50% sucrose) was performed for isolation of mRNA associated to monosomes (fractions 4 to 7), light polysomes (fractions 8 to 10) or heavy polysomes (fractions 11 to 16). The ATM kinase inhibitor KU55933 was added 1 hour prior induction of DNA damage with etoposide.

first: Manuel

last: Diaz-Muñoz

first: Vladimir

middle: Y

last: Kiselev

first: Nicolas

last: Le Novere

first: Tomaz

last: Curk

first: Jernej

last: Ule

first: Martin

last: Turner


title: Characterization  of the small RNAome in acute myeloid leukemia and discovery of novel small RNA species by deep sequencing (Illumina)

city: Cantanhede

first: Jacek

middle: Dariusz

last: Marzec

address: Biocant Park

country: Portugal

institute: CoLAB AccelBio

summary: We used small RNA seq (Illumina) to characterise and quantify the miRNA and small non-coding (snc)RNA transcriptome of 38 libraries of size-fractionated RNA obtained from AML patients and normal bone marrow. We detected the expression of 765 known miRNAs and 2554 uniquely located species of sncRNAs. A total of 575 potential miRNA candidate hairpins were identified. We also identified 37 C/D Box and 51 H/ACA Box, potential novel snoRNAs.

overall_design: We sequenced 38 libraries obtained from 34 cytogenetically distinct cases of AML and 1 normal bone marrow from healthy donor. Duplicate experiments, which involved 2 independent RNA size fractionation and library preparation, were performed for 2 patient samples and for the normal bone marrow.

first: Jun

last: Wang

first: Floriana

last: Manodoro

first: Charles

last: Mein

first: Alessandra

last: Curtotti

first: Bryan

last: Young

first: Silvana

last: Debernardi


title: Regulation of mRNA translation and subcellular location controls protein synthesis of key modulators of the DNA damage response during B cell activation [RNA-seq]

overall_design: Splenic B cells from C57BL/6Babr mice were isolated and activated with LPS for 48 hours prior induction or not of DNA damage with etoposide. Total RNA from control or etoposide-treated B cells was isolated 4 hour later. The ATM kinase inhibitor KU55933 was added 1 hour prior induction of DNA damage with etoposide.


title: Regulation of mRNA translation and subcellular location controls protein synthesis of key modulators of the DNA damage response during B cell activation [CLIP-seq]

overall_design: Analysis by individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) of Tia1-RNA interactions in the cytoplasm of B cells activated with LPS for 48 hours. 2 biological replicates perfomed.


title: PTP4A1 phosphatase is overexpressed in systemic sclerosis fibroblasts and promotes TGFb signaling

status: Public on Sep 12 2017

city: La Jolla

first: Cristiano

last: Sacchetti

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

summary: We show that silencing of tyrosine phosphatase PTP4A1 attenuates pro-fibrotic TGFb signaling in human dermal fibroblasts

overall_design: Cell-permeable antisense morpholino oligonucleotide (ASO) was designed against the pre-mRNA splicing junction between intron 2 and exon 3. ASO treatment enabled nearly complete knockdown of PTP4A1. Next, using next generation sequencing, we determined the transcriptional profile of 3 normal human dermal fibroblast lines lines treated with PTP4A1 ASO (PRL-1 samples), compared to the same lines treated with a control non-targeting ASO (Vivo samples).

first: Yunpeng

last: Bai

first: Stephanie

last: Stanford

first: Paola

last: Di Benedetto

last: Cipriani

first: Eugenio

last: Santelli

first: Sonsoles

last: Piera-Velazquez

last: Chernitskiy

first: William

last: Kiosses

first: Arnold

last: Ceponis

first: Klaus

middle: H

last: Kaestner

first: Francesco

last: Boin

first: Sergio

last: Jimenez

first: Roberto

last: Giacomelli

first: Zhong-Yin

last: Zhang

first: Nunzio

last: Bottini


title: RNA Seq analysis of WT haploid and Disome 10 in Saccharomyces cerevisiae

city: Baltimore

first: Wahid

last: Mulla

address: 855 North Wolfe Street

institute: Johns Hopkins University

summary: Aneuploidy and epigenetic alterations have long been associated with carcinogenesis, but it was unknown whether aneuploidy could disrupt the epigenetic states required for cellular differentiation. In this study, we found that ~3% of random aneuploid karyotypes in yeast disrupt the stable inheritance of silenced chromatin during cell proliferation. Karyotype analysis revealed that this phenotype was significantly correlated with gains of chromosomes III and X. Chromosome X disomy alone was sufficient to disrupt chromatin silencing and yeast mating-type identity as indicated by a lack of growth response to pheromone. The silencing defect was not limited to the cryptic mating type loci but was associated with global changes in histone modifications and chromatin localization of Sir2 histone deacetylase. The chromatin-silencing defect of disome X can be partially recapitulated by increasing the copy number of several genes on chromosome X. These results suggest that aneuploidy can directly cause epigenetic instability and disrupt cellular differentiation.

overall_design: WT haploid vs Disome 10 in triplicates

first: Chris

last: Seidel


title: RNA-Seq of SHEP TET21N cells upon Doxorubicin treatment

city: Heidelberg

first: Tatsiana

last: Ryl

address: Im Neuenheimer Feld 280

department: Theoretical Systems Biology

institute: German Cancer Research Center

summary: MYCN-high and MYCN-low neuroblastoma cells differ in their responses to Doxorubicin treatment. To explain this difference we compared the global trancriptomes of MYCN-high and MYCN-low cells before, during and after treatment.

overall_design: MYCN-high cells without doxycyline and MYCN-low cells with doxycycline were treated with 0.1µg/ml Doxorubicin.  Transcriptome was measured for the following time points: in untreated cells,  in cells which were treated with Doxorubicin for 72 hours, and in cells collected three, eight and fourteen days after Doxorubin washout.  Experiment was performed in biological duplicate.


title: ATRX is necessary for cellular senescence and represses HRAS to drive cells from quiescence into senescence

first: Andrew

last: Koff

address: 1275 York Avenue

institute: Sloan Kettering Institute


title: Skeletal muscle ERalpha action is critical for the maintenance of mitochondrial dynamics and metabolic homeostasis in male mice

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

summary: Impaired estrogen production and action are associated with obesity and insulin resistance in male males however the tissues critical for estrogen action in the maintenance of metabolic homeostasis remain inadequately understood.  Moreover, the cell specific target genes and molecular actions of estrogen in males remain unknown. We generated male mice with a muscle-specific ERa knockout (MERKO) to determine the role of this hormone nuclear receptor in controlling metabolic function and insulin action in skeletal muscle. Male MERKO mice became insulin resistant with age and accumulated more adipose tissue than floxed control mice.  Skeletal muscle was distinguished by enlarged hyper-fused mitochondria that produced increased amounts of superoxide, and this was associated with enhanced proinflammatory signaling.  The striking mitochondrial phenotype was accompanied by reduced protein abundance of electron transport chain proteins and the mitochondrial biogenesis marker Pgc1a.  Muscle from MERKO mice showed imbalanced protein abundance of mitochondrial fission-fusion proteins most notably marked reductions in total DRP1, MFN1, and OPA1 were observed compared with f/f control.  To recapitulate the reduction in DRP1 protein leading to impairment in mitochondrial fission, we generated mice with a muscle-specific heterozygous deletion in Drp1 (mDrp1+/-).  mDrp1+/- mice phenocopied the aberrant muscle mitochondrial morphology and dysfunction of the MERKO mice and developed insulin resistance with age.  Skeletal muscle ERa is critical for the maintenance of mitochondrial function and metabolic homeostasis in male mice.

overall_design: Quadriceps mRNA profiles of male 20-week old wild type (WT) and muscle-specific Erα knockout (MERKO) mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000.

first: Andrea

last: Hevener


title: Analysis of transcriptome profiling in liver tissues of wild-type and SREBP1c knockout mice using RNA-seq

status: Public on Sep 11 2017

city: Seoul

first: Jae Bum

last: Kim

country: South Korea

institute: Seoul National University

summary: Sterol regulatory element-binding protein 1c (SREBP1c) plays important roles in lipid metabolism and cell proliferation. To identify novel target genes of SREBP1c, particularly, in cell cycle regulation, we analyzed transcriptome profiling (RNA-seq) in liver tissue of wild-type and SREBP1c knockout mice. Liver transcriptome profiles of 12-week-old wild-type (C57BL/6) and SREBP1c KO mice were generated by mRNA-seq, in duplicate, using Illumina HiSeq4000 by MACROGEN, Inc (Korea).

overall_design: Analysis of transcriptome profilings (RNA-seq) in liver tissue of wild-type and SREBP1c knockout mice

first: Jae Ho

last: Lee

first: Yong Geun

last: Jeon

first: Hagoon

last: Jang

first: Jeu

last: Park


title: Autocrine BMP-4 signaling promotes survival of colorectal cancer cells.

city: Wakayama

first: Shogo

last: Ehata

state: Wakayama

address: Kimiidera 811-1

department: School of Medicine

country: Japan

institute: Wakayama Medical University

summary: Prognoses are poor for colorectal cancer (CRC) patients with metastatic lesions, leading to high demand for the development of novel molecular target therapies. Here, we demonstrate that expression of bone morphogenetic protein 4 (BMP4) is universally up-regulated and endogenous BMP signaling is activated in human CRC cells and tissues. Inhibition of endogenous BMP signaling by the BMP type I receptor inhibitor LDN-193189 led to elevated expression of dual specificity phosphatase 5 (DUSP5) in CRC cells, inducing apoptosis through the dephosphorylation of Erk MAP kinase. Administration of LDN-193189 to mice diminished tumor formation of CRC cells in vivo. Our findings thus suggest that inhibition of autocrine BMP-4 by BMP inhibitors represents a promising candidate method for treatment of CRC.

overall_design: Target genes for BMPs in CRC cells were identified using LDN-193189.

first: Yuichiro

last: Yokoyama

first: Toshiaki

last: Watanabe

first: Yusuke

last: Tamura

first: Yoshinobu

last: Hashizume

first: Kohei

last: Miyazono


title: Single-cell transcriptomics reveals gene signatures and alterations associated with aging in distinct neural stem cell subpopulations

city: Shanghai

first: shi

last: zhanping

address: 1239 siping road

institute: Tongji University

summary: We report single-cell transcriptomics reveals gene signatures and alterations associated with aging in mouse SVZ.

overall_design: Examination of single-cell transcriptomics in distinct neural stem cell subpopulations

first: Z

last: Shi


title: DLK inhibitor treated Optic nerve crush

city: South San Francisco

first: Josh

last: Kaminker

address: 1 DNA Way

department: Bioinformatics and Computational Biology

country: USA

institute: Genentech

summary:
RNA was purified from retinas following crush in the presence of vehicle or DLKi
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0010360

overall_design: RNA from mouse retinas following optic nerve crush


title: Differential expression of microRNAs in productively HIV-1 infected and bystander macrophages in culture.

city: Montreal

first: Eric

last: Cohen

state: Quebec

address: 110 Ave des Pins Ouest

institute: IRCM

summary: Macrophages are heterogeneous immune cells with distinct origins, phenotypes, functions and tissue localization. Their susceptibility to HIV-1 is subject to variations from permissiveness to resistance, owing in part to regulatory microRNAs. Here, we used RNAseq to examine the expression of >400 microRNAs in productively infected and bystander cells of HIV-1-exposed macrophage cultures. Two micro-RNAs up regulated in bystander macrophages, miR-221 and miR-222, were identified as negative regulators of CD4 expression and CD4-mediated HIV-1 entry. Both microRNAs were enhanced by TNF-α, an inhibitor of CD4 expression. MiR-221/miR-222 inhibitors recovered HIV-1 entry in TNF-α-treated macrophages by enhancing CD4 expression, and increased HIV-1 replication and spread in macrophages by countering TNF-α-enhanced miR-221/miR-222 expression in bystander cells. In line with these findings, HIV-1-resistant intestinal myeloid cells express higher levels of miR-221 than peripheral blood monocytes. Thus, miR-221/miR-222 act as effectors of the antiviral host response activated during macrophage infection that restrict HIV-1 entry.

overall_design: Macrophages derived from the blood of 3 different adults (n=3 adults) were used. MicroRNAseq was performed on uninfected, productively HIV-1 infected (GFP+) and bystander (GFP-) macrophages.

first: Robert

last: Lodge

first: Éric


title: Distinct mesenchymal lineages and niches promote epithelial self-renewal and myofibrogenesis in the lung

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Using flourescence activated cell sorting, we gated on cells negative for CD45, CD326 and CD31, from single cell suspension generated from Adult mice. We then isolated subsets of YFP-, GFP- or TdTomato expressing cells from the indicated reporter mice. tdTomato indicates Wnt-responsive cells, GFP reports Pdgfr-alpha expression and YFP- was used to isolate lineaged Wnt2-positive cells. Additionally we included cells that were negative for the aforementioned reporters. We performed RNAseq on biological duplicates for each subset.

overall_design: Adult Axin2CreERT2:tdT:PdgfraEGFP and Wnt2CreERT2:R26REFYP mice lungs were FACS sorted into five corresponding lineages for RNAseq.

first: Jarod

last: Zepp

first: Edward

last: Morrisey


title: Bone Morphogenetic Protein and Retinoic Acid Synergistically Specify Female Germ Cell Fate in Mice

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: The mechanism for sex determination in mammalian germ cells remains unclear. Here, we reconstitute the female sex determination in mouse germ cells in vitro under a defined condition without the use of gonadal somatic cells. We show that retinoic acid (RA) and its key effector, STRA8, are not sufficient to induce the female germ-cell fate. In contrast, bone morphogenetic protein (BMP) and RA synergistically induce primordial germ cells (PGCs)/PGC-like cells (PGCLCs) derived from embryonic stem cells (ESCs) into fetal primary oocytes. The induction is characterized by the entry into the meiotic prophase, occurs synchronously and recapitulates cytological and transcriptome progression in vivo faithfully. Importantly, the female germ-cell induction necessitates a proper cellular competence–most typically, DNA demethylation of relevant genes–which is observed in appropriately propagated PGCs/PGCLCs, but not in PGCs/PGCLCs immediately after induction. This provides an explanation for the differential function of BMP signaling between PGC specification and female germ-cell induction. Ou findings represent a framework for a comprehensive delineation of the sex-determination pathway in mammalian germ cells, including humans.

overall_design: Transcriptome analysis of mouse PGCs and cultured PGCLCs using SC3-seq technology

first: Hidetaka

last: Miyauchi

first: Hiroshi

last: Ohta

first: So

last: Nagaoka

first: Fumio

last: Nakaki

first: Kotaro

last: Sasaki

first: Katsuhiko

last: Hayashi

first: Tomonori

last: Nakamura

first: Takuya

last: Yamamoto

first: Mitinori

last: Saitou


title: Transcriptome profile of a murine renal bilateral ischemia reperfusion model 2 hours to 12 months post injury

first: Jing

last: Liu

state: California

address: 1425 San Pablo St.

department: Department of Regenerative Medicine  & Stem Cell Biology

institute: University of Southern California

summary: Acute kidney injury (AKI) is associated with an increased risk of chronic kidney disease (CKD). To extend our understanding of renal repair, and its limits, we performed a detailed molecular characterization of a murine ischemia reperfusion injury (IRI) model for 12 months post injury. RNA-seq analysis highlights a cascade of temporal specific gene expression patterns related to tubular injury/repair, fibrosis, innate and adaptive immunity.

overall_design: Murine renal bilateral ischemia reperfusion injury (IRI) was performed on 10- to 12-week-old (25- 28g) C57Bl/6NCrl male mice (Charles River). The mice were anesthetized with an intraperitoneal injection of a ketamine/xylazine mix (105 mg ketamine/kg; 10 mg xylazine/kg). The body temperature was maintained at 36.5~ 37°C throughout the procedure. Kidneys were exposed by a midline abdominal incision and both renal pedicles were clamped for 21 min using non-traumatic microaneurysm clips. Sham-operated mice underwent the same procedure except for clamping of the pedicles.  Cohorts of 3 to 4 biological replicates for injured, sham and uninjured kidneys were collected for RNA-seq at 10 different time points following IRI: 2, 4 hours; 1, 2, 3 days; 1, 2, 4 weeks; and 6, 12 months.

first: Sanjeev

last: Kumar

first: Andrew

last: McMahon