title: Transcriptional profiling through RNA-seq of zebrafish larval liver after exposure to biliatresone, a biliary toxin.

city: Philadelphia

first: Xiao

last: Zhao

state: PA

address: 411 Curie Blvd, Rm 1126

department: Medicine/DIgestive Diseases

institute: University of Pennsylvania

summary: We sequenced liver mRNA isolated from biliatresone-treated zebrafish larvae and DMSO-treated controls in order to elucidate the molecular pathways induced by biliatresone, a biliary toxin that is responsible for outbreaks of biliary atresia in Australian liverstock.

overall_design: Liver mRNA profiles of biliatresone-treated zebrafish larvae and DMSO-treated controls were generated by deep sequencing, in duplicates.

first: Michael

last: Pack


title: DNase Hypersensitivity Peaks from Rat Schwann Cells

status: Public on Aug 24 2017

city: Ann Arbor

first: Anthony

last: Antonellis

state: MI

address: 1241 E Catherine St.

department: Human Genetics

country: USA

institute: University of Michigan

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We utilized DNase-Seq to identify open chromatin regions within Schwann cells. This data was used in conjunction with sequence conservation and transcription factor binding site prediction to identify putative cis-regulatory elements critical for Schwann cells. We used three independent biological replicates, and for our studies used sample 'barcode4' as a representative sample for all three. DNase HSS peaks were identified using F-Seq and HOMER, and overlapped to prioritize candidate regions. These regions were then verified using luciferase assays.

overall_design: Performed DNase HSS on three independent biological replicates of S16 rat Schwann cells

first: William

middle: D

last: Law


title: DNA methylation in Vav-IDH1-KI mouse haematopoietic stem cells

status: Public on Aug 23 2017

city: Toronto

first: Alan

last: Tseng

state: ON

address: 610 University Avenue

country: Canada

institute: The Campbell Family Cancer Research Institute

type: Methylation profiling by high throughput sequencing

summary: Mutations in isocitrate dehydrogenase-1 (IDH1 R132) and -2 (IDH2 R140 and R172), which confer neomorphic enzymatic activity converting αKG (α-ketoglutarate) to D-2-hydroxyglutarate (D2HG), occur commonly in acute myeloid leukemia (AML). Mutant IDH1 alters epigenetics and increases haematopoietic progenitors in vivo, consistent with D2HG-mediated inhibition of TET2 5-methylcytosine hydroxylase. As TET2 mutations are mutually exclusive with IDH1/2 mutations and confer a similar phenotype, it has been widely believed that the oncogenicity of mutant IDH1/2 is due to TET2 inhibition. However, IDH1/2 mutations may have additional effects explaining the clinical features of MDS/MPN/AML. Here we show that mutant IDH1 downregulates ATM, thereby inhibiting DNA damage responses and increasing genomic instability. To investigate potential mechanisms of ATM downregulation, we examined ATM promoter DNA methylation in Vav-IDH1-KI long term  haematopoietic stem cells (LT-HSC), short term haematopoietic stem cells (ST-HSC) and multipotent progenitors (MPP).

overall_design: LT-HSC, ST-HSC, and MPP were sorted from pooled bone marrow of aged male Vav-IDH1-KI mice and control litermates (n=6/groups) and subjected to enhanced reduced representation bisulfite sequencing (eRRBS).

first: Satoshi

last: Inoue

first: Wanda

middle: Y

last: Li

first: Zhenyue

last: Hao

first: Aline

last: Planello

first: Daniel

last: De Carvalho

first: Tak

middle: W

last: Mak


title: RNA-seq Analysis of Tfcp2l1ΔCP2-regulated Genes in Human ESCs

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

country: China

institute: Anhui University

type: Expression profiling by high throughput sequencing

summary: Purpose:The goal of this study is to analyze the candidate genes motified by Tfcp2l1ΔCP2 to regulate the human embryonic stem cell (ESC) fate through RNA-seq approach.

overall_design: HES2 human ESCs expressing PB or PB-Tfcp2l1ΔCP2 were cultured in 10% KSR basal media supplemented with 10 ng/ml FGF2 and 10 ng/ml Activin A for two passages and then were collected by using Trizol. These samples were sent to BGI (China) company to do deep sequencing by using BGISEQ-500.

first: Shoudong

last: Ye


title: ChIP-seq Analysis of Estrogen Receptor-alpha on Treatment with Fulvestrant with internal and spike-in controls

status: Public on Aug 22 2017

city: York

first: Andrew

middle: Nicholas

last: Holding

address: Wentwork Way

department: Biology

country: United Kingdom

institute: University of York

summary: A key challenge in quantitative ChIP-seq is the normalisation of data in the presence of genome-wide changes. Data-based methods often rely on assumptions that do not hold true. Misapplication of these methods to ChIP-seq data results in the suppression of the biological signal or erroneous measurement of differential occupancy.     To develop methods that address this challenge, we generated three ChIP-seq datasets, each measuring Estrogen Receptor-alpha (ER) binding in MCF7 before and after 100 nm Fulvestrant treatment for 48 hours. The three methods were: a novel internal control using CTCF binding to normalise (SLX-14229 & SLX-14438); a spike-in control using H2av binding to D. Melanogaster chromatin (SLX-8047); and a spike-in control using the cross reactivity of ER antibody against M. Musculus chromatin (SLX-12998).

overall_design:
3 ER ChIP-seq experiments implimenting internal or spike-in normalisation stratergies

Please note that there is no processed data for one dataset (SLX-12998) as these form part of a study to evaluate multiple methods and it is concluded at an early stage that this method isn't suitable, however the sequencing raw data is still relevant and provided for those who may be interested in re-evaluating the methods.

first: Florian

last: Markowetz

middle: N


title: Multiple RNA structures affect translation initiation and UGA redefinition efficiency during synthesis of selenoprotein p

city: Salt Lake City

middle: T

last: Howard

state: UT

institute: University of Utah

summary: Mice carrying genomic deletions of SECIS1 or SECIS2 in the Selenop gene were euthanized and liver tissue was harvested and processed for RNA-Seq and ribosome profiling. From these studies, we determined the affect of SECIS1 and SECIS2 on UGA redifinition across the Selenop gene.

overall_design: Gene expression analysis of liver tissue from mice carrying genomic deletions of the 3' UTR SECIS1 or SECIS2 elements of Selenop


title: Sequence dependency and regulatory function of dimeric NOTCH1/RBPJ complexes on coding and non-coding transcription in T-lymphoblastic leukemia

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

type: Non-coding RNA profiling by high throughput sequencing

summary: NOTCH/RBPJ/MAML ternary transcriptional complex binds to regulatory element and drives gene expression. The complex can function as monomer and dimer. How dimeric complexes regulate gene expression in human cancer is not well studied. Here, we integrate genomic data sets and analyze Notch dimeric complexes-regulated transcriptome and cis-regulatory elements. A subset of coding and non-coding RNA is Notch dimeric complexes-associated. Dimeric complexes recognition sequence enriched in functional dynamic Notch sites and majority of dimer recognition sequence located in (super-)enhancers.

overall_design: Gene expression profiling for Notch-sensitive TLL cell lines using RNA-seq, with replicates

first: Hongfang

last: Wang

first: Sujun

last: Chen

first: X

middle: S

last: Liu

first: Jon

middle: C

last: Aster


title: UPF1 helicase promotes Tudor-SN-mediated miRNA decay

city: Rochester

first: Lynne

last: Maquat

state: New York

address: 601 Elmwood Ave

department: Biochemistry and Biophysics

institute: University of Rochester

summary: The helicase activity of UPF1 remodels miRNPs so as to render miRNAs susceptible to Tudor-SN (TSN)-mediated miRNA decay

overall_design: We performed miR-seq on five biological replicates of Control siRNA-, TSN siRNA or UPF1 siRNA-treated T24 human bladder cancer cells. We aimed to define the pool of miRNAs that are upregulated in TSN-knockdown and UPF1-knockdown cells relative to Control siRNA-treated cells

first: Reyad

middle: A

last: Elbarbary

first: Keita

last: Miyoshi

first: Omar

last: Hedaya

first: Jason

middle: R

last: Myers

middle: E


title: Genome-wide chromatin conformation capture (Hi-C) analysis in fission yeast.

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

summary: The dynamic nature of genome organization impacts critical nuclear functions including the  regulation of gene expression, replication and DNA damage repair. Despite significant progress,  the mechanisms responsible for reorganization of the genome in response to cellular stress, such as  aberrant DNA replication, are poorly understood. Here we show that fission yeast cells carrying a  mutation in the DNA binding protein Sap1 show defects in DNA replication progression and  genome stability, and display extensive changes in genome organization.

overall_design: Two biological replicates of Hi-C experiments were done in sap1-1.

first: Takeshi

last: Mizuguchi

first: Nitika

last: Taneja

first: Emiko

last: Matsuda

first: Jon-Matthew

last: Belton

first: Peter

last: FitzGerald

first: Job

last: Dekker


title: High throughput sequencing of small RNAs from black pepper (Piper nigrum L.)

city: Trivandrum

first: Soniya

last: E V

state: KERALA

department: Plant Molecular Biology

country: India

institute: Rajiv gandhi Centre for Biotechnology

summary: In this study, we used the illumina high throughput sequencing approach (Sequencing-By-Synthesis, or SBS) to develop the sequence resource of black pepper. To identify micro RNAs functioning in stress response of the black pepper plant, small RNA libraries were prepared from the leaf and root of Phytophthora capsici infected plants, leaves from drought stressed and  control plants.

overall_design: Stress responsive small RNAome profiling from black pepper

first: E

middle: V

last: Soniya

first: Asha

last: Srinivasan

first: Sweda

last: Sreekumar

first: Divya

last: Kattuppalli


title: Recessive mutation in EXOSC3 associates with mitochondrial dysfunction and pontocerebellar hypoplasia

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

country: Germany

institute: Charite

summary: Recessive mutations in EXOSC3, encoding a subunit of the human RNA exosome complex, cause Pontocerebellar hypoplasia type 1b (PCH1B). We report a boy with severe muscular hypotonia, psychomotor retardation, progressive microcephaly, and cerebellar atrophy. Biochemical abnormalities comprised mitochondrial Complex I and PDHc deficiency. Whole exome sequencing uncovered a known EXOSC3-mutation p.(D132A) as the underlying cause. In patient fibroblasts, >50% of the EXOSC3 protein was trapped in the cytosol. mtDNA-copy numbers in muscle were reduced to 40%, but mutations in the mtDNA and nuclear mitochondrial genes were excluded. RNA-seq of patient muscle showed highly increased mRNA-copy numbers, especially for genes encoding structural subunits of OXPHOS-complexes I, III, and IV, possibly due to reduced degradation by a dysfunctional exosome complex. This is the first case of mitochondrial dysfunction associated with an EXOSC3 mutation, which expands the phenotypic spectrum of PCH1B. We discuss the links between exosome and mitochondrial dysfunction.

overall_design: comparison of n=1 patient sample with 3 male and 3 female control samples from the GEO database


city: Freising

first: Elena

last: Ferrari

address: Weihenstephaner Berg 3

department: ZIEL, Department of Microbiology

institute: Technische Universität München

summary: Adaptation of Listeria weihenstephanensis to anaerobiosis. Trascriptional profiling at two different temperatures of L. weihenstephanensis

overall_design: Genome sequence and trascriptional profiling at two different temperatures of L. weihenstephanensis

first: Mathias

last: Walter

first: Christopher

last: Huptas

first: Siegfried

last: Scherer

first: Stefanie

last: Müller-Herbst


title: Transcriptome characterization of murine ventricular cardiomyocytes

city: Bern

first: Jean-Sebastien

last: ROUGIER

address: Bühlstrasse 28

department: IBMM

country: Switzerland

institute: University of Bern

summary: We collected comprehensive RNAseq data from wildtype murine ventricular cardiomyocytes. Moreover, a cardiomyocyte-specific knockout mouse model for the ion channel regulator CASK was included, since CASK can translocate to the nucleus and regulate gene expression. Knockout models for SAP97 and dystrophin, two ion channels regulators, were also investigated.

overall_design: Sequencing of cardiomycyte RNA from WT mice as well as CASK KO, SAP97 KO and MDX mice. Three replicated experiments were performed for CASK KO and SAP97 KO conditions, and five replicated experiments for the MDX condition.

first: Morgan

last: Chevalier

first: Sarah

last: Vermij

first: Kurt

last: Wyler

first: Irene

last: Keller

first: Ludovic

last: Gillet

first: Hugues

last: Abriel


title: The histone variant H2A.Z promotes splicing of weak introns (ChIP-Seq)

city: San Francisco

first: Kelly

last: Nissen

state: CA

address: 600 16th Street

institute: UCSF

summary: Multiple lines of evidence implicate chromatin in the regulation of pre-mRNA splicing. However, the influence of chromatin factors on co-transcriptional splice-site usage remains unclear. Here we investigated the function of the highly conserved histone variant H2A.Z in pre-mRNA splicing using the intron-rich model yeast, Schizosaccharomyces pombe. Using Epistatic Mini-Array Profiles (EMAPs) to survey the genetic interaction landscape of the Swr1 nucleosome remodeling complex, which deposits H2A.Z, we uncovered evidence for functional interactions with components of the spliceosome. In support of these genetic connections, splicing-specific microarrays show that H2A.Z and the Swr1 ATPase are required during temperature stress for the efficient splicing of a sub-set of introns. Notably, affected introns are enriched for H2A.Z occupancy, and more likely to contain non-consensus splice sites. To test the significance of the latter correlation, we mutated the splice sites in an affected intron to consensus and found this suppressed the requirement for H2A.Z in splicing of that intron. These data suggest that H2A.Z occupancy promotes co-transcriptional splicing of sub-optimal introns that may otherwise be discarded via proofreading ATPases. Consistent with this model, we show that over-expression of splicing ATPase Prp16 suppresses both the growth and splicing defects seen in the absence of H2A.Z.

overall_design: ChIP-Seq of H2A.Z association in Schizosaccharomyces pombe using the HiSeq 2500 platform

first: Christina

middle: M

last: Homer

first: Colm

middle: J

last: Ryan

first: Michael

last: Shales

first: Nevan

last: Krogan

first: Kristin

middle: L

last: Patrick

first: Christine

last: Guthrie


title: Next Generation Sequencing of Lung Primary Fibroblast Responding to Eosinophil-Degranulation Products

city: Madison

first: Yury

last: Bochkov

state: WI

address: 600 Highland Ave, K4/945 CSC

department: Pediatrics

institute: University Of Wisconsin-Madison

summary:
Methods: Two human lung primary fibroblast (HLF) lines were activated for 24 h with eosinophil conditioned media obtained from two blood eosinophil donors. Total RNA was extracted from HLF and treated with DNase. RNA quality was analyzed via Agilent 2100 Bioanalyzer platform. The sequencing library from mRNA was prepared using TruSeq Stranded mRNA Library Preparation Kit (Illumina; San Diego, CA, USA) and RNA-seq (1x100 bases; 25 million reads per sample) was carried out using Illumina HiSeq 2500 platform. SeqMan Ngen (v.13) and ArrayStar with Qseq module (v.13) software packages (DNAStar, Madison, WI) were used to map sequence reads to human reference genome (GRCh38), apply statistical analyses and identify global gene expression changes.
Results: Compared to control HLF cultures, conditioned medium from IL-3-primed degranulated eosinophils on IgG upregulates 169 genes and downregulates 131 genes in both HLF lines.
Conclusions: Our study represents the first detailed analysis of gene expression in HLF activated with degranulated products from eosinophils, generated by RNA-seq technology. Analyses of the genes which expression level is changed by conditioned media from degranulated eosinophils should inform on the function of eosinophils on fibroblasts.

overall_design: Human lung primary fibroblast mRNA profiles after activation with conditioned media from degranulated eosinophils were generated by deep sequencing, using Illumina HiSeq 2500 platform. Two eosinophils donors and two HLF lines were used.

first: Stephane

last: Esnault


title: Target-Enrichment Sequencing for Detailed Characterization of Small RNAs

city: Brisbane

first: Quan

middle: Hoang

last: Nguyen

state: Queensland

address: Queensland Bioscience Precinct (Building 80) The University of Queensland. 306 Carmody Road. St

department: Australian Institute for Bioengineering and Nanotechnology

country: Australia

institute: The University of Queensland

summary: Identification of important, functional small RNA (sRNA) species is presently hampered by the lack of reliable and sensitive methods to isolate and characterize them. We have developed a method termed Target-Enrichment of small RNAs (TEsR), which enables targeted sequencing of rare sRNAs and diverse precursor and mature forms of sRNAs not detectable by current standard sRNA sequencing methods. It is based on the amplification of full length sRNA molecules, production of biotinylated RNA probes, hybridization to one or multiple targeted RNA, removal of non-targeted sRNAs, and sequencing. By this approach, target sRNAs can be enriched by a factor of 500-30,000 while maintaining strand specificity. TEsR enriches for sRNAs irrespective of length or different molecular features, such as the presence or absence of a 5’-cap or of secondary structures or abundance levels, and allows the detection of the complete sequence (including sequence variants, 5’ and 3’ ends) of precursors, intermediate and mature forms, and all this quantitatively.

overall_design: RNA extracted from mouse embryonic fibroblast cell lines (MEFs), induced or uninduced for TRF2 conditional knock out, were used for targeted enrichment sequencing of small RNA (TEsR) and MiSeq sequencing or standard TruSeq small RNA sequencing. Each treatment had at least two replicates.

first: Julio

last: Aguado

first: Fabio

last: Iannelli

first: Ana-Maria

last: Suzuki

first: Francesca

last: Rossiello

first: Fabrizio

last: dʼAdda di Fagagna

first: Piero

last: Carninci


title: DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A [RNA-Seq]

city: HOUSTON

first: Jianzhong

last: Su

state: TEXAS

address: 1 Baylor Plaza

institute: Baylor college of Medicine

summary: We demonstrate that dCas9-SunTag-DNMT3A dramatically increased CpG methylation at the HOXA5 locus in human embryonic kidney 293T cells (HEK293T). Furthermore, using a single sgRNA, dCas9-SunTag-DNMT3A was able to methylate a 4.5 kb genomic region and repress HOXA5 gene expression. Reduced representation bisulfite sequencing (RRBS) and RNA-seq showed that dCas9-SunTag-DNMT3A methylated regions of interest with minimal impact on the global DNA methylome and transcriptome.

overall_design: I)PCR amplicon deep sequencing of dCas9-SunTag-DNMT3A treated HEK2937 samples  using Illumina Nextseq sequencing system. II) Reduced representation bisulfited sequencing (RRBS) of plasmid transfected HEK 293T cells using Illumina Hiseq2000 sequencing system. III)  Whole genome bisulfite sequencing of dCas9-SunTag-DNMT3A treated HEK2937 samples. IV) RNA sequencing of dCas9-SunTag-DNMT3A treated HEK2937 samples

first: Yung-Hsin

last: Huang

first: Wei

last: Li

first: Margaret

last: Goodell


title: Transcriptional and mutational profiling of an aminoglycoside resistant Pseudomonas aeruginosa small colony variant

city: Hannover

first: Michal

last: Koska

state: Deutschland

address: Feodor-Lynen-Straße 7

department: Molecular Bacteriology

institute: Twincore GmbH

summary: In this study we have profiled a clinical tobramycin resistant P. aeruginosa strain that exhibited a small colony variant (SCV) phenotype. Both, the resistance and the colony morphology phenotypes were lost upon passaging the isolate under rich medium conditions. Transcriptional and mutational profiling revealed that the SCV harbored activating mutations in the two two-component systems AmgRS and PmrAB. Introduction of these mutations singularly into the type strain PA14 conferred tobramycin and colistin resistance, respectively. However, their combined introduction had an additive effect on the tobramycin resistance phenotype. Activation of the AmgRS system slightly reduced the colony size of the PA14 wild-type, whereas the simultaneous overexpression of gacA, the response regulator of the GacSA two component system, further reduced colony size. In conclusion, we uncovered combinatorial influences of two-component systems on clinically relevant phenotypes, such as resistance and the expression of the SCV phenotype. Our results clearly demonstrate that combined activation of P. aeruginosa two-component systems exhibit pleiotropic effects with unforeseen consequences.

overall_design: Transcriptional and mutational profiling of SCV revertants

first: Monika

last: Schniederjans

first: Susanne

last: Häussler


title: The histone variant H2A.Z promotes splicing of weak introns

first: Kelly

last: Nissen

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

overall_design: Refer to individual Series


title: DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A [BS-Seq]

summary: Here, we demonstrate that dCas9-SunTag-DNMT3A dramatically increased CpG methylation at the HOXA5 locus in human embryonic kidney 293T cells (HEK293T). Furthermore, using a single sgRNA, dCas9-SunTag-DNMT3A was able to methylate a 4.5 kb genomic region and repress HOXA5 gene expression. Reduced representation bisulfite sequencing (RRBS) and RNA-seq showed that dCas9-SunTag-DNMT3A methylated regions of interest with minimal impact on the global DNA methylome and transcriptome.


title: BAP1 inhibits the ER stress gene regulatory network and modulates metabolic stress response

city: Houston

first: Boyi

last: Gan

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary: BRCA1 associated protein 1 (BAP1) is a tumor suppressor with de-ubiquitinating (DUB) enzyme activity and has been implicated in chromatin regulation of gene transcription. The goal of this study is to identify BAP1-dependent transcriptional alterations under both basal (25 mM glucose) and glucose starvation (0 mM glucose) conditions. To this end, we established UMRC6 cell lines (a BAP1 deficient renal cancer cell line) stably expressing Flag-tagged BAP1 wild-type (U6-F), and the empty vector control cells (U6-EV), and performed RNA sequencing (RNA-Seq) analysis in U6-EV and U6-F stable cell lines at 0, 4, and 8 hour upon glucose starvation. The RNA-Seq datasets allow us to compare BAP1-dependent transcriptional alterations under both basal and glucose deprivation conditions.

overall_design: Two cell line described above (U6-F: UMRC6 cells with stable expression of Flag-BAP1, and U6-EV: UMRC6 cells with stable expression of empty vector) were cultured under three conditions: T0 (cell cultured in 25mM glucose-containing medium for 8 hours), T4 (cells cultured in 0 mM glucose-containing medium for 4 hours), and T8 (cells cultured in 0 mM glucose-containing medium for 8 hours). The samples (Two replicates per cell line per condition) were then subjected to RNA sequencing analysis.

first: Hui

last: Yao

first: Xiaoping


title: Next Generation Sequencing Facilitates Quantitative Analysis of FoxO3 or Geminin/FoxO3 depletion on MDA-MB-231 cells Transcriptomes

city: Xiamen

first: Lei

last: Zhang

state: Fujian

address: Xiang'an Nan Road

department: School of Life Sciences

institute: Xiamen University

summary: We generated 2 Gb of high-quality sequencing data (~1 Gb per sample) and catalogued the expression profiles of 48,162 annotated human genes in each sample. The analysis showed differences of transcriptomes between Control and Geminin/FoxO3 co-depletion expression changes. We identified numerous differentially expressed genes that exhibited distinct expression patterns. These genes are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms by Geminin and FoxO3 .

overall_design: MDA-MB-231 mRNA profiles of Control, FoxO3 and Geminin/FoxO3 co-depletion were generated by deep sequencing,  using Illumina HiSeq4000.

first: H

last: You

first: L


title: Regulatory Functions and Chromatin Loading Dynamics of Linker Histone H1 During Endoreplication in Drosophila

city: Bronx

first: Travis

last: Bernardo

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

summary:
Purpose: In Drosophila larval tissues that undergo endoreplication without cell division, the latest-replicating regions occasionally fail to complete endoreplication, resulting in the establishment of underreplicated (UR) domains of polytene chromosomes. The cause of this phenomenon is poorly understood.
Methods: Freshly dissected salivary glands were crosslinked, nuclei were sonicated to shear DNA at an average size of 200 bp, and DNA was purified using a QiaQuick PCR Purification Kit. Sequencing libraries were prepared using the Illumina HiSeq 2500 system. UR regions were identified in aligned reads of the control knockdown by scanning along 5-kb windows, with regions designated as under-replicated if 20 consecutive windows fell below the average per-chromosome read count. Fold change was then calculated between the H1-depleted and control-depleted samples.
Results: We found that H1 is required for the underreplication phenomenon in Drosophila salivary glands, as UR regions show substantial increase in copy number upon H1 depletion.
Conclusions: Our findings implicate H1 as a critical factor in the formation of UR regions and as an important upstream effector of SUUR.

overall_design:
UR region genomic DNA copy number in salivary gland cells of H1-depleted and Nautilus-depleted wandering L3 larvae was determined by deep sequencing, in duplicate, using Illumina HiSeq 2500.
pINT-Nau_UR.bed: called UR domains
pINT-NaU_RelCopy_1K.bgr: Genomic Relative Copy Number, Nau KD (1 kilobase intervals)
pINT-H15M_RelCopy_1K.bgr: Genomic Relative Copy Number, H1 KD (1 kilobase intervals)


title: Exosomal microRNA analysis of patients with multiple myeloma and healthy adults

city: Boston

first: Chia-Jen

last: Liu

state: MA

address: 4 Blackfan Circle, 2nd Floor, Suite 240

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: We report the microRNA expression in patients with multiple myeloma and healthy adults. RNA sequencing was performed for circulating exosomes obtained from the serum of 10 MM patients and 5 healthy individuals.

overall_design: Exosomal microRNAs in multiple myeloma patients and healthy adults were extracted and sequenced.

first: Salomon

last: Manier

first: Irene

last: Ghobrial


title: RNA-sequencing of brain ECs isolated at P8 from mice with EC-specific deletion of YAP/TAZ

city: Irvine

first: Hosung

last: Bae

address: 839 Health Sciences Road Sprague Hall, Room 150

institute: UC Irvine

summary: To investigate the role of Hippo-YAP signaling in angiogenesis, we performed RNA-sequencing by using brain ECs isolated from mice with EC-specific deletion of indicated components of Hippo pathway.

overall_design: Bung ECs were isolated from mice with indicated genotype at P8 and mRNA profiles was generated by deep sequencing, in quadruplicate, using Illumina NextSeq 500.

first: Gou

last: Koh

first: Jongshin

last: Kim


title: Expression level is a key determinant of E2F1-mediated cell fate

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Drive, 2179 CIEMAS

department: Biostatistics and Bioinformatics

institute: Duke University

summary:
Purpose: dose response analysis of E2F1 target genes expression in flow-sorted fractions with increasing amounts of fluorescently labled E2F1
Methods:U2OS pTRIPZ-YFP-ER-E2F1 cells were grown in full serum-containing growth medium and treated with 500 ng/ml doxycycline for 48 hours followed by addition of 90 nM OHT for an additional 20 hours. Cells from different YFP fractions were sorted by flow cytometry. mRNA profiles were generated by deep sequencing  using Illumina HiSeq 4000.
Results: different target genes have different E2F1 activation thresholds. Numerous proliferation-related target genes are induced already by the lowest E2F1-levels. Intermediate E2F1 levels induce cdk inhibitors, which might be responsible for cell cycle arrest. Finally, although some apoptotic E2F1 targets are induced already by low E2F1 levels, many key apoptotic genes require higher E2F1 levels for induction.
Conclusions: induction of different cell fates by increasing E2F1 levels might pertain to differential affinities of the targets.

first: Igor

last: Shats

first: Lingchong

first: Dinesh

last: Manandhar


title: CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: Identification of in vivo direct RNA targets for RNA binding proteins (RBP) provides critical insight into their regulatory activities and mechanisms. Recently, we described a methodology for enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP-seq) using antibodies against endogenous RNA binding proteins. However, in many cases it is desirable to profile targets of an RNA binding protein for which an immunoprecipitation-grade antibody is lacking. Here we describe a scalable method for using CRISPR/Cas9-mediated homologous recombination to insert a peptide tag into the endogenous RNA binding protein locus. Further, we show that TAG-eCLIP performed using tag-specific antibodies can yield the same robust binding profiles after proper control normalization as eCLIP with antibodies against endogenous proteins. Finally, we note that antibodies against commonly used tags can immunoprecipitate significant amounts of antibody-specific RNA, emphasizing the need for paired controls alongside each experiment for normalization. TAG-eCLIP enables eCLIP profiling of new native proteins where no suitable antibody exists, expanding the RBP-RNA landscape.

overall_design: eCLIP-seq performed in wild-type and endogenously tagged HEK293T cell lines

first: Eric

last: Van Nostrand

first: Chelsea

last: Gelboin-Burkhart

first: Ruth

last: Wang

first: Gabriel

last: Pratt

first: Steven

last: Blue


title: RNA-sequencing of lung ECs isolated at P5 from mice with EC-specific deletion of LATS1/2 and LATS1/2;YAP/TAZ

summary: To investigate the role of Hippo-YAP signaling in angiogenesis, we performed RNA-sequencing by using lung ECs isolated from mice with EC-specific deletion of indicated components of Hippo pathway.

overall_design: Lung ECs were isolated from mice with indicated genotype at P5 and mRNA profiles was generated by deep sequencing, in quadruplicate, using Illumina NextSeq 500.


title: Study gene expression of KDR-expressing GL261 tumor associated hematopietic progenitor cells

city: New York

first: Yujie

last: Huang

state: NY

address: 510E 70st Street

department: Neurological Surgery

institute: Weill Cornell Medicine

summary:
Purpose: Using NGD techinque to profile the gene expression in KDR+ hematopietic progenitor cells (HPC) and KDR- HPC during tumor progression. The goal is to study how KDR signaling within hematopieosis respond to tumor progression by analyzing transcriptome of KDR+ HPC
Method: Isolate KDR + HPC and KDR- HPC from late stage GL261 tumor mice, and HPC from non tumor mice. Compare their transcriptomes.by deep sequencing, in triplicate. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks.
Results: Basedl analysis of transcirptome  and expression pattern of 11650 genes, KDR+ HPC resprent a different population compared with KDR- HPC in tumor mice or HPC in non-tumor mice.

overall_design: GL261 tumor were implanted into KDR-GFP knockin mice, the GFP+ Lin-C-kit+sca-1- bone marrow cells were isolated by flowcytometery, RNA from ~20000 cells were extracted and subjected for sequencing

first: Jefftrey

last: Greenfield


title: Transcriptome profile in INT cells following Cryptosporidium parvum infection

city: Omaha

first: Xianming

last: Chen

state: NE

address: 2500 california plaza

institute: creighton university

summary: Cryptosporidium parvum is an important opportunistic parasite pathogen for immunocompromised individuals and a common cause of diarrhea in young children in developing countries. Certain parasite molecules can be delivered into host epithelial cells and may act as effector molecules for parasite intracellular development.  This study aims to measure the impact of transfection of a parasite low-protein coding potential RNA transcript, Cdg7_FLc_0990, on the transcriptome profile in intestinal epithelial cells. Human intestinal epithelial INT (FHs 74 Int) cells were grown to 80% confluence and transfected with the Cdg7_FLc_0990 full-length or the empty vector for 48h. Total RNA was collected for the genome-wide analysis. RNA from INT cells following C. parvum infection for 48h and from cell of the non-infected control was also collected for the analysis. The Agilent SurePrint G3 Human Gene Expression Microarray (G4851B) was used for the genome-wide analysis, which provides full coverage of genes and transcripts with the most up-to-date content, including mRNAs and lincRNAs (http://www.chem.agilent.com/store/en_US/Prod-G4851B/G4851B)

overall_design: The FHs 74 Int  were grown to 80% confluence for four groups:  control (Group 00-C), C. parvum infection (Group 00-D, cells treated with C. parvum), pcDNA3.1(+) empty vector (Group CP-A, cells transfected with pcDNA3.1(+) empty vector), and pcDNA3.1(+)_Cdg7_FLc_0990 full-length (Group CP-D, cells transfected with pcDNA3.1(+)_Cdg7_FLc_0990 full-length ). 48h later, total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.


title: Gene expression profiles in retinas from miRNA183/182/96 cluster knockout mice versus wild type controls by RNA-seq

city: Bethesda

first: Jianguo

last: Fan

address: 6 Center Drive Rm 108A

institute: National Eye Institute

summary: Retinas from various developmental stages at postnatal p5, p11, and p27 from miRNA183/182/96 cluster knockout mice versus wild type controls were used to prepare total RNA for RNA-sequencing.

overall_design: Differential mRNA expression between miR183C knockout mice and age matched C57bl6/J control mice was quantified by RNA-seq data analysis using the Tuxedo package (i.e. the Tophat-Cufflinks pipeline)

first: Lijin

last: Dong

first: Graeme

last: Wistow


title: DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A [WGBS]

first: Jianzhong

last: Su

first: Yung-Hsin

first: Wei

last: Li

first: Margaret

last: Goodell


title: Whole genome RNA-sequencing from root tips ofArabidopsis thalianalow-phosphate insensitive mutants under High and Low phosphate

city: Irapuato

first: Luis

middle: Rafael

last: Herrera-Estrella

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera León

department: Langebio

country: Mexico

institute: Cinvestav - Langebio

summary: Phosphate limitation constrains plant development in natural and agricultural systems. Under phosphate-limiting conditions plants activate genetic, biochemical and morphological modifications to cope with phosphate starvation. One of the morphological modifications that plants induce under phosphate limitation is the arrest of primary root growth and it is induced by the root tip contact with low phosphate media. The sensitive to proton rhizotoxicity (stop1) and aluminium activate malate transporter 1 (almt1) mutants of Arabidopsis thaliana continue primary root growth under in vitro Pi-limiting conditions, thus, to get insight into the molecular components that control primary root growth inhibition under low phosphate conditions we extracted and sequenced mRNA from the root tips (2-3 mm from the root apex) of wild-type plants (Col-0 accession) and low-phosphate-insensitive mutants almt1 and stop1 grown under low and high phosphate conditions 5 days after germination using an RNA-seq methodology.

overall_design: Analysis of 9 different treatments, 3 different genotypes (Col-0,stop1,almt1), 4 different Phosphate treatments (High Pi, Low Pi, Low Pi -Fe, Low Pi +M), 1 biological replicate for treatment

first: Jonathan

middle: O

last: Ojeda-Rivera

first: Javier

last: Mora-Macías


title: mRNA exrpession patterns in response to RelA siRNA

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

institute: University Clinic of Schleswig Holstein

summary:
The experiment aims to identify mRNAs regulated in response to RelA
overall aim: elucidate the role of CCL20 mediated immune cell recruitment in NF-[gamma]B mediated TRAIL resistance of pancreatic cancer

overall_design: compare 3 different experimental groups: 1) controls, TRAIL stimulated 2) controls unstimulated 3) TRAIL stimulated with RelA si-RNA

first: R

last: Häsler


title: Treating the placenta to prevent adverse effects of gestational hypoxia on fetal brain development

city: Cardiff

first: Hannah

last: Scott

address: Hadyn Ellis Building, Maindy Road

department: UK Dementia Research Institute

institute: Cardiff University


title: Treating the placenta to prevent adverse effects of gestational hypoxia on fetal brain development [RNAseq]

summary: Some neuropsychiatric disease, including schizophrenia, may originate during prenatal development, following periods of gestational hypoxia and placental oxidative stress. Here we investigated if gestational hypoxia promotes damaging secretions from the placenta that affect fetal development and whether a mitochondria-targeted antioxidant MitoQ might prevent this. Gestational hypoxia caused low birth-weight and changes in young adult offspring brain, mimicking those in human neuropsychiatric disease. Exposure of cultured neurons to fetal plasma or to secretions from the placenta or from model trophoblast barriers that had been exposed to altered oxygenation caused similar morphological changes. The secretions and plasma contained altered microRNAs whose targets were linked with changes in gene expression in the fetal brain and with human schizophrenia loci. Molecular and morphological changes in vivo and in vitro were prevented by a single dose of MitoQ bound to nanoparticles, which were shown to localise and prevent oxidative stress in the placenta but not in the fetus. We suggest the possibility of developing preventative treatments that target the placenta and not the fetus to reduce risk of psychiatric disease in later life.

overall_design: 16 samples (4 biological replicates per group) were analysed using RNA sequencing. The 4 groups were: Normoxia+Saline (control sample), Normoxia+MitoQ-NP, Hypoxia+Saline and Hypoxia+MitoQ-NPs. Pair-wise comparison between all groups was performed.

first: Tom

last: Phillips

first: David

last: Menassa

first: Ashleigh

last: Bignell

first: Aman

last: Sood

first: Jude

last: Morton

first: Takami

last: Akagi

first: Koki

last: Azuma

first: Mark

middle: F

last: Rogers

first: Catherine

last: Gilmore

first: Gareth

last: Inman

first: Simon

last: Grant

first: Yealin

last: Chung

first: Mais

last: Aljunaidy

first: Christy-Lynn

last: Cooke

first: Bruno

last: Steinkraus

first: Andrew

last: Pocklington

first: Angela

last: Logan

first: Gavin

middle: P

last: Collett

first: Helena

last: Kemp

first: Peter

last: Holmans

first: Michael

last: Murphy

first: Tudor

last: Fulga

last: Coney

first: Mitsuru

last: Akashi

first: Sandra

last: Davidge

first: Charles

last: Case


title: The Cdc42/Rac1 regulator CdGAP is a novel E-cadherin transcriptional co-repressor with Zeb2 in breast cancer

city: Montreal

first: Ariane

last: Pelletier

state: QC

address: 110 Avenue Des Pins Ouest

institute: IRCM

summary: The loss of E-cadherin causes dysfunction of the cell-cell junction machinery, which is an initial step in epithelial-to-mesenchymal transition (EMT), facilitating cancer cell invasion and the formation of metastases. A set of transcriptional repressors of E-cadherin (CDH1) gene expression, including Snail1, Snail2 and Zeb2 mediate E-cadherin down-regulation in breast cancer. However, the molecular mechanisms underlying the control of E-cadherin expression in breast cancer progression remain largely unknown. Here, by using global gene expression approaches, we uncover a novel function for Cdc42 GTPase-activating protein (CdGAP) in the regulation of expression of genes involved in EMT. We found that CdGAP used its proline-rich domain to form a functional complex with Zeb2 to mediate the repression of E-cadherin expression in ErbB2-transformed breast cancer cells. Conversely, knockdown of CdGAP expression led to a decrease of the transcriptional repressors Snail1 and Zeb2, and this correlated with an increase in E-cadherin levels, restoration of cell-cell junctions, and epithelial-like morphological changes. In vivo, loss of CdGAP in ErbB2-transformed breast cancer cells impaired tumor growth and suppressed metastasis to lungs. Finally, CdGAP was highly expressed in basal-type breast cancer cells, and its strong expression correlated with poor prognosis in breast cancer patients. Together, these data support a previously unknown nuclear function for CdGAP where it cooperates in a GAP-independent manner with transcriptional repressors to function as a critical modulator of breast cancer through repression of E-cadherin transcription. Targeting Zeb2-CdGAP interactions may represent novel therapeutic opportunities for breast cancer treatment.

overall_design: Total RNA profiles of ErbB2-expressing control mammary tumor explants cells (shCON) and CdGAP-depleted cells (shCdGAP) were generated by deep sequencing, in triplicate, using Illumina HiSEq2000.

first: Yi

last: He

first: Jason

last: Northey

first: Zuzana

last: Kos

first: Liliane

last: Meunier

first: Benjamin

last: Haibe-Kains

first: Anne-Marie

last: Mes-Masson

first: Jean-François

last: Côté

last: Siege

first: Nathalie

last: Lamarche-Vane


title: Chromatin-associated protein interactions drive megadomain formation in NUT midline carcinoma

last: Kharchenko

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

summary: To investigate the mechanism that drives dramatic mistargeting of active chromatin in NUT-midline carcinoma, we have identified protein interactions unique to the BRD4-NUT fusion oncoprotein compared to wild type BRD4.  Using crosslinking, affinity purification, and mass spectrometry, we identify the p300 acetyltransferase as ectopically associated with BRD4 through the NUT fusion in both NMC and non-NMC cell types. We also identify ZNF532 among a number of candidates uniquely associated with BRD4-NUT in NMC patient cells but not present in 293T cells.  p300 and ZNF532 are both implicated in feed-forward regulatory loops leading to propagation of the oncogenic regulatory complex in BRD4-NUT patient cells.  Extending our biochemical findings, we independently identified a novel ZNF532-NUT translocation fusion in a newly diagnosed NMC patient. ChIP-seq of key players: NUT, ZNF532, BRD4, p300, and anti-H3K27ac, reveals the formation of ZNF532-NUT-associated hyperacetylated megadomains, distinctly localized, but otherwise analogous to those found in BRD4-NUT patient cells. Our results support a model in which NMC is caused by a cascade of misregulation that is initiated by ectopic protein-protein interactions on chromatin between NUT and several distinct, but interacting, components of BRD4 regulatory complexes.

overall_design: ChIP-seq and nascent RNA sequencing of patient-derived cancer cell lines.

first: Tibor

last: Pakozdi


title: JAK dependent survival of ALK- ALCL

first: Jing

last: Chen

address: 10 center drive

institute: NEI

summary: Activating JAK and STAT mutations were discovered in many T-cell malignancies including ALK- anaplastic large cell lymphomas (ALCL). However, such mutations often occur in a minority of patients. To investigate the clinical application of targeting Janus Kinase (JAK) for ALK- ALCL, we treated ALK- cell lines of different histologic origins with JAK inhibitors. Interestingly, most exogenous cytokine independent cell lines responded to JAK inhibition regardless of JAK mutation status. JAK inhibitor sensitivity correlated with STAT3 phosphorylation status of tumor cells. Employing retroviral shRNA knockdown, we demonstrated that these JAK inhibitor sensitive cells were dependent on both JAK1 and STAT3 for survival. JAK1 and STAT3 gain-of-function mutations were found in some but not all JAK inhibitor sensitive cells. Moreover, the mutations alone could not explain the JAK1/STAT3 dependency as wild-type JAK1 or STAT3 was sufficient to promote cell survival in the cells that had either JAK1or STAT3 mutations. To investigate whether other mechanisms were involved, we knocked down upstream receptors GP130 or IL-2Rγ. Knockdown of GP130 or IL-2Rγ induced cell death in select JAK inhibitor sensitive cells. High levels of cytokine expression including IL-6 were demonstrated in cell lines as well as in primary ALK- ALCL tumors. Finally, ruxolitinib, a JAK1/2 inhibitor, was effective in vivo in a xenograft ALK- ALCL model. Our data suggest cytokine receptor signaling was required for tumor cell survival in diverse forms of ALK- ALCL even in the presence of JAK1/STAT3 mutations. Therefore, JAK-inhibitor therapy might benefit patients with ALK- ALCL that are pSTAT3+.

overall_design: We performed RNA-seq to examine whether JAK and STAT genes were mutated in these JAK inhibitor sensitive ALK-ALCL cell lines: Mac-1, Mac-2A, Mac-2B, Fe-Pd, TLBR1, and TLBR2,(n=6). pSTAT3 negative ALK-ALCL cell lines DL40 and TLBR3 (n=2) (also JAK inhibitor insensitive) were used as negative cell controls. All ALK- cell lines grew independent of exogenous cytokines with the exception of TLBR4, which needed exogenous IL-2 to grow.


title: Kap1 in liver physiology

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

institute: EPFL

summary: Hepatocellular carcinoma (HCC) represents the fifth most common form of cancer worldwide and carries a high mortality rate due to lack of effective treatment. Males are eight times more likely to develop HCC that females, an effect largely driven by sex hormones, albeit through still poorly understood mechanisms. We previously identified TRIM28, a scaffold protein capable of recruiting a number of chromatin modifiers, as a crucial mediator of sexual dimorphism in the liver, with Trim28hep-/- mice displaying sex-specific transcriptional deregulation of a wide range of bile and steroid metabolism genes and development of liver adenomas in males. We now demonstrate that obesity and ageing precipitate alterations of TRIM28-dependent transcriptional dynamics, leading to a metabolic infection state responsible for highly penetrant male-restricted hepatic carcinogenesis. Molecular analyses implicate aberrant androgen receptor stimulation, biliary acid disturbances and altered responses to gut microbiota in the pathogenesis of Trim28hep-/--associated HCC. Correspondingly, androgen deprivation markedly attenuates the frequency and severity of tumors, and raising animals under axenic conditions completely abrogates their abnormal phenotype, even upon high-fat diet challenge. This work underpins how discrete polyphenic traits in epigenetically unstable conditions can contribute to a cancer-prone state, and more broadly provides new evidence linking hormonal imbalances, metabolic disturbances, gut microbiota and cancer.

overall_design: Transcriptome profiling of liver tissues from TgAlbCre or TgAlbCreKap1lox mice in HFD settings

first: Marco

last: Cassano


title: shRNA screens for mediators of anti-proliferative effects of p53 in SJSA cell line

city: Aurora

first: Ahwan

last: Pandey

state: CO

department: Pharmacology

institute: University of Colorado Anschutz Medical Center

summary: To identify genes required for anti-proliferative function of p53 we performed genome-wide and p53TARGET screens in SJSA cells treated with Nutlin.

overall_design: SJSA cells were transduced with the pooled libraries in triplicate and propagated for at least 7 days. Next, cells were exposed to either DMSO or 10 microM Nutlin for 48 hours. After recovery, cells were treated one more time for 48 hours. Following final recovery period, gDNA was harvested and shRNA expression casettes were amplified by PCR. Purified reaction product was used for preparation of sequencing library.

first: Anna

last: Guarnieri

first: Zdenek

last: Andrysik

first: Joaquín

last: Espinosa


title: p53 ChIP-seq in Nutlin-treated HCT116, MCF7, and SJSA cell lines

summary: To identify genomic loci occupied by p53, we performed p53 ChIP-seq analysis of colorectal carcinoma cell line HCT116, breast carcinoma line MCF7, and osteosarcoma line SJSA treated with MDM2 inhibitor Nutlin.

overall_design: HCT116, MCF7, and SJSA cells were treated with either DMSO or Nutlin for 12 hours. Samples from formaldehyde cross-linked cells were subjected to chromatin immunnoprecipitation and recovered DNA was sequenced.


title: Total RNA-seq from HCT116, MCF7 and SJSA cell lines treated with DMSO and Nutlin

summary: To determine effects of p53 activation on steady-state mRNA levels, we performed RNA-seq analysis of colorectal carcinoma cell line HCT116 (p53+/+ and p53 -/-), breast carcinoma line MCF7, and osteosarcoma line SJSA treated with MDM2 inhibitor Nutlin.

overall_design: Total RNA was sequenced from HCT116 (p53+/+ and p53 -/-), MCF7 and SJSA cells treated with DMSO or 10 microM Nutlin for 12 hours.

first: Matthew

middle: D

last: Galbraith


title: GRO-seq from HCT116, MCF7 and SJSA cell lines treated with DMSO and Nutlin

summary: To identify loci with transcriptionally engaged RNA polymerase, we performed GRO-seq analysis of colorectal carcinoma cell line HCT116, breast carcinoma line MCF7, and osteosarcoma line SJSA treated with MDM2 inhibitor Nutlin.

overall_design: HCT116, MCF7, and SJSA cells were subjected to a run-on experiment after 1 hour of treatment with either DMSO or 10 microM Nutlin.


title: Effect of PPAR Gamma Agonist Rosiglitazone on Carotid Artery Gene Expression after Knockout of Retinol Binding Protein 7 (RBP7)

city: Iowa City

first: Henry

last: Keen

state: IA

institute: University of Iowa

summary: To examine the role of retinol binding protein 7 (RBP7) in PPAR gamma mediated regulation of target gene expression in the carotid artery, RNA-Seq was used to quantitate gene expression in carotid artery from both wild-type and RBP7 knockout mice after ligand-mediated activation of PPAR gamma with Rosiglitazone.

overall_design: Carotid artery were removed from wild-type (WT) and RBP7 knockout (KO) mice and treated with either Rosliglitazone (ROSI, 10 uM) or vehicle DMSO (CONT) for 24 hrs.

first: Chunyan

last: Hu

first: Curt

last: Sigmund


title: The Molecular Mechanism for EZH2 Function in DSS-induced Colitis

city: shanghai

first: Yongfeng

last: Liu

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: The Institute of Health Sciences, SIBS, CAS / SJTUSM

summary:
Here we employed the genetically engineered mice models (GEM) to uncover the role of gut epithelial EZH2 in the pathogenesis of colitis. To dissect the underlying mechanism, Chip-Seq analysis is used for mechanistic study.
From the result we find EZH2 mainly targeted in the TSS region. As we have known TNF-alpha pathway can be regulated by EZH2, we try and find TRAF2/5 may be the key point for EZH2 to regulated TNF-alpha pathway. At the same time Bad, BAX, PUMA.etc which promote cell apoptosis can be find in the result, which means EZH2 may inhibit apoptosis of IEC in colitis by targenting these genes.

overall_design: Wild-type mice were treated with 2% DSS for 3 days and IECs were isolated by EDTA isolation buffer, and each sample contains pooled IECs from 5 mice. Flash frozen cells were then sent to Active Motif, Inc. for chromatin extraction and followed by immunoprecipitation using anti-EZH2 antibody (Active Motif, cat # 39901).

first: Jun

last: Qin


title: Genomic deletion of malic enzyme 2 confers collateral lethality in pancreas cancer

city: Houston

first: Jennifer

last: Wang

state: TX

address: 1515 Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary: Comparison of malic enzyme 3 (ME3) depleted vs non-depleted xenograft tumors. ME3 is an isoform of ME2.

overall_design: Sub-cutaneous tumors of nude mice injected with PATU-ishME3 (shRNA against ME3) and treated +/- Dox to knockdown ME3. 4 tumors off-dox and 2 tumors on-dox

first: Ronald

last: DePinho


title: The Role of Epithelium EZH2 in Experimental Colitis

summary:
Despite recent progress, the contribution of epigenetic mechanisms to govern Inflammatory bowel disease (IBD) pathogenesis remains elusive. Here we show that epithelial EZH2, the catalytic subunit of PRC2 is critical for experimental colitis. Depletion of EZH2 in intestinal epithelial cells sensitized the cells to DSS-induced colitis in mice. To dissect underlying mechanism, we conducted gene expression profile analysis (RNA-Seq) by using primary Intestinal epithelial cells (IECs) isolated from EZH2 WT and KO mice to gain molecular insights into the affected biological processes. To this end, colorectal epithelial cells were isolated after 3 days of 2% DSS treatment, in which day EZH2-depleted mice did not display the obviously morphological defects in comparison with control littermates. IECs were isolated by EDTA isolation buffer. Each sample contains pooled prostate RNA from 5 mice, and was subjected to Hiseq RNA-Seq, performed by BGI Tech Solutions Co., Ltd.
There was total 1018 genes up-regulated after EZH2 depletion, respectively. Gene ontology (GO) analysis revealed that the most prominent biological processes altered were associated with immune and inflammatory response. Likewise, unbiased Ingenuity Pathway Analysis (IPA) indicated that TNF-alpha and INF-gamma serve as the top upstream regulators to modulate gene changes in EZH2-depleted cells. In addition, a sub-set of apoptotic were altered after EZH2 depletion.

overall_design: Genome-wide expression profiling of primary colon epethelial cells isolated form EZH2 WT and EZH2-IEC-KO mice which are treated with 2% DSS for 3 days.Each is tested in duplicate.


title: cis-regulatory landscape in ccRCC [cell lines]

city: Singapore

first: Xiaosai

last: Yao

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

summary: VHL loss is the most common genetic alteration event in ccRCC, but its effect on epigenetic landscape has not been elucidated previously. By performing histone modifications (H3K27ac, H3K4me1, H3K4me3) from ccRCC cell lines, we describe the genome-wide cis-regulatory landscapes of VHL-deficient ccRCC tumors. We show that ccRCCs exhibit a pervasive gain of enhancers around hypoxic and metabolic transcriptional targets.

overall_design: Histone ChIP-Seq in ccRCC cell lines

first: Patrick

last: Tan


title: cis-regulatory landscape in ccRCC [tissue]

overall_design: Histone ChIP-Seq in primary normal-tumor tissue pairs of ccRCC


title: RNAseq from polysomal RNA harvested from HCT116, MCF7 and SJSA cell lines treated with DMSO and Nutlin

summary: To determine effects of p53 activation on levels of RNA associated with polysomes, we performed RNA-seq analysis of colorectal carcinoma cell line HCT116, breast carcinoma line MCF7, and osteosarcoma line SJSA treated with MDM2 inhibitor Nutlin.

overall_design: Polysomal RNA was extracted from HCT116, MCF7 and SJSA cells treated with Nutlin, polyA enriched and subjected to RNA-seq protocol.

first: Sara

last: Zaccara


title: CRIG identifies a novel population of highly phagocytic peritoneal macrophages associated with disease severity in patients with cirrhosis and ascites

city: Brisbane

first: Katharine

last: Irvine

address: 306 Carmody Rd

institute: Institute for Molecular Bioscience

summary: Infections are an important cause of morbidity and mortality in patients with decompensated cirrhosis and ascites. Hypothesising that innate immune dysfunction contributes to susceptibility to infection, we assessed ascitic fluid macrophage phenotype and function. The expression of complement receptor of the immunoglobulin superfamily (CRIg) and CCR2 defined two phenotypically and functionally distinct peritoneal macrophage sub-populations. The proportion of CRIgHi macrophages differed between patients, and in the same patient over time, and a high proportion of CRIgHi macrophages was associated with reduced disease severity (Model for End Stage Liver Disease (MELD)) score. As compared to CRIgLow macrophages, CRIgHi macrophages were highly phagocytic and displayed enhanced antimicrobial effector activity. Transcriptional profiling by RNA Sequencing and comparison with human macrophage and murine peritoneal macrophage expression signatures highlighted similarities between CRIgHi cells, human macrophages and mouse F4/80Hi resident peritoneal macrophages, and between CRIgLow macrophages, human monocytes and mouse F4/80Low monocyte-derived peritoneal macrophages. These data suggest CRIgHi and CRIgLow macrophages may represent a tissue-resident population and a monocyte-derived population, respectively. In conclusion, ascites fluid macrophage subset distribution and phagocytic capacity is highly variable between patients with chronic liver disease. Regulating the numbers and/or functions of these macrophage populations could provide therapeutic opportunities in cirrhotic patients.

overall_design: CRIg-High and CRIg-Low macrophages (CD14+ cells) sorted by flow cytometry from ascites fluid from 6 patients were analyzed (total 12 samples, 6 replicates per cell type).

first: Gregory

last: Baillie


title: Genomics insights into high pressure adaptation in a Thermococcus sp. from the world’s deepest hydrothermal vents

first: Priya

last: Narasingarao

address: 8750 Biological Grade

institute: Scripps Institution of Oceanography

summary: The present study describes the isolation of a Thermococcus sp. strain 175 from the world‘s deepest hydrothermal vent sites known thus far – The Mid-Cayman Rise.consisting of two hydrothermal venting systems Bee Bee (or Piccard), at 4950m depth and Von Damm (or Walsh) at 2300m The strain is capable of growth over 0.1MPa (atm. Pressure) to 120MPa, the widest known range of pressure dependent growth. The study further explores piezophilic adaptation using comparative genomic tools. Insights into the transcriptome of this strain providers the first look into the transcriptional machinery of peizophilic Thermococci.

overall_design: RNA was extracted from cells grown at HighPressure (three replicates HP1,HP2,HP3) and at atmospheric pressure (reference also in triplicate Atm1,Atm2.Atm3) and sequenced.

first: Douglas

middle: H

last: Bartlett

first: Haythem

last: Latif

first: Karsten

last: Zengler


title: Identification of a core p53 transcriptional program with highly fractionated tumor suppressive activity

first: Ahwan

last: Pandey

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

overall_design: Refer to individual Series


title: Alloimmune responses of humanized mice to human pluripotent stem cell therapeutics

status: Public on Aug 21 2017

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

summary: Temporal tracking of transcriptional changes of human T cells in humanized mice.  In this experiment, we studied the ability of immunodeficient NOD-SCID IL2Rgamma-null mice with reconstituted human immune systems to recapitulate graft vs host disease against engrafted tissues. Interestingly, we found that the mice failed to fully reject engrafted tissues, and evaluation of T-cells isolated from grafts demonstrated decreased expression of inflammatory cytokines. We hypothesized this phenotype was due to the devlopment of an "exhausted phenotype." To assess this, we tracked the development of human T-cells in these mice beginning 8 weeks after engraftment of human immune components, and monitored their transcriptional profiles to assess for markers of anergy, exhaustion, and immune activation.

overall_design: RNA-seq (3 samples + 1 control) - Samples are T cells pooled from 5 mice with reconstituted human immune systems at three time points. Control sample represents T cells from healthy human adult. Circulating T cells isolated from whole blood via flow cytometry.

first: Jonathan

last: Stack

first: Ning-Yi

last: Shao


title: Plasmodium berghei transcriptome for female gametocytes, male gametocytes, and asexual erythrocytic stages

city: Parkville

first: Lee

middle: Ming

last: Yeoh

state: VIC

address: Bio21 Institute, 30 Flemington Rd

institute: The University of Melbourne

overall_design: These transcriptomes are derived from isolated female and male gametocytes, and asexual erthythrocytic stages of Plasmodium berghei. Samples are of 820cl1m1cl1 parasites, which express RFP and GFP in female and male gametocytes respectively. Gametocytes were purified by flow cytometry, and asexual stages were derived from mouse blood depleted of host cells by CF11 columns followed by saponin lysis.

first: Christopher

last: Goodman

first: Vanessa

last: Mollard

first: Geoffrey

middle: I

last: McFadden

first: Stuart

last: Ralph


title: Telomere Length Protects Mice from Human Disease Phenotype Caused By Notch1 Haploinsufficiency

city: San Francisco

first: Christina

last: Theodoris

state: California

address: 1650 Owens Street

institute: Gladstone Institutes, University of California, San Francisco

summary: Diseases caused by gene haploinsufficiency in humans commonly lack a phenotype in mice heterozygous for the orthologous factor, although the source of this discrepancy is unknown. The inability to accurately model human disease in mice impedes the study of complex phenotypes and critically limits the discovery and testing of potential therapeutics. Laboratory mice have longer telomeres (>40 kilobases (kb)) compared to humans (~5-15 kb), potentially protecting them from age-related disease caused by haploinsufficiency. In humans, heterozygous non-sense mutations in the transcription factor, NOTCH1 (N1), lead to severe age-dependent aortic valve (AV) calcification. However, mice heterozygous for N1 do not develop calcific AV disease (CAVD)5. Here, we show that telomere shortening is sufficient to elicit age-dependent cardiac valve disease in N1+/- mice that closely mimics the human disease and that progressive shortening correlates with severity of disease, extending to AV thickening in the neonate. N1 haploinsufficiency led to increased proliferation in valves that further reduced telomere length. Calcified AVs exhibited downregulation of osteoclast factors and upregulation of pro-calcific regulatory nodes concordant with gene network alterations in human N1 heterozygous endothelial cells. Dysregulated genes in valves were enriched for those that have promoters normally contacted by telomere looping. These findings reveal a critical role for telomere length in a mouse model of age-dependent human disease that may have broader implications and provides an in vivo model in which to test therapeutic candidates to prevent or delay the progression of CAVD.

overall_design: RNA-sequencing of aortic valves dissected from mice WT or heterozygous for Notch1 in the setting of long (Terc WT) or shortened (generation 2 Terc-/-) telomeres

first: Deepak

last: Srivastava


title: Bag101 overexpression in S. pombe

city: Copenhagen

first: Rasmus

last: Hartmann-Petersen

address: Ole Maaloes Vej 5

department: Department of Biology

country: Denmark

institute: University of Copenhagen

summary: Bag101 overexpression causes growth defects. The purpose of the experiment was to quantify gene expression differences caused by bag101 overexpression.

overall_design: 5 independent repeats of control (no bag101 overexpression) and 5 independent repeats of bag101 overexpression.

first: Jens

last: Johansen


title: N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis

city: Hinxton

first: Rik

last: Lindeboom

address: Wellcome Trust Genome Campus

department: Cellular Genetics

institute: Wellcome Sanger Institute

summary: RNA modifications are integral to regulation of RNA metabolism. One such abundant mRNA modification is m6A, which impacts various aspects of RNA metabolism including splicing, transport and degradation. Current knowledge about proteins recruited to m6A to carry out these molecular processes is still limited. Here we describe a comprehensive and systematic mass spectrometry-based screening of m6A interactors in various cell types and species. Amongst the main findings, we identified G3BP1 as a protein, which is repelled by m6A and which positively regulates mRNA stability in an m6A regulated manner.  Furthermore, we identified FMR1 as a novel, RNA sequence context dependent m6A reader, thus revealing a connection between an mRNA modification and an autism spectrum disorder. Collectively, our data represents a rich resource for the community and sheds further light on the complex interplay between m6A, m6A interactors and mRNA homeostasis.

overall_design: Transcriptome wide profiling of G3BP1 and G3BP2 binding sites and mRNA half-live measurement after G3BP1 overexpression or knockdown.

first: Raghu

last: Edupuganti

first: Michiel

last: Vermeulen


title: Cooperative and Antagonistic Transcriptional Regulation by BRG/BRM [RNA-seq]

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

summary: We monitored the transcription changes associated with loss of BRG1, BRM, or both combined I HepG2 cells to understand the functional relationship between two mutually exlusive subunits of SWI/SNF

overall_design: Cells were transduced with shRNA targeting the subunits of interested and subjected to RNAseq.


title: RNAseq in mast cells

city: ROCHESTER

first: Longze

last: Zhang

address: 55 FAIRHILL DR.

institute: University of Rochester

summary: Investigations of teriparatide (rPTH) as a potential treatment for critical defects have demonstrated the predicted anabolic effects on bone formation, and significant non-anabolic effects on healing via undefined mechanisms. Specifically, studies in murine models of structural allograft healing demonstrated that rPTH treatment increased angiogenesis (vessels <30μm), and decreased arteriogenesis (>30 μm) and mast cell numbers, which lead to decreased fibrosis and accelerated healing. To better understand these non-anabolic effects, we interrogated osteogenesis, vasculogenesis and mast cell accumulation in mice randomized to placebo (saline), rPTH (20µg/kg/2days), or the mast cell inhibitor sodium cromolyn (SC) (24µg/kg/2days), via longitudinal micro-CT and multiphoton laser scanning microscopy (MPLSM), in a critical calvaria defect model. Micro-CT demonstrated that SC significantly increased defect window closure and new bone volume versus placebo (p<0.05), although these effects were not as great as rPTH.  Interestingly, both rPTH and SC has similar inhibitory effects on arteriogenesis versus placebo (p<0.05) without affecting total vascular volume. MPLSM time course studies in untreated mice revealed that large numbers of mast cells were detected 1 day post-op (43 +/- 17), peaked at 6 days (76 +/- 6), and were still present in the critical defect at the end of the experiment on day 30 (20 +/- 12). In contrast, angiogenesis was not observed until day 4, and functional vessels were first observed on 6 days, demonstrating that mast cell accumulation precedes vasculogenesis. To confirm a direct role of mast cells on osteogenesis and vasculogenesis, we demonstrated that specific diphtheria toxin-α deletion in Mcpt5-Cre-iDTR mice results in similar affects as SC treatment in WT mice.  Collectively, these findings demonstrate that mast cells inhibit bone defect healing by stimulating arteriogenesis associated with fibrotic scaring, and that an efficacious non-anabolic effect of rPTH therapy on bone repair is suppression of arteriogenesis and fibrosis secondary to mast cell inhibition.And then, we need to figure out how rPTH works on mast cells. So we used the co-culture of osteoblast and mast cells, and perform RNAseq, by which we aim to screen out the factors in mast cells that are potential mediators for rPTH effects in bone formation, blood vessel formation, and fibrosis formation.

overall_design: Both cell lines were purchased from ATCC®. Osteoblast cell line, 7F2(ATCC® CRL-12557TM). Mast cell line, MC/9(ATCC® CRL-8306TM). The culture methods for both cell lines are the same with those provided by ATCC®. To prepare cells for RNAseq, osteoblasts were seeded and then mast cells were transferred in on the following day. Final concentration 10nM of rPTH was used to treat the cell co-culture for 24 hours. The mast cells were then collected for RNAseq, which was performed at the UR Genomic Research Center at URMC, University of Rochester. The genes with p < 0.05 compared with the average factor of all groups were screened out as candidate genes.


title: Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis

first: Daniel

middle: Antony

last: Pass

state: South Glamorgan

address: Museum Avenue

institute: Cardiff University

summary:
Background:
Analysis of the effect that chromatin structure has on the expression patterns of eukaryotic genes has recently expanded knowledge of the complex influence genome accessibility has on genome function. Interlaced with regular nucleosomal patterning are other mobile and labile sub-nucleosomal-sized protein structures bound to the genome such as transcription factors (TF), initiation complexes, and modified nucleosomes.
Results:
We present chromatin structure maps of the A. thaliana Col-0 wild-type (in vitro cell culture) combining differential micrococcal nuclease (MNase) digestion and analysis by paired-end next-generation sequencing with RNASeq data to provide insight into the sensitive genomic regions and variable DNA-bound particle size related to transcriptional activity. The landscape of sub-nucleosomal sized particles (subNSPs) has been investigated, revealing the DNA-binding complex positioning genome-wide. We observe the dynamic changes in the distribution of these complexes surrounding genomic features, particularly at transcription start sites (TSS). Differential digestion reveals the presence of MNase-sensitive smaller particles and a labile -1 nucleosome upstream of the TSS of active genes. These changes correlate with gene expression differences resulting from different environmental conditions of light- or dark growth both globally and locally, and a complex profile of bound particles is directly visualised.
Conclusions:
Analysis of the A. thaliana genome reveals that resolution of chromatin particle size by differential MNase digestion allows detection of the sensitive features in chromatin structure that have hereto been obfuscated. The concomitant analysis of transcript levels reveals the impact of transient extrinsic factors in modifying the sub- nucleosomal landscape in association with transcriptional changes, giving insight into the binding of transcription-associated factors.

overall_design: 2x Light grown, 2x Dark grown Arabidopsis thaliana Col0 under High or Low MNase digestion with 4x associated RNAseq per condition

first: Emily

last: Sornay

first: Angela

last: Marchbank

first: Margret

last: Crawford

first: Konrad

last: Paszkiewicz

first: Nicholas

last: Kent

first: James

last: Murray


title: RNA-sequencing of human leukemia cells and mouse hematopoietic progenitors

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: human leukemia cells treated with vitamin C for 12 and 72hrs and mouse hematopoietic progenitor cells with knockdown and Tet2 restoration

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: examination of 2 mouse hematopietic progenitor cell lines and 2 human leukemia cell lines

first: Luisa

last: Cimmino

first: Iannis

last: Aifantis


title: Ikk2 regulates cytokinesis during vertebrate development (Trancriptome profiling from the wild-type and Ikk2 maternal-zygotic mutant zebrafish)

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

state: Singapore

address: 60, Biopolis street

department: Computational and Systems Biology

summary:
Purpose: The Ikk2 maternal-zygotic mutants are the only vertebrates animals completely depleted globally of the Ikk2 function which is expected to block an activity of the canonical NFkB signaling pathway. Transcriptome profiling of embryos before the midblastula transition (MBT) and after MBT may provide a clean strategy to identify the NFkB target genes.
Methods: Zebrafish lines were maintained under standard laboratory procedures.
Results: Using an optimized data analysis workflow, we identified 54,276 transcripts in the embryos at 2 hours postfertilization (hpf) and 4 hpf. RNA-seq data confirmed lack of expression of a number of genes in the mutant both prior to and after the MBT, including genes linked to angiogenesis, skin development, cytokinesis, innate immunity and cytoskeletonT, and 4 of these were validated with qRT–PCR. M. add here if required.
Conclusions: Our study represents the first detailed analysis of transcriptomes of vertebrates globally depleted of activity of Ikk2, with two biologic replicates, generated by RNA-seq technology.The data reported here should provide a framework for understanding of maternal and zygotic genes which expression is controlled by Ikk2 activity. Our results expands a list of transcripts which expression may be controlled by the canonical NFkB signaling. We conclude that RNA-seq based transcriptome characterization improves analysis of NFkB regulated genes.

overall_design: Zebrafish Ikk2 mutants were obtained using zinc-finger nuclease-mediated mutagenesis. Some of the mutant homozygotic embryos grow into fertile adults able to produce embryos totally deplated of maternal and zygotic Ikk2.

first: Mathavan

last: Sinkaruppan

first: Korzh

last: Vladimir


title: Transcriptome analysis of root-knot nematode (Meloidogyne incognita)-infected tomato (Solanum lycopersicum) roots reveals complex gene expression profiles and metabolic networks of both plant and nematode during susceptible and resistance responses.

city: Brno

first: Neha

last: Shukla

address: Kamenice 753

department: Plant Molecular Biology

country: Czech Republic

institute: CEITEC

summary:
Purpose: To understand the molecular mechanisms involved in disease development during plant-nematode interactions.
Methods: We have taken a comprehensive transcriptomic approach to investigate the expression of both tomato and RKN genes in tomato roots at five infection time points from susceptible plants (PR: Pusa Ruby) and two infection time points from resistant plants (M36: Transgenic MM line), grown under soil conditions.
Results: Differentially expressed genes during susceptible (1827 tomato, 462 RKN) and resistance (25 tomato, 160 RKN) interactions were identified and a set of genes were validated by qRT-PCR.
Conclusion: Our findings, for the first time, provide insights into the transcriptome dynamics of both tomato and RKN during susceptible and resistance interactions and reveal involvement of a complex network of biosynthetic pathways during disease development.

sample_organism:
Solanum lycopersicum
Meloidogyne incognita

overall_design: Five infected stages from susceptible tomato plants (PR) and two infected stages from resistant tomato plants (M36) along with their corresponding uninfected controls (water inoculated) were analysed, in duplicates.

first: Rachita

last: Yadav

first: Pritam

last: Kaur

first: Simon

last: Rasmussen

first: Shailendra

last: Goel

first: Manu

last: Agarwal

first: Arun

last: Jagannath

first: Ramneek

last: Gupta

first: Amar

last: Kumar


title: Transcriptional profiling of wilt-resistant and wilt-susceptible chickpea cultivars after Fusarium oxysporum f.sp. ciceri (Foc) inoculation

city: Pune

first: Narendra

last: Kadoo

state: Maharashtra

address: Dr. Homi Bhabha Road, Pashan

department: Biochemical Sciences

institute: CSIR-National Chemical Laboratory

summary: Purpose: Molecular analysis of chickpea-Foc interaction; Methods: Four LongSAGE libraries of wilt-resistant and wilt-susceptible chickpea cultivars prepared after Foc inoculation and sequenced using Ion Torrent PGM. Results: Transcriptome analyses revealed expression of several plant defense and pathogen virulence genes with their peculier expression patterns in wilt-resistant and wilt-susceptible chickpea cultivars. Conclusion: The study identified several candidate Foc resistant genes, which can be used for crop improvement after their functional validation.

overall_design: Two chickpea cultivars were used: Digvijay (DV, wilt-resistant) and JG62 (JG, wilt-susceptible). One week old chickpea plants were inoculated with pathogen spores (or mock-inoculated with sterile distilled water) and tissues were collected from 11 timepoints after inoculation. Four LongSAGE libraries [resistant inoculated (DVI),  resistant control (DVC), susceptible inoculated (JGI) and susceptible control (JGC)] were generated by normalizing and pooling RNA from the 11 time-points. The libraries were sequenced using Ion Torrent PGM sequencer.

first: Medha

last: Upasani

first: Bhakti

last: Bhagwat

first: Gayatri

last: Gurjar

first: Sunitha

last: Kasibhatla

first: Rajendra

middle: R

last: Joshi

first: Vidya


title: Host mechanisms potentially associated with foodborne pathogen Escherichia coli O157 shedding in feedlot beef cattle

city: Edmonton

first: Ou

last: Wang

state: AB

address: 410 Agriculture/Forestry Centre, University of Alberta

department: AFNS

institute: University of Alberta

summary: Cattle shedding > 10e4 CFU of Escherichia coli O157 per g of feces are defined as super-shedders. RNA-sequencing was performed to identify the transcriptome of tissues, including duodenum, proximal jejunum, distal jejunum, distal jejunum, cecum, spiral colon and descending colon of super-shedder cattle in comparison with non-shedders. The total number of genes detected in gut tissues ranged from 16,846 ± 639 (cecum) to 18,137 ± 696 (distal jejunum), and immune functions were enriched for the transcriptomes of small intestinal tissues, reflecting their greater immune activity than large intestine. Totally 351 differentially expression genes were identified between super-shedders and non-shedders, including 101 up-regulated and 250 down-regulated in super-shedders. Differential gene expression analysis suggested increased T-cell responses and cholesterol absorption in distal jejunum and descending colon, and inhibited B-cell maturation in intestines of super-shedders. distal jejunum of super-shedders. Our findings suggested that host genetics and E. coli O157 activities are involved in super-shedding phenomenon.

overall_design: We performed a differential analysis of transcriptomes of gut tissues collected from E. coli O157 super-shedders and non-shedders (control), to study molecular mechanisms of super-shedding phenomenon. It is a case control study.

first: Leluo

last: Guan


title: Integrated analysis of mRNA-seq and miRNA-seq reveals the potential roles of sex-biased miRNA-mRNA pairs in gonad tissue of dark sleeper (Odontobutis potamophila)

city: Nanjing

first: Shaowu

last: Yin

state: jiangsu

address: College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road,  210023, China.

institute: Nanjing Normal University

summary: We used next-generation sequencing technology to characterize mRNA-seq and miRNA-seq of testes and ovaries of Odontobutis potamophila to elucidate the molecular mechanisms of sex determination and differentiation. We were able to find miRNA-mRNA pairs using bioinformatics analysis and miRNA prediction algorithms.

overall_design: mRNA-seq and miRNA-seq examination of testes and ovaries in Odontobutis potamophila (Each sample type has three biological replicates).

first: Cheng

last: Zhao


title: Dual role of Act1 in keratinocyte differentiation and host defense: TRAF3IP2 silencing alters keratinocyte differentiation while inhibiting IL-17 responses

city: Ann Arbor

first: William

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

summary: TRAF3IP2 is a candidate psoriasis susceptibility gene encoding Act1, a ubiquitin ligase that couples the IL-17 receptor to downstream signaling pathways. We investigated the role of Act1 in keratinocyte responses to IL-17 using a tetracycline inducible shRNA targeting TRAF3IP2. Tet exposure for seven days effectively silenced TRAF3IP2 mRNA and Act1 protein, resulting in 761 genes with significant changes in expression (495 down, 266 up, >1.5-fold, p<0.05). Gene Ontology analysis revealed that genes affected by TRAF3IP2 silencing are involved in epidermal differentiation, with early differentiation genes (KRT1, KRT10, DSC1, DSG1) being downregulated and late differentiation genes (SPRR2, SPRR3, LCE3) being upregulated.  AP1 binding sites were enriched upstream of genes up-regulated by TRAF3IP2 silencing. Correspondingly, nuclear expression of FosB and Fra1 was increased in TRAF3IP2-silenced cells.  Many genes involved in host defense were induced by IL-17 in a TRAF3IP2-dependent fashion. Inflammatory differentiation conditions (serum addition for 4 days postconfluence) markedly amplified these IL-17 responses, while increasing basal levels and TRAF3IP2 silencing-dependent upregulation of late differentiation genes. These findings suggest that TRAF3IP2 may alter both epidermal homeostasis and keratinocyte defense responses to influence psoriasis risk.

overall_design: Immortalized N/TERT-2G keratinocytes were either untreated or treated with tetracycline (TET) for TRAF3IP2 knockdown. Additionally, cells were either untreated or treated with IL17, TNF, or IL17+TNF. The experiment was replicated 4 times (batch IDs 2, 3, 4 and 5). A total of 32 samples were generated for RNA-seq analysis (8 treatments x 4 replicated experiments = 32 RNA-seq samples).

first: Sylviane

last: Lambert

first: Lam

middle: C

last: Tsoi

first: Stefan

middle: W

last: Stoll

first: James

middle: T

last: Elder


title: Transcriptomics analysis of gene expressions of EC and HSPC in zebrafish CHT

status: Public on Aug 20 2017

city: Beijing

first: Yuanyuan

last: Xue

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology，Chinese Academy of Sciences

summary: RNA  isolated from sorted cells from zebrafish CHT using HiSeq4000 (Illumina) in paired-read mode.

overall_design: Examination of gene expressive levels in EC and HSPC of zebrafish CHT

first: Feng

last: Liu


title: Hypoxic transcriptome of SQ20B human head and neck cancer cells

city: Philadelphia

first: Constantinos

last: Koumenis

state: PA

address: 13400 Civic Center Blvd

department: Radiation Oncology

institute: University of Pennsylvania

summary: We have carried out deep directional sequencing of  mRNA isolated from normoxic (control) SQ20B cells (N=4) and hypoxic (16h at 0.5% oxygen) cells (N=4).

overall_design: Normoxic compared to hypoxic, with 4 biological replicates.

first: Lauren

middle: K

last: Brady


title: Transcriptome analysis of Foxj3 or Zbtb18 stable expressed embryonic stem (ES) cell lines

city: Yangling

first: Haibo

last: Wu

address: 3rd, Taicheng Road

institute: Northwest A&F University

summary: To understand the specific mechanism by which Foxj3 and Zbtb18 control RA-induced neural directional differentiation of ESCs, total mRNAs of Foxj3-ES and Zbtb18-ES were extracted and used for RNA seq and transcriptome analyses. Compared with the control, 1331 genes were differentially expressed (P < 0.05) by twofold in Foxj3-ES (557 were underexpressed and 774 were overexpressed), and 1175 genes were differentially expressed (P < 0.05) by twofold in Zbtb18-ESCs (548 were underexpressed and 627 were overexpressed). Through Gene ontology and gene co-expression network analysis, we identified four critical genes in the neural regulatory networks: Olig1, Zic5, Erbb2, and Olig2. Our study shows that Foxj3 and Zbtb18 could trigger the gene regulatory networks of neurodevelopment by mediating the expression of Olig1, Zic5, Erbb2, and Olig2.

overall_design: mRNA profiles of  Foxj3 or Zbtb18 stable expressed embryonic stem cell lines by deep sequencing

first: Yan

last: Zhang

first: Jiaxing

last: Lv

first: Yong


title: Thymic epithelial cells induce formation of mesenchymal network structure after abrogation of thymic crosstalk

status: Public on Aug 19 2017

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

summary: In the earliest step of thymic organogenesis, mesenchymal cells support the growth of thymic epithelial cells (TECs). It is established that TECs and thymocytes influence each other for their growth/differentiation, a process called thymic crosstalk. However, little is known about the influence of developing thymocytes or TECs on mesenchymal cells. Here, we show that during normal thymus development fibroblast ingrowth occurs towards hypoxic areas. Similar overgrowth of mesenchymal cells is seen in a fetal thymic organ culture system under low oxygen conditions. However, when thymocytes were depleted by deoxyguanosine treatment, mesenchymal cells were also induced, precluding the direct effect of hypoxia. In the fetal thymus of hCD3εTg mice, which lack T lineage cells, an overgrowth of mesenchymal cells can be seen at a very early stage of thymic organogenesis. The growth of the mesenchymal cells is due to extensive proliferation and not mere enrichment.  With RNA sequencing analysis comparing hCD3εTg with wild type TECs, we identified candidate factors that could be involved in mesenchymal network formation.

overall_design: Comparison of thymic epithelial cells of different in vivo situations; one in presence of thymocytes, the other in the absence of thymocytes

first: Rumi

last: Satoh

first: Kiyokazu

last: Kakugawa

first: Hiroshi

last: Kawamoto


title: Identify and characterize the circular RNAs expressed in lactating rat mammary glands

city: Xuzhou

first: Yanhong

last: Wang

address: shanghai road number101

institute: Jiangsu Normal University

summary:
Purpose: A novel member of RNAs, circular RNAs (circRNAs), has recently been evidenced to play key role on biological process regulation. However, the global landscape of circular RNA remains largely unknown. In the present study, deep RNA-sequencing technique was employed to identify and characterize the circular RNAs expressed in lactating rat mammary gland.compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods:Deep RNA-sequencing technique was employed
Results: A total of 6824 and 4523 circRNAs were identified from rat mammary glands at two lactation stages, respectively. Numerous circRNAs seem to be specifically expressed in different lactation stages, as only 1314 circRNAs were detected in both libraries. Majority of the candidate circRNAs maps to intronic and intergenic regions, namely noncoding regions. There existed the circular preference or specificity of some genes. Interestingly, 4 protein coding genes (Rev3l, IGSF11, MAML2, and LPP) that also tanscripted high level circRNAs have been reported to be involved in cancer. The distribution of specific miRNA binding sites and RNA binding proteins binding sites also implied the role of circRNAs in mammary gland development and tumorigenesis.
Conclusions:The results provide the basis for comparisons with breast cancer profiles and for selection of representative circRNA candidates for future functional characterization in breast development and breast cancer.

overall_design: The rat mammary glands at different lactation stages were investigated

first: ChunLei


title: CTCF counter-regulates cardiomyocyte development and maturation programs in the embryonic heart [RNA-seq]

city: Madrid

first: Miguel

last: Manzanares

address: Melchor Fernandez Almagro, 3

department: Cell and Developmental Biology

country: Spain

institute: National Center of Cardiovascular Diseases

summary: Analysis of chromatin architecture suggests that the 3D structure of the genome plays a major role in regulating gene expression, orchestrating the compartmentalization of chromatin and facilitating specific enhancer-promoter interactions. However, the mechanisms that control this structuring of the genome are not fully understood. We have addressed this issue by analyzing the role of CTCF, a major architectural factor in chromatin structure, in the embryonic heart. Loss of CTCF triggered an overall downregulation of the cardiac developmental program, suggesting that CTCF facilitates enhancer-promoter interactions in the developing heart. Detailed analysis of the IrxA gene cluster showed that CTCF loss leads to disruption of the heart-specific regulatory domain that surrounds Irx4, resulting in changes in expression of IrxA cluster genes and neighboring genes. In contrast to the critical role proposed for CTCF in organizing large-scale chromatin domains, our results show that CTCF preferentially mediates local regulatory interactions.

overall_design: RNAseq of mouse embryonic E10.5 hearts in three conditions: 1) control (labeled as WT), 2) heterozygous (labeled as HET) and  3) homozygous (labeled as KO). Three replicates were performed for each condition, each consisting of a pool of 6 hearts. Tissue was mechanically disaggregated and RNA extracted with trizol and purified through columns.

first: Melisa

last: Gómez-Velázquez

first: Claudio

last: Badía


title: RNASeq to identify the in vivo mechanism of anti-Ox40 mAb treatment exacerbated lupus in NZB/W F1 Mice

status: Public on Aug 18 2017

city: South San Francisco

first: Jonathan

last: Sitrin

state: CA

address: 1 DNA Way

department: OMNI Human Genetics

institute: Genentech, Inc.

summary: We've recently shown that we can accelerate disease in a model of SLE (the NZB/W F1 model) using an anti-Ox40 mAb treatment regimen. The disease acceleration is rapid (within 2 weeks) but its unclear, mechanistically, how OX40 functions to promote disease. To that end we want to perform RNASeq on the sorted OX40-expressing CD4 T cells during treatment to understand how they function in response to OX40 signaling in vivo

overall_design: RNASeq was performed on FACS sorted CD4 T cells from the spleen and kidney of NZB/W F1 lupus mice following anti-Ox40 agonist mAb treatment and disease acceleration

first: Art

last: Wuster


title: The neuropeptide Neuromedin U stimulates innate lymphoid cells and promotes type 2 inflammation [NMU]

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

summary: The type 2 cytokines interleukin (IL)-4, IL-5, IL-9 and IL-13 play critical roles in stimulating innate and adaptive immune responses required for resistance to helminth infection and promotion of allergic inflammation, metabolic homeostasis and tissue repair.  Group 2 innate lymphoid cells (ILC2s) are a potent source of type 2 cytokines and while significant advances have been made in understanding the cytokine milieu that promotes ILC2 responses, there are fundamental gaps in knowledge regarding how ILC2 responses are regulated by other stimuli. In this report, we demonstrate that ILC2s in the gastrointestinal tract co-localize with cholinergic neurons that express the neuropeptide neuromedin U (NMU). In contrast to other hematopoietic cells, ILC2s selectively express the NMU receptor 1 (NMUR1). In vitro stimulation of ILC2s with NMU induced rapid cell activation, proliferation and secretion of type 2 cytokines IL-5, IL-9 and IL-13 that was dependent on cell-intrinsic expression of NMUR1 and Gaq protein. In vivo administration of NMU triggered potent type 2 cytokine responses characterized by ILC2 activation, proliferation and eosinophil recruitment that was associated with accelerated expulsion of the gastrointestinal nematode Nippostrongylus brasiliensis or induction of lung inflammation. Conversely, worm burden was higher in Nmur1-/- mice compared to control mice. Further, use of gene-deficient mice and adoptive cell transfer experiments revealed that ILC2s were necessary and sufficient to mount NMU-elicited type 2 cytokine responses. Together, these data indicate that the NMU-NMUR1 neuronal signaling circuit provides a selective and previously unrecognized mechanism through which the enteric nervous system and innate immune system integrate to promote rapid type 2 cytokine responses that can induce anti-microbial, inflammatory and tissue-protective type 2 responses at mucosal sites.

overall_design: To assess changes in gene expression in ILC2s due to NMU treatment, RNAseq was performed on 3 samples from NMU-treated mice and 4 samples from PBS-treated mice.

middle: G


title: The neuropeptide Neuromedin U stimulates innate lymphoid cells and promotes type 2 inflammation [ILC2 and ILC3]

overall_design: Transcriptional differences between ILC2s and ILC3s were determined by RNAseq using 3 ILC2 samples and 3 ILC3 samples.


title: RNASeq to identify the in vitro molecular signature of Ox40 signaling in conjunction with TCR signaling in CD4 T cells from NZB/W F1 Mice

summary: We've recently shown that we can accelerate disease in a model of SLE (the NZB/W F1 model) using an anti-Ox40 mAb treatment regimen. The disease acceleration is rapid (within 2 weeks) but its unclear, mechanistically, how Ox40 promotes disease. To that end we performed RNASeq on in vitro cultured CD4 T cells during Ox40 and TCR stimulation (in a reductionist setting) to understand how Ox40 signaling impacts cellular phenotype and function, including with and without TCR stimulation

overall_design: RNASeq was performed on in vitro cultured CD4 T cells from the spleen of NZB/W F1 lupus prone mice, following anti-Ox40 mAb and anti-CD3/CD28 bead stimulation


title: Functional astrocytes differentiated from hiPSCs

first: Kristen

middle: J.

last: Brennand

address: 1425 Madison Ave

department: Department of Neuroscience & Friedman Brain Institute

institute: Icahn School of Medicine at Mount Sinai

summary: Growing evidence implicates the importance of glia, particularly astrocytes, in neurological and psychiatric diseases. Here, we describe a rapid and robust method for the differentiation of highly pure populations of astrocytes from human induced pluripotent stem cells (hiPSCs), via a neural progenitor cell (NPC) intermediate.  Using this method, we generated hiPSC-derived astrocyte populations (hiPSC-astrocytes) from 42 NPC lines (derived from 30 individuals) with an average of ~90% S100β-positive cells. Transcriptomic analysis demonstrated that the hiPSC-astrocytes are highly similar to primary human fetal astrocytes and characteristic of a non-reactive state. hiPSC-astrocytes respond to inflammatory stimulants, display phagocytic capacity and enhance microglial phagocytosis. hiPSC-astrocytes also possess spontaneous calcium transient activity. Our novel protocol is a reproducible, straightforward (single media) and rapid (<30 days) method to generate homogenous populations of hiPSC-astrocytes that can be used for neuron-astrocyte and microglia-astrocyte co-cultures for the study of neuropsychiatric disorders.

overall_design: 6 hiPSC-derived astrocyte lines were generated. Total RNA were extracted from these hiPSC-astrocytes as well as 2 primary astrocyte lines and analyzed by RNA sequencing.

first: Julia

last: TCW

first: Minghui

first: Anna

middle: A

last: Pimenova

first: Kathryn

last: Bowles

first: Brigham

middle: J

last: Hartley

first: Emre

last: Lacin

first: Saima

last: Machlovi

first: Rawan

last: Abdelaal

first: Celeste

middle: M

last: Karch

first: Hemali

last: Phetnani

first: Paul

last: Slesinger

first: Bin

first: Alison

last: Goate


title: Paramutation of natural epialleles in tomato [BiSulfite-seq]

city: Heidelberg

first: Quentin

last: Gouil

address: Studley Road

institute: Olivia Newton-John Cancer Research Institute

summary: By using DNA methylation of introgression lines as a marker of past paramutation, we characterise in details the paramutation of the \textit{H06} locus in crosses between Solanum lycopersicum and a range of tomato relatives and cultivars. Paramutation of H06 depends on the timing of sRNA production and conforms to the RNA-directed model of paramutation. By scanning the methylomes of tomato introgression lines for shared regions of differential methylation, thousands of candidate regions for paramutation are identified. Analysing the segregation of the methylation patterns for a subset of these regions shows variations in the penetrance of paramutation-like interactions.

sample_organism: Solanum lycopersicum x Solanum pennellii

overall_design: sRNA of M82, S. pennellii and their F1 for leaf/flower/pollen, sRNA for Micro-Tom and S. pimpinellifolium seedlings, methylome data of M82 and introgression lines IL1-1, IL2-5 and IL8-3