title: Next Generation Sequencing Study of Circadian Changes in Transcriptome of Rhesus Macaque Pineal Gland and Retina

city: New York

first: Marjan

last: Bozinoski

address: 1305 York Avenue, Box 140

department: Physiology and Biophysics

institute: Weill Cornell Medicine

summary:
Purpose: We performed an NGS study on the circadian changes in Rhesus Macaque retina and pineal gland transcriptome in order to elucidate novel elements in the primate circadian clock.
Methods: Total RNA from retina and pineaal glands of Rhesus Macauqes euthanized at 4 timepoints (Dawn, Day, Dusk and Night) was deep sequenced, in triplicate, using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2.
Results: We discover a variety of novel genes that show circadian activivty in both retina and pineal gland of the Rhesus Macaque. A particular set of genes involved in the production of N-acetyltryptamine in Rhesus Macaque retina appears to be responsible for the circadian oscillations of the concentrations of N-acetyltriptamine in the plasma, thereby accentuating N-acetyltriptamine as a retina derived signaling molecule in primates.
Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Retinal and Pineal gland Total RNA reads were generated by deep sequencing, in triplicate, using Illumina HiSeq2000. Control samples consisting of same amount of RNA extracted from corpus callosum, frontal cortex, cerebellum, thalamus, hippocampus, caudate, medulla, pituitary, heart, liver, lung, kidney, skeletal muscle, small intestine, testis and ovary, at mid-day (12 P.M.) and midnight (12 A.M.).

first: David

last: Klein

first: Steven

middle: L

last: Coon


title: CD133hi, Notchhi, DP (double positive) and DN (double negative) in GBML8 and GBML20, both patient-derived glioblastoma tumorsphere cultures

status: Public on May 22 2017

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

country: USA

institute: NYU Grossman School of Medicine

type: Expression profiling by high throughput sequencing

summary: CD133hi, Notchhi, DP and DN cells were FACS-isolated from GBML8 and GBML20 cultures and analyzed with RNA-seq, in order to find cell type-specific gene signatures.

overall_design: CD133hi, Notchhi, DP and DN cells were FACS-isolated and subjected to RNA isolation and RNA-seq. The experiment represents averaged data of 2 independent FACS isolations from GBML8 and 1 isolation from GBML20.

first: Nermin

middle: S

last: Bayin

first: Dimitris

middle: G

last: Placantonakis


title: Identification of Candida albicans traits that sustain its commensal dwelling in the mammalian gut

status: Public on Aug 01 2017

city: Würzburg

first: Tobias

last: Ludwig

address: Josef-Schneider-Straße 2

country: Germany

institute: Institute for Molecular Infection Biology

summary:
Goal: We employed RNA-seq to identify targets of regulation of five Candida albicans transcription regulators (Try4, Zfu2 and Zcf8). These regulators were identifyed through a genetic screen in a gnotobiotic mouse model of Candida albicans gut colonization.
Results: We found that the five regulators comprise a complex transcriptional network (>500 targets of regulation) that partitions in two sub-networks. One sub-network is formed by Rtg1 and Rtg3. The other comprises the regulators Try4, Zfu2 and Zcf8.

overall_design: Comparison of the transcriptome of Candida albicans wild-type reference strain vs. five transcription regulator deletion mutants. One growth condition, two biological replicates per sample. RNA-seq data generated with Illumina HiSeq2500.

first: J

middle: C

last: Perez


title: DNA methylation and gene expression profiling of primary medulloblastoma samples

status: Public on Jun 13 2017

city: Toronto

first: Florence

middle: M G

last: Cavalli

state: Ontario

address: PGCRL, 686 Bay Street

department: Developmental and Stem Cell

country: Canada

institute: The Hospital for Sick Children

type:
Expression profiling by array
Methylation profiling by array

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

overall_design: Refer to individual Series


title: CTCF and cohesin regulate chromatin loop stability with distinct dynamics

status: Public on May 03 2017

city: Berkeley

first: Robert

last: Tjian

state: CA

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The study investigates the nuclear organization and the binding dynamics of CTCF and cohesin by super-resolution microscopy and ChIP-seq. We determined the genome-wide binding profile of CTCF and Rad21 cohesin subunit in wild type mouse ES cells and compared them to a double FLAG-Halo-mCTCF/mRad21-SNAPf-V5 knock-in mES line, generated by CRISPR/Cas9-mediated genome editing to perform imaging experiments.

overall_design: ChIP-Seq of CTCF and Rad21 cohesin subunit in wild type mouse ES cells (WT) and in mouse ES cells homozygous for FLAG-Halo-CTCF and Rad21-SNAPf-V5 (C59 clone). ChIP-Seq libraries were prepared independently from two ChIP biological replicates, using normal serum IgGs as a control, and including total inputs as reference datasets.

first: Anders

last: Sejr Hansen

first: Claudia

last: Cattoglio

first: Iryna

last: Pustova

first: Xavier

last: Darzacq


title: Bacterial endosymbionts control host sexuality and reveal reproductive genes of early divergent fungi

status: Public on May 13 2017

city: Ithaca

first: Stephen

middle: James

last: Mondo

state: NY

address: 334 Plant Science Building, Tower Road

department: Plant Pathology and Plant-Microbe Biology

institute: Cornell University

summary: Through transcriptome profiling using RNA-seq, we investigated the mechanisms behind bacterial endosymbiont (Burkholderia rhizoxinica) control over host (Rhizopus microsporus) reproductive biology. By analyzing differential expression across six different conditions, including fungal opposite mates growing independently with or without endosymbionts, as well as opposite mates growing together with endosymbionts (mating) or without endosymbionts (no mating), we were able to identify that endosymbionts control expression of a Ras signaling protein critical for sexual reproduction in many fungi (Ras2). As little is known regarding sexual reproduction in Mucoromycotina, we also used these data to investigate conservation of sex-related genes across all fungi, as well as predict potential genes involved in sensing of trisporic acid, the mating pheromone used by these fungi.

overall_design: 6 different conditions were analyzed, each consisting of two biological replicates. These included Rhizopus microsporus ATCC52813 (sex +) growing alone with endosymbionts, R. microsporus ATCC52814 (sex -) growing alone with endosymbionts, ATCC 52813 growing alone without endosymbionts, ATCC52814 growing alone without endosymbionts, ATCC52813 and ATCC52814 growing together with endosymbionts (successfully mating), and ATCC52813 and ATCC52814 growing together without endosymbionts (failure to mate). In each condition, fungi were cultivated on half-strength PDA and plugs of mycelium were placed at the edge of the plate. After 6 days, approximately 2.5 cm of tissue were harvested from the center of the plate. Each biological replicate consists of 5 plates which were pooled prior to RNA extraction to ensure sufficient tissue was collected.

middle: J

last: Riley

first: Hui

last: Sun

first: Gregoriev

middle: V

last: Igor

first: Teresa

middle: E

last: Pawlowska


title: CP190 and CTCF mediated enhancer blocking is augmented by SUMOylation

status: Public on Aug 07 2017

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

summary: Chromatin insulators shield promoters and chromatin domains from neighbouring enhancers or chromatin regions with opposing activities. Insulator binding proteins and their cofactors mediate the boundary function. In general, covalent modification of proteins by the Small Ubiqutin-like Modifier (SUMO) is an important mechanism to control the interaction of proteins within complexes. Here we addressed the impact of SUMO in respect to insulator function, chromatin binding of insulator factors and formation of insulator speckles. SUMOylation augments the enhancer blocking function of four different insulator sequences and increases the genome-wide binding of the insulator cofactor CP190. A model is discussed with enhanced chromatin binding of SUMOylated CP190 causing fusion of insulator speckles, which may allow for more efficient insulation.

overall_design: ChIP-seq of FLAG-tagged SUMO, CTCF and CP190 before and after induction of FLAG-SUMO

first: Theresa

last: Jox

first: Rainer

last: Renkawitz


title: Contribution of STAT3, IRF1 and PGAM5 to androgen response in prostate cancer cells

status: Public on May 01 2017

city: buffalo

first: Dan

last: Wang

address: Elm & Carlton Streets

institute: RPCI

summary: To decipher the contribution of STAT3, IRF1 and PGAM5 to androgen-responsive gene expression, effect of siRNA-mediated silencing of STAT3, IRF1 and PGAM5 on expression of androgen-dependent genes was studied.

overall_design: Human LNCaP prostate cancer cells were transfected with individual siRNA SmartPools targeting STAT3, IRF1 or PGAM5 or a non-targeting siRNA SmartPool.  Forty-two hours after transfection, cells were treated with synthetic androgen R1881 (5nM) or vehicle.  Three biological replicates were generated per treatment group.  Forty-eight hours later, total RNA was isolated and processed for Illumina oligoarray analysis.

first: Hannelore

last: Heemers

first: Xiwei

last: Chen

first: Song

last: Liu


title: Emerging pathways of dystonia pathogenesis: eIF2α and neuroplasticity defects in DYT6

status: Public on Nov 11 2017

city: Tempe

first: Ben

last: Readhead

state: AZ

address: 797 E. Tyler Street

institute: ASU-Banner Neurodegenerative Disease Research Center

summary: Dystonia is characterized by involuntary muscle contractions. Its many forms are genetically, phenotypically and etiologically diverse and it is unknown whether their pathogenesis converges on shared pathways. Mutations in THAP1, a zinc-finger transcription factor, cause DYT6, but its neuronal targets and functions are unknown. We used RNA-Seq to assay the in vivo effect of a heterozygote Thap1C54Y or Exon2 allele on the gene transcription signatures in neonatal mouse striatum and cerebellum. Enriched pathways and gene ontology terms include eIF2α Signaling, Mitochondrial Dysfunction, Neuron Projection Development, Axonal Guidance Signaling, and Synaptic Long Term Depression pathways, which are dysregulated in a genotype and tissue-dependent manner. Electrophysiological and neurite outgrowth assays confirmed the functional significance of those findings. Notably, several of these pathways were recently implicated in other forms of inherited dystonia, including DYT1. We conclude that dysfunction of these pathways may represent a point of convergence on the pathogenesis of unrelated forms of inherited dystonia.

overall_design: We used RNA-Seq to assay the in vivo effect of a heterozygote Thap1C54Y or deltaExon2 allele on the gene transcription signatures in neonatal mouse striatum and cerebellum

first: Zakirova

last: Zuchra

first: Ehrlich

last: Michelle


title: Gene expression profile in freshly isolated monocytes from patients with diffuse cutaneous scleroderma (dcSSc) compared to healthy donors (HDs)

status: Public on Jun 12 2017

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
Monocytes/macrophages are activated in several autoimmune diseases, including systemic sclerosis (scleroderma, SSc), with increased expression of IFN-regulatory genes and inflammatory cytokines, suggesting dysregulation of the innate immune response in autoimmunity. Recently, we found that EBV is deregulated in SSc with abnormal expression of viral lytic-genes in PBMCs and skin. Since monocytes/macrophages are involved in innate immune recognition of EBV/lytic infection, we sought to determine whether EBV might contribute to their activation in SSc.
In this study, using recombinant-EBV we infected monocytes from SSc and healthy donors (HDs), we found that viral replication is essential for inducing the expression of TLR8 in EBV-infected primary monocytes. Markers of activated monocytes, such as IFN-regulated genes and chemokines, were up-regulated in SSc- and HD-EBV-infected monocytes. Inhibiting TLR8 expression reduced virally-induced-TLR8 in THP-1 infected cells, demonstrating that innate immune activation by infectious EBV is partially dependent on TLR8. Viral lytic-mRNA and -proteins were detected in freshly isolated SSc monocytes. Microarray analysis substantiated the evidence of an increased IFN signature and altered level of TLR8 expression in SSc monocytes carrying infectious EBV compared to HD monocytes.

overall_design: Four dcSSc monocytes tested positive for EBV lytic genes were compared to age-matched monocytes from HDs.

first: Giuseppina

middle: A

last: Farina


title: Differential gene expression profiles of corneal epithelium from Keratoconus patients

status: Public on Apr 30 2017

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: The gene expression profile of various cell signaling pathway associated genes were compared between the different clinical grades of keratoconus corneal epithelium, controls

overall_design: Organism : Homo sapiens, Agilent's Human Gene Expression  8x60k Array (AMADID: 039494)

first: Nallathambi

last: Jeyabalan

first: Rohit

last: Shetty

first: Arka

last: Subhra Ghosh


title: Global gene expression kinetics of early human lung development modeled by directed differentiation of human PSCs using an NKX2-1GFP iPSC reporter

status: Public on May 02 2017

summary:
It has been postulated that during human fetal development all cells of the lung epithelium derive from an embryonic endodermal NKX2-1+ precursor, however, this hypothesis has not been formally tested due to an inability to purify or track this theorized cell for detailed characterization. Here we engineer and developmentally differentiate NKX2-1GFP reporter pluripotent stem cells (PSCs) in vitro to generate and isolate a human primordial lung progenitor that expresses NKX2-1 but is initially devoid of markers of differentiated lung lineages. As these progenitors move through the earliest moments of lung lineage specification from definitive endoderm they can be imaged in real time or isolated for time-series global transcriptomic profiling. We performed microarray analysis of 5 timepoints of human iPSC to lung directed differentiation compared to week 21 human fetal lung and Neural NKX2-1+ cell controls.  These profiles indicate that evolutionarily conserved, stage-dependent developmental gene signatures are expressed in primordial human lung progenitors.
Using a TALEN-targeted fluorescent reporter to purify iPSC-derived lung progenitors (C17 NKX2-1GFP) we analyzed cells at major developmental time points in vitro (undifferentiated iPSC, definitive endoderm, anterior foregut endoderm and sorted NKX2-1GFP+ and NKX2-1GFP- cells on day 15 and day 28 of the protocol). We also differentiated NXK2-1GFP iPSC in a neural protocol and isolated neural NKX2-1GFP+ cells. Approximately 90% pure human fetal lung epithelial cells from week 21 embryos were used as controls.

overall_design: We prepared time series microarray expression profiles representing the following 5 key stages of iPSC lung-directed differentiation: undifferentiated iPSC (day 0), sorted CXCR4+ definitive endoderm (day 3), anterior foregut-like endoderm (day 6), sorted NKX2-1GFP+ and NKX2-1GFP- primordial progenitors (day 15), sorted NKX2-1GFP+ and NKX2-1GFP- differentiated cells (day 28). For positive and negative controls we included primary distal fetal lung epithelial cells (21 weeks of human gestation) and forebrain-like iPSC-derived neural NKX2-1GFP+ cells. Biological triplicates of all samples except human fetal lung were prepared. Biological triplicates were used for each sample except human fetal lung control samples where biological duplicates from one embryo (“uncultured naïve lung epithelium”) and a singlicate from a different embryo (“differentiated AT2 cells”) were prepared. Fetal lung samples were prepared using previously described protocols that result in approximately 90% epithelial cells. Global gene expression in all 27 samples was analyzed by Affymetrix GeneChip Human Gene 2.0 ST arrays

first: Finn

last: Hawkins

first: Darrell

last: Kotton


title: A genome-wide microRNA profiling indicates miR-424-5p and miR-503-5p as regulators of ALK expression in neuroblastoma (NB cell lines)

city: Genova

first: Sara

last: Stigliani

address: largo R Benzi 10

country: Italy

institute: IRCCS AOU San Martino-IST

summary: The discovery of either missense mutations or amplification of ALK (Anaplastic Lymphoma Kinase) gene identified this receptor tyrosine kinase as a therapeutic target in neuroblastoma (NB). Moreover, a high ALK expression has been associated with cases of metastatic NB and with a worse prognosis. In order to identify miRNAs involved in the regulation of ALK expression in NB we therefore analyzed their expression profile in 16 NB cell lines and in 22 patients by qPCR. We then identified miRNAs which were differentially expressed between two groups of samples showing high (ALK+) or low (ALK-) expression levels of ALK by using microarrays containing 866 human miRNA probes (Agilent). Next, the differential expression analysis between the two groups (ALK+ and ALK-) was performed using R. Our analysis showed a higher expression of 30 and 23 miRNAs (p-value <0.05) in NB lines and samples, respectively, both belonging to the ALK- group. Validation analysis and filtering according to in silico suggested miR-424-5p as a potential ALK regulator candidate. Dual luciferase assay indicated a direct binding of this miRNA to ALK-3’UTR. Moreover, we observed a down-regulation of ALK protein expression following transfection of miR-424-5p mimic as well as inhibition of cell viability in ALK+ NB cell lines. In conclusion, our data suggest miR-424-5p as involved in the regulation of ALK expression in NB.

overall_design: A total of 16 cell lines (divided in ALK+ and ALK- according to gene and protein expression analysis) were studied to obtain microRNA profile. After quality control SKNBE2 (belonging to ALK+ group) were removed from further analysis.

first: Marilena

last: DeMariano

first: Stefano

last: Moretti

first: Luca

last: Longo


title: Investigation of tolvaptan induced liver damage using expression data of Collaborative Cross (CC) mice

status: Public on Jun 25 2017

city: chapel hill

first: Yunjung

last: Kim

state: North Carolina

address: 120 Mason farm road

institute: UNC at Chapel Hill

summary:
We evaluate tolvaptan induced liver injury using 8-10 weeks old, male mice.
We used microarray to study gene expression changes in mouse liver after tolvaptan treatment.

overall_design: We examined liver transcriptome profiles from 354 mice (175 tolvaptan-treated, 179 vehicle-treated) after 24 hours of tolvaptan treatment.

first: Kim

last: Yunjung


title: Transcriptional Profiling of Biofilm Regulators Identified by an Overexpression Screen in S. cerevisiae

status: Public on Apr 25 2017

city: Seattle

first: Aimee

last: Dudley

state: Washington

address: 720 Broadway

institute: PNDRI

summary: Biofilm formation by microorganisms is a major cause of recurring infections and removal of biofilms has proven to be extremely difficult given their inherent drug resistance. Understanding the biological processes that underlie biofilm formation is thus extremely important and could lead to the development of more effective drug therapies, resulting in better infection outcomes. Using the yeast S. cerevisiae as a biofilm model, overexpression screens identified DIG1, SFL1, HEK2, TOS8, SAN1 and ROF1/YHR177W as regulators of biofilm formation. Subsequent RNA-seq analysis of biofilm and non-biofilm forming strains revealed that all of the overexpression strains, other than DIG1 and TOS8, were adopting a single differential expression profile, although induced to varying degrees. TOS8 adopted a separate profile, while the expression profile of DIG1 reflected the common pattern seen in most of the strains, plus substantial DIG1-specific expression changes. We interpret the existence of the common transcriptional pattern seen across multiple, unrelated overexpression strains as reflecting a real transcriptional state, that the yeast cell can access through regulatory signaling mechanisms, allowing an adaptive morphological change between biofilm-forming and non-biofilm states.

overall_design: RNA-seq from overexpression screen in yeast identifying genes whose overexpression causes a reduction in complex colony morphology.Twenty samples from strains over-expressing SAN1, TOS8, ROF1, SFL1, or HEK2. Four biological replicate samples of each strain.

first: Gareth

last: Cromie

first: Zhihao

last: Tan

first: Michelle

last: Hays

first: Amy

last: Sirr

first: Eric

middle: W

last: Jeffery

first: Aimée

middle: M


title: Time-course expression data from HEK293∆RAF1:ER cells stimulated with 4OHT and labelled with 4SU

status: Public on Apr 28 2017

first: Florian

last: Uhlitz

address: 1275 York Avenue

department: Computational Oncology

institute: Memorial Sloan Kettering Cancer Center

summary: We integrate experimental data and mathematical modelling to unveil how ERK signal duration is translated to mRNA dynamics.

overall_design: HEK293 cells were transfected with an inducible form of RAF (∆RAF1:ER), labelled with 4-thiouridine (4SU) one hour before harvesting and induced with tamoxifen (4OHT) for different periods of time (0h-8h).

first: Anja

last: Sieber

first: Emanuel

last: Wyler

first: Raphaela

last: Fritsche-Günther

first: Johannes

last: Meisig

first: Markus

last: Landthaler

first: Bertram

last: Klinger

first: Nils

last: Blüthgen


title: A genome-wide microRNA profiling indicates miR-424-5p and miR-503-5p as regulators of ALK expression in neuroblastoma(NB Samples)

first: Sara

last: Stigliani

overall_design: A total of 22 NB samples (divided in ALK+ and ALK- according to gene expression analysis) were studied to obtain microRNA profile. After quality control 2 samples were excluded from further analysis

first: Marilena

last: DeMariano

first: Stefano

last: Moretti

first: Luca

last: Longo


title: A genome-wide microRNA profiling indicates miR-424-5p and miR-503-5p as regulators of ALK expression in neuroblastoma


title: BPTF Depletion Enhances NK Cell Mediated Antitumor Immunity

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

summary:
In mouse models, the bromodomain PHD finger transcription factor (BPTF) chromatin remodeling subunit in tumor cells suppresses natural killer (NK) cell antitumor activity.
In vitro, BPTF suppresses NK cell cytolytic activity to mouse and human cancer cell lines, demonstrating a conserved function.

overall_design: BPTF-depleted tumors from BALB/c or NSG mice were compared to control tumors using gene expresion microarray experiments.

first: Joseph

last: Landry

middle: I

first: Kimberly

last: Mayes


title: Whole genome-wide expression profiles of hemp (Cannabis sativa L.) in response to drought stress

status: Public on Apr 22 2017

city: changsha

first: chunsheng

last: gao

address: No.348 Xianjiahu West Rd

department: Institute of Bast Fiber Crops and Center of Southern Economic Crops

country: China

institute: Chinese Academy of Agricultural Sciences

summary: Drought stress is the main environmental factor influencing hemp growth and yield. However, little is known about the response mechanism of hemp to drought stress. A total of 44.10 M tags and 8.91G bases were sequenced in the control hemp (CK) and drought stress hemp (DS) libraries. A total of 1292 differentially expressed genes (DEGs), including 883 up-regulated genes and 409 down-regulated genes, were identified. These results may contribute toward improving our understanding about the drought stress regulatory mechanism of hemp, and improving its drought tolerance ability.

overall_design: 3' tag-based DGE libraries were generated to exam the differentially expressed gene between drought-stressed and well-watered hemp

first: Chunsheng

last: Gao


title: Time-course expression data from HEK293∆RAF1:ER cells stimulated with 4OHT, U0126, CYHX, ActD, EGF, FGF, or IGF and labelled with 4SU

first: Florian

last: Uhlitz


title: Epigenomic Analysis Reveals Chromatin States and Regulators Associated with Melanoma Progression

status: Public on Apr 24 2017

city: Houston

first: Kadir

middle: Caner

last: Akdemir

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary: The extent and nature of the changes in epigenome and their association with cancer progression are not completely understood. Here we profiled 35 epigenetic modifications and gene expression to understand changes in the epigenome during melanoma progression using a primary cell line based melanoma progression model representing non-tumorigenic and tumorigenic states based on constitutively active BRAF and PTEN knockdown. Identification of chromatin states based on the combinatorial and spatial pattern of the histone modifications revealed specific changes in them during transition to tumorigenesis.  Major changes in chromatin states comprised of loss of histone acetylation events in combination with H3K4 methylation. These chromatin state changes primarily enriched for enhancers and promoter states. The putative gene targets of these enhancers and promoters that changed genes were most enriched in cancer-regulatory pathways including cell cycle, apoptosis, cell adhesion and immune response. A ChIP-String assay was used to validate some of the chromatin state changes in human tumor samples.

overall_design: We generated a cell line based model of melanoma tumorigenesis using partially transformed melanocytic line (two clonal variants are referred as HMEL or PMEL). This cell-line was generated using primary foreskin melanocytes, immortalized by overexpression of TERT, CDK4R24C, dominant negative p53 and BRAFV600E derivatives. HMEL-shGFP and PMEL-shGFP cells are referred as non-tumorigenic variants as  they have poor tumorigenic abilities (at 1million cells per injection tumors appear by 22 weeks with 10-20% penetrance). HMEL-shPTEN and PMEL-shPTEN  cells are called tumorigenic cells as they form tumors readily (at 1million cells per injection tumors appear by 8-9 weeks with ~80% penetrance) We profiled 33 histone marks, histone H3, H4 and IgG using a high-throughput ChIP-Sequencing (chromatin immunoprecipitation followed by next-generation sequencing) approach in non-tumorigenic and tumorigenic cells.

first: Kunal

last: Rai

first: Lynda

last: Chin


title: Paget's associated osteosarcoma

status: Public on Apr 18 2017

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

country: United Kingdom

institute: University of Oxford

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Refer to individual Series


title: Endogenous tRNA fragments are expressed in a phosphaturic mesenchymal tumor and Paget's associated osteosarcoma

city: Norwich

first: Darrell

last: Green

address: Earlham Road

department: Norwich Medical School

institute: University of East Anglia

summary: We profiled the differential expression of microRNAs and tRNA fragments between a case of a patient harbouring an FGF23-producing tumor and malignant osteosarcoma.

overall_design: We profiled normal tissue versus tumor tissue in an attempt to identify differential expression of small RNAs.

first: Jeremy

last: Turner

first: Andoni

last: Toms

first: John

last: Nolan

first: Richard

last: Ball

first: Iain

last: McNamara

first: Tamas

last: Dalmay

first: William

last: Fraser


title: Differentially expressed lncRNAs in placentas from patients with late-onset preeclampsia

city: Guangzhou

first: Xin

last: Wang

address: Duobao Road, No. 63

department: Department of Obstetrics and Gynecology

institute: Third Affiliated Hospital of Guangzhou Medical University

summary: To identify lncRNA expression in placentas from patients with late-onset preeclampsia (LOPE), we have employed whole genome microarray expression profiling as a discovery platform to identify differential expression of lncRNAs in placental samples from LOPE patients and normal controls. For microarray analysis, 8 randomly and blindly selected placental samples from LOPE patients and matched controls (4 samples per group) were used to extract total RNA. The expression profiles of the placental lncRNAs were detected using the Agilent Human lncRNA Microarray V4.0(OE Biotech, Shanghai, China). The threshold for a dysregulated lncRNA was set as a fold-change (FC) value of 2.0 or greater. A totle of 163 differentially expressed lncRNAs were identified.  Expression of nine lncRNAs (NONHSAT145880, ENST00000587240, NONHSAT116812, NONHSAT104536, FR339600, NONHSAG018907, TCONS_l2_00014782, NONHSAT134432 and NONHSAG024318) from this microarray was quantified n placental tissues from the LOPE patients (n = 40) and controls (n = 35) delivered by caesarean section by real-time PCR, confirming low variability between the qRT-PCR results and the microarray data.

overall_design: LOPE patients (n = 40) and controls (n = 35) delivered by caesarean section. For each sample, the RNA Integrity Number (RIN) was greater than or equal to 7, the value of 28S/18S was greater than or equal to 0.7, and the total RNA can meet 2 or more than 2 experiments.


title: Transcriptome profiling of drug resistant cell lines (NGP-127).

status: Public on Apr 14 2017

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

summary: The aim of this research was to uncover transcriptome changes in NGP-127 cells during the acquisition of resistance to anticancer drugs Sorafenib, Sunitinib, Pazopanib, Everolimus, Temsirolimus.

overall_design: NGP-127 cells resistant to five target anticancer drugs were generated by growing naive cells serially treated with an increasing doses of Sunitinib up to 6 µM, Pazopanib up to 25 µM, Sorafenib up to 10 µM, Everolimus up to 20 µM and Temsirolimus up to 15 µM. Transcriptome analisys was made at the following time points: 4, 8, 14 and 18 weeks. Simultaneously untreated control sells were grown for the same period, transcriptome analisys was performed at 4, 8, 10,14 and 18 weeks.

first: Roman

last: Kholodenko

first: Elena

last: Ilnitskaya

first: Maksim

last: Sorokin

first: Anton

last: Buzdin


title: Dehydration and Fixed-Carbon Starvation of Brassinosteroid related mutants in Arabidopsis

status: Public on Apr 11 2017

city: Ames

first: Yanhai

last: Yin

state: IA

address: 1035D Roy J. Carver Co-Lab

department: Genetic Development and Cell Biology

institute: Iowa State University

summary: We report global gene expression profilies of Brassinosteroid related Arabidopsis mutants in response to dehydration and fixed-carbon starvation stresses by RNA-seq

overall_design: Arabidopsis plants of listed genotypes were grown for 4 weeks under long day (16 hour light) conditions before being subjected to control, 4 hour dehydration, or 5 day fixed carbon starvation treatments.


title: Trisomy detection by PCR and comparative genomic hybridization

status: Public on Apr 19 2017

city: México

first: Esther

last: Lopez-Bayghen

address: Av. IPN 2508 San Pedro Zac

department: Toxicología

country: Mexico

institute: Cinvestav-IPN

summary: PCR based detection of trisomy 18 and trisomy 21 compared against results obtained by CGH microarrrays in Preimplantation Genetic Screening

overall_design:
Three-condition experiment: subjects classified by results from PCR as lacking trisomies in either chromosome 18 or 21 were labeled "non-trisomy". If a trisomy was otherwise present and detected by PCR, subjects were labeled "trisomy 18" or "trisomy 21". These classifications were then matched against the results of CGH. Biological replicates: 9 "non-trisomy" embryos, 5 "trisomy 18" embryos and 7 "trisomy 21" embryos.

Please note that the row counts for the raw data files vary from 2,101 to 2,878. Even with the standard protocol according Illumina's 24sure instructions for the microarrays, each run generates a set of analyzed probes that varies from sample to sample. However all the different combinations represent a uniform sampling of the genome.

first: Elizabeth

last: Schaeffer

first: Bruno

last: López Bayghen

first: Adina

last: Neumann

first: Azucena

last: Ocampo


title: Loss of miR-16 mediated silencing of SQSTM1 is associated with Paget's associated osteosarcoma

first: Irina

last: Mohorianu

summary: We report an upregulation of miR-16 in Paget's disease of bone which is to target the SQSTM1. When miR-16 is lost in Paget's disease, there is malignant transformation.

overall_design: Paget's bone tissue was obtained from the NRP biorepository. We then performed small RNA sequencing using HD adapters.

first: Darrell

last: Green


title: Transcriptome profiling of drug resistant cell lines (SKOV3).

summary: The aim of this research was to uncover transcriptome changes in SKOV3 cells during the acquisition of resistance to anticancer drugs Sorafenib, Sunitinib, Pazopanib, Everolimus, Temsirolimus.

overall_design: SKOV3 cells resistant to five target anticancer drugs were generated by growing naive cells serially treated with an increasing doses of Sunitinib up to 6 µM, Pazopanib up to 25 µM, Sorafenib up to 10 µM, Everolimus up to 20 µM and Temsirolimus up to 15 µM. Transcriptome analisys was made at the following time points: 4, 8, 12 and 16 weeks. Simultaneously untreated control sells were grown for the same period, transcriptome analisys was performed at 8, 10,12, 14 and 16 weeks.


title: Differential gene expression in Jagged1 treated human dental pulp cells.

status: Public on Apr 04 2017

city: Pathumwan

first: Thanaphum

last: Osathanon

state: Bangkok

address: 34 Henri-dunant Rd. Wongmai

country: Thailand

institute: Chulalongkorn University

summary: The present study aimed to determine mRNA expression profilling of indirect immobilized Jagged1 treated human dental pulp cells. Human dental pulp cells were seeded on indirect immobilized Jagged1 surface for 24 h. Cells on hFc immobilized surface was employed as the control. RNA sequencing was performed using NextSeq500, Illumina. Data were processed on FastQC and FastQ Toolkit and subsequently mapped with Homo sapiens hg38 using TopHat2. Mapped data were processed through Cufflink2 and Cuffdiff2. Results demonstrated 1,465 differentially expressed genes in Jagged1 treated cells compared with the control. Enriched pathway analysis revealed that Jagged1 treated cells upregulated genes mainly involved in extracellular matrix organization, disease, and signal transduction categories. However, genes related to cell cycle, DNA replication and DNA repair categories were downregulated. In conclusion, Jagged1 activates Notch signaling and regulates cell cycle pathway in hDPs.

overall_design: The mRNA profiles of human dental pulp cells treated with indirect immobilized Jagged1 (10nM) for 24 h was evaluated by next genereation RNA sequencing (NextSeq 500, Illumina) in triplicates. Cells on hFc immobilized surface was used as the control. In some condition, cells were pretreated with a gamma secretase inhibitor (DAPT; 20 uM) for 30 mins prior to Jagged1 exposure.

first: Jeeranan

last: Manokawinchoke

first: Praphawi

last: Nattasit

first: Tanutchaporn

last: Thongngam

first: Prasit

last: Pavasant

first: Kevin

last: Tompkins

first: Hiroshi

last: Egusa


title: Detection of Y chromosome

status: Public on Apr 05 2017

summary: PCR based detection of Y-chromosome compared against results obtained by CGH microarrrays in Preimplantation Genetic Screening

overall_design:
Two-condition experiment: subjects classified by PCR results as male (y-chromosome present) or female (y-chromosome absent). Biological replicates: 10 male, 11 female.

Please note that the row counts for the raw data files vary from 1,755 to 2,888. Even with the standard protocol according Illumina's 24sure instructions for the microarrays, each run generates a set of analyzed probes that varies from sample to sample. However all the different combinations represent a uniform sampling of the genome.

last: Lopez Bayghen


title: Ion Channel Expression Patterns in Glioblastoma Stem Cells with Functional and Therapeutic Implications for Malignancy

status: Public on Apr 21 2017

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: Ion channels and transporters have increasingly recognized roles in cancer progression through the regulation of cell proliferation, migration, and death. Glioblastoma stem-like cells (GSCs) are a source of tumor formation and recurrence in glioblastoma multiforme, a highly aggressive brain cancer, suggesting that ion channel expression may be perturbed in this population. However, little is known about the expression and functional relevance of ion channels that may contribute to GSC malignancy. Using RNA sequencing, we assessed the enrichment of ion channels in GSC isolates and non-tumor neural cell types. We identified a unique set of GSC-enriched ion channels using differential expression analysis that stratify by molecular subtype and are associated with distinct gene mutation signatures. In support of potential clinical relevance, expression of selected GSC-enriched ion channels evaluated in human glioblastoma databases of The Cancer Genome Atlas and Ivy Glioblastoma Atlas Project correlated with patient survival times. Finally, genetic knockdown or pharmacological inhibition of individual or classes of GSC-enriched ion channels constrained growth of GSCs compared to normal neural stem cells. This first-in-kind global examination characterizes ion channels enriched in GSCs and explores their potential clinical relevance to glioblastoma molecular subtypes, gene mutations, survival outcomes, regional tumor expression, and experimental responses to loss-of-function. Together, the data support the potential biological and therapeutic impact of ion channels on GSC malignancy and provide strong rationale for further examination of their mechanistic and therapeutic importance.

overall_design: Ion channel expression in glioblastoma stem cells

first: Julia

last: Pollak

first: Karan

last: Rai

first: Cory

last: Funk

first: Eunjee

last: Lee

first: Jun

last: Zhu

first: Nathan

middle: D

last: Price

first: Patrick

last: Paddison

first: Jan

last: Ramirez

first: Robert

last: Rostomily


title: Transcriptomic differences in bovine blastocysts following vitrification and slow freezing at morula stage [EmbryoCryoSF]

status: Public on Mar 31 2017

city: Saskatoon

first: Fernanda

last: Dias

address: 52 Campus Dr

institute: University of Saskatchewan

summary: This study aimed to compare the transcriptome of vitrified and slow frozen embryos with the untreated control. Bovine embryos (compact morulae) were vitrified or slow frozen and post-warm embryos were cultured to expanded blastocyst stage. The vitrified- and slow frozen-derived were subjected to microarray analysis and compared with untreated control embryos for differential gene expression. Morula to blastocyst conversion rate was higher (P<0.05) in control (72%) and vitrified (77%) embryos compared to slow frozen (34%) embryos. Total 20 genes were upregulated and 44 genes were downregulated in the vitrified embryos (fold change ≥ +-2, P<0.05). In slow frozen embryos, 102 genes were upregulated and 63 genes were downregulated (fold change ≥ +-1.5, P<0.05) in comparison with untreated embryos. Vitrified embryos exhibited significant changes in gene expression mainly involving embryo implantation (PTGS2, CALB1), lipid peroxidation and ROS generation (HSD3B1, AKR1B1, APOA1) and cell differentiation (KRT19, CLDN23). The slow frozen embryos, however, showed significant changes in the expression of genes related to cell signaling (SPP1), cell structure and differentiation (DCLK2, JAM2 and VIM), and lipid metabolism (PLA2R1 and SMPD3). In silico comparison between vitrified and slow-frozen (reference) embryos revealed similar changes in gene expression as between vitrified and untreated embryos. In conclusion, the vitrified bovine embryos demonstrated better post-warming embryo development than slow-frozen bovine embryos but their gene expression related to lipid metabolism, steroidogenesis, cell differentiation and placentation changed significantly. Slow freezing killed more embryos than vitrification, and the survived embryos did not express significant change in their gene expression.

overall_design: Slow freezen embryos intensities compared with fresh bovine embryos (control)

first: Alisha

last: Gupta

first: Jaswant

last: Singh

first: Isabelle

last: Dufort

first: Claude

last: Robert

first: Muhammad

last: Anzar


title: Gene expression from armored CAR T cell

status: Public on Apr 03 2017

city: NEW YORK

first: Mauro

middle: Pellegrino

last: Avanzi

address: 427 east 73rd street apt 5B

summary: Compare the gene expression profile among armored IL-18 secreting CAR T cells and second-generation CAR T cells

overall_design: CAR T cells were cocultured with NALM6 tumor cells, sorted on day 1 and day 8, RNA extracted and gene expression was analyzed with Nanostring

first: M

middle: P

first: R

last: Brentjens


title: Transcriptomic differences in bovine blastocysts following vitrification and slow freezing at morula stage

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


title: RNA-seq of mouse cultured retinal pigment epithelium (RPE) challenged with photoreceptor outer segments (POS).

city: Cleveland

first: Aleksander

last: Tworak

state: Ohio

address: 2109 Adelbert Rd

department: SOM Pharmacology

institute: Case Western Reserve University

summary: Primary culture of mouse RPE cells (C57BL/6J background) was challenged with POS for 90 min and subjected for RNA-seq.

overall_design: Cells treated with POS (Trt) compared with untreated culture (Veh).

first: Brian

last: Kevany

first: Krzysztof

last: Palczewski


title: Broadly protective monoclonal antibodies against influenza B virus target highly conserved neuraminidase epitopes

city: Cambridge

first: Benjamin

middle: Robert

last: tenOever

address: 7 Divinity Avenue

institute: Harvard University

summary: Purpose: To identify viral escape mutants to NA antibodies

sample_organism: Influenza B virus (B/Malaysia/2506/2004)

overall_design: Amplify virus in the present of antibody

middle: R


title: Transcriptomic differences in bovine blastocysts following vitrification and slow freezing at morula stage [EmbryocryovitSF]

overall_design: Vitrification intensities compared with Slow freezing of bovine embryos

middle: C


title: Identification of a Cell-of-Origin for Fibroblasts Comprising the Fibrotic Reticulum in Idiopathic Pulmonary Fibrosis

status: Public on Mar 27 2017

city: Minneapolis

first: Ying

last: Zhang

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: Idiopathic pulmonary fibrosis (IPF) is a progressive disease of the middle aged and elderly with a prevalence of one million persons worldwide. The fibrosis spreads from affected alveoli into contiguous alveoli, creating a reticular network that leads to death by asphyxiation. Lung fibroblasts from patients with IPF have phenotypic hallmarks, distinguishing them from their normal counterparts: pathologically activated Akt signaling axis, increased collagen and a-smooth muscle actin expression, distinct gene expression profile, and ability to form fibrotic lesions in model organisms. Despite the centrality of these fibroblasts in disease pathogenesis, their origin remains uncertain. Here, we report the identification of cells in the lungs of patients with IPF with the properties of mesenchymal progenitors. In contrast to progenitors isolated from nonfibrotic lungs, IPF mesenchymal progenitor cells produce daughter cells manifesting the full spectrum of IPF hallmarks, including the ability to form fibrotic lesions in zebrafish embryos and mouse lungs, and a transcriptional profile reflecting these properties. Morphological analysis of IPF lung tissue revealed that mesenchymal progenitor cells and cells with the characteristics of their progeny comprised the fibrotic reticulum. These data establish that the lungs of patients with IPF contain pathological mesenchymal progenitor cells that are cells of origin for fibrosis-mediating fibroblasts. These fibrogenic mesenchymal progenitors and their progeny represent an unexplored target for novel therapies to interdict fibrosis.

overall_design: RNA-seq of lung fibroblasts from IPF or healthy control patients at day 0 or day 21 of culture.

first: Hong

last: Xia

first: Vidya

last: Bodempudi

first: Alexey

last: Benyumov

first: Polla

last: Hergert

first: Damien

last: Tank

first: Jeremy

last: Herrera

first: Jeff

last: Braziunas

first: Ola

last: Larsson

first: Matthew

last: Parker

first: Daniel

last: Rossi

first: Karen

last: Smith

first: Mark

last: Peterson

first: Andrew

last: Limper

first: Jose

last: Jessurun

first: John

last: Connett

first: David

last: Ingbar

first: Sem

last: Phan

first: Peter

middle: B

last: Bitterman

first: Craig

last: Henke


title: B cells expressing the IgA receptor FcRL4 participate in the autoimmune response in patients with rheumatoid arthritis

city: Stockholm

last: Ramsköld

address: Nobels väg 3

country: Sweden

institute: Karolinska Institutet

summary: The clinical efficacy of B cell targeting therapies highlights the pathogenic potential of B cells in inflammatory diseases. Expression of Fc Receptor like 4 (FcRL4) identifies a memory B cell subset, which is enriched in the joints of patients with rheumatoid arthritis (RA) and in mucosa-associated lymphoid tissue. The high level of RANKL production by this B cell subset indicates a unique pathogenic role. In addition, recent work has identified a role for FcRL4 as an IgA receptor, suggesting a potential function in mucosal immunity. Here, the contribution of FcRL4+ B cells to the specific autoimmune response in the joint of patients with RA was investigated. Single FcRL4+ and FcRL4- B cells were sorted from synovial fluid and tissue from RA patients and their immunoglobulin genes characterized. Levels of hypermutation in the variable regions in both populations were largely consistent with memory B cells selected by an antigen- and T cell-dependent process. Recombinant antibodies were generated based on Ig variable region sequences and investigated for antigen specificity. A significantly larger proportion of the recombinant antibodies generated from the IgH and IgL variable regions of individual synovial FcRL4+ B cells showed reactivity towards citrullinated autoantigens. Furthermore, both in analyses based on heavy chain sequences and flow cytometric detection, these cells have significantly increased usage of the IgA isotype. Their low level of expression of immunoglobulin and plasma cell differentiation genes does not suggest current antibody secretion. We conclude that these activated B cells are a component of the local autoimmune response, and through their RANKL expression, can contribute to joint destruction. Furthermore, their expression of FcRL4 and their enrichment in the IgA isotype points towards a potential role in the link between mucosal and joint inflammation for these cells.

overall_design: B cells were sorted from synovial fluid of 4 individuals with rheumatoid arthritis into FcRL4 positive and negative fractions, and RNA-seq was performed.

first: Elizabeth

last: Clay

first: Vivianne

last: Malmström

first: Dagmar

last: Scheel-Toellner


title: Circularized RNA sequencing of wild-type and Mrpp3 knock out mouse heart mitochondria

status: Public on Mar 23 2017

city: Perth

first: Stefan

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

summary: Here we find that circularization of RNA prior to deep sequencing enables the discovery and characterization of unprocessed mitochondrial RNAs. Using this approach we identify the most stable processing intermediates and the presence of intermediate processing products that are partially degraded and polyadenylated. Analysis of libraries constructed using RNA from mice lacking the nuclease subunit of the mitochondrial RNase P reveals the identities of stalled processing intermediates, their order of cleavage, and confirms the importance of RNase P (MRPP3) in generating mature mitochondrial RNAs. Using RNA circularization prior to library preparation should provide a generally useful approach to studying RNA processing in many different biological systems.

overall_design: RNA from purified mouse mitochondria from wild-type and Mrpp3 knock out mouse hearts was circularized and the resulting libraries were sequenced usingan Illumina MiSeq.

first: Irina

last: Kuznetsova

first: Aleksandra

last: Filipovska

first: Oliver

last: Rackham


title: Constitutive Activation of HH-GLI Signaling in the Metanephric Mesenchyme causes Ureteropelvic Junction Obstruction during Mammalian Embryogenesis

status: Public on Mar 29 2017

city: Cincinnati

last: Potter

state: OH

address: 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

summary: This study explores the underlying pathogenic mechanisms of congenital intrinsic obstruction of the ureteropelvic junction. A hedgehog-dependent mechanism underlying mammalin intrinsic ureteropelvic obstruction is defined.

overall_design: Tissue was microdissected from the kidney-ureter junction at E13.5, one day after the onset of Ptc2-lacZ expression, from PTC-/-MM mice; 2 PTC2+ and 2 PTC2- cell populations were isolated using antibodies specific for PTC2 and FACS sorting.

first: S

last: Sheybani-Deloui

first: L

last: Chi

first: M

last: Staite

first: J

last: Cain

first: B

last: Nieman

first: R

last: Henkelman

last: Wainright

middle: S

first: D

last: Bagli

first: A

last: Lorenzo

first: N

last: Rosenblum


title: Small RNA sequencing of wild-type and Mrpp3 knock out mouse heart mitochondria

middle: J

summary: Small RNA sequencing was used to examine RNA degradation products in mitochondria from mice lacking the nuclease subunit of the mitochondrial RNase P (MRPP3).

overall_design: RNA from purified mouse mitochondria from wild-type and Mrpp3 knock out mouse hearts was sequenced using Illumina TruSeq Small RNA Library methods.


title: Transcriptomic insights into human decidual and peripheral blood CD4 T cells

city: shanghai

first: wang

last: yujie

state: Shanghai

address: Chi Feng road No:65

institute: Shanghai JiaYin Biological technology co., LTD

summary: We performed the analysis of transcriptional and alternative splicing landscapes for paired decidual and peripheral blood CD4 T cells during human pregnancy by high-throughput mRNA sequencing.

overall_design: Healthy women during early pregnancy were recruited, and FACS was performed to isolate and purify the CD4+ T cells from the decidua and peripheral blood. We sequenced the RNA samples on an Illumina HiSeq 2500 platform.

first: Weihong

last: Zeng

first: Yi

last: Lin


title: Osteogenic programming of adipose-derived mesenchymal stem cells using a fungal metabolite that suppresses the Polycomb protein EZH2

status: Public on Mar 21 2017

city: Seattle

first: Pritha

last: Chanana

address: 1100 Fairview Ave N, PO Box 19024

department: Shared Resources

institute: Fred Hutchinson Cancer Center

summary: We report genome-wide expression changes that occur in adipose-derived mesenchymal stem cells upon treatment with CytoD cytoskeletal drug. mRNA-Seq analysis shows that CytoD-treated samples cluster together. In addition, we also see that cells treated with CytoD show upregulation of osteogenic markers, epiregulators, and a number of key molecular function pathways including extracellular matrix, cell membrane gene expression.

overall_design: Adipose MSCs were cultured in Advanced-MEM base (Life Technologies), 5% platelet lysate, and 1% non-essential amino acids (Life Technologies), and 2U/ml heparin. Cells used for experiments were of passage 6. Adipose MSCs were seeded at 3,000 cells per cm2 in maintenance medium in 6-well plates and incubated under standard culture conditions for 24 hours before being changed to osteogenic medium containing vehicle (DMSO) or 0.1 µg/ml cytochalasin D (Sigma). Osteogenic medium maintenance media supplemented with 10 nM dexamethasone, 25 µg/ml ascorbic acid, and 10 mM β-glycerophosphate. Cells in culture were prepared for RNA isolation by lysing with Qiazol. Purified RNA was then submitted for RNA-sequencing.

first: Andre

last: van Wijnen

first: Rebekah

last: Samsonraj


title: Transcriptomic differences in bovine blastocysts following vitrification and slow freezing at morula stage [EmbryocryoVit]

first: Fernanda

last: Dias

overall_design: Vitrified embryos intensities compared with fresh bovine embryos (control)

first: Alisha

last: Gupta

first: Jaswant

last: Singh

first: Isabelle

last: Dufort

first: Claude

last: Robert

first: Muhammad

last: Anzar


title: Transcriptomic responses in the spider mite Tetranychus urticae to bacterial infection

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

summary:
Genome annotation of the chelicerate Tetranychus urticae revealed the absence of many canonical immunity genes.
T. urticae either does not mount an immune response or it induces uncharacterized immune pathways.
To disentangle these two hypotheses, we performed transcriptomic analysis of mites injected with bacteria vs mites injected with LB-buffer.
Two types of bacteria were injected: E. coli and B. megaterium and transcriptomes were sampled 3, 6 and 12 hrs after injection.
We found no consistent differential expression after bacterial infection, supporting the hypothesis that spider mites do not mount an immune response.
We hypothesize that the apparent absence of inducable immunity pathways in T. urticae is a result of relaxed selective pressure due to ecological factors.

overall_design:
Six major comparisons were made, having 4 replicates each.
Each replicate consisted of 300 injected mites.
After 3, 6 and 12 hours of injection, bacteria-injected mites (cy5-labelled) were directly compared to LB buffer-injected mites (cy3-labelled). Samples of non-injected mites are also included.

first: Gonçalo

last: Matos

first: Nelson

last: Martins

first: Thomas

middle: V

last: Leeuwen

first: Sara

last: Magalhães

first: Élio

last: Sucena


title: Association between DNA methylation profiles in leukocytes and serum levels of persistent organic pollutants in Dutch men

status: Public on Mar 06 2017

city: Wageningen

first: Myrthe

last: van den Dungen

address: Tuinlaan 5

country: Netherlands

institute: Wageningen University

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling was performed in Dutch men consuming eel from relatively low- or high-polluted areas, resulting in a broad range of serum POP levels. The Illumina Infinium 450K Human DNA methylation Beadchip v1.0HD was used to measure DNA methylation in these men and associate this with serum levels of persistent organic pollutants (POPs). In total 48 POPs were measured, of which 30 POPs had levels above the detection limit in at least 60% of the participants. Furthermore, 11 different clinical parameters were measured as biomarkers for health. The leukocyte count was measured in each sample to adjust DNA methylation values. Furthermore, participants reported possible confounders in a questionnaire.

overall_design: Bisulfite converted DNA from 34 men (40-70 years old) was hybridized to the Illumina Infinium 450K Human Methylation Beadchip. DNA methylation was analyzed using linear regression against serum levels of dioxins and dioxin-like compounds, sum of seven indicator PCBs, and PFOS.

last: Van den Dungen

first: Albertinka

last: Murk

first: Ellen

last: Kampman

first: Wilma

middle: T

last: Steegenga

first: Dieuwertje

middle: E

last: Kok


title: A novel role for SALL4 during scar-free wound healing in axolotl

status: Public on Mar 07 2017

city: Woods hole

first: Karen

last: Echeverri

address: 7 MBL ST

department: Eugene Bell Center for Regeneration Biology and Tissue Engineering

institute: MARINE BIOLOGICAL LAB

summary: Salamanders, such as the Mexican axolotl, are some of the few vertebrates fortunate in their ability to regenerate diverse structures after injury. Unlike mammals they are able to regenerate a fully functional spinal cord after injury. Throughout human life, many cells and certain tissues, such as hair follicle stem cells and liver, can be continuously replaced to maintain functional integrity in response to normal daily wear and tear. However, the human response to more serious tissue damage is limited to relatively primitive wound healing, whereby collagenous scar tissue fills the injury site, assuring the tissue’s structural integrity but often resulting in a debilitating loss of functionality. In contrast many vertebrates, including axolotls, have remarkable regenerative capacity including the functional regeneration of full thickness wounds. Here, we have identified a novel role for SALL4 in regulating collagen transcriptional after injury that is essential to ensure perfect skin regeneration in axolotl.

overall_design: All axolotls used in these experiments were bred in the axolotl facility at the University of Minnesota under the IACUC protocol1411-32049A. Adult axolotls and larval axolotls of 2–3 cm were used for all in vivo experiments, and animals were kept in separate containers and fed daily with artemia; water was changed daily. Animals were anesthetized in 0.01% p-amino benzocaine (Sigma) before microinjection was performed.      Experimental Design: Ivermectin injection  Ivermectin or vehicle only (water) was pressure injected into the central canal of the spinal cord, and this was visualized by the addition of Fast Green into the solution. Directly after injection, a portion of the spinal cord was surgically removed and the animals were placed back into water in individual containers. One day post injury (1dpi) animals were anesthetized again and the area of the injury was removed. Tissue from 10 animals were pooled for each microarray replicate.

first: Jami

last: Erickson

first: Micah

last: Gearhard

first: Drew

last: Honson

first: Branden

last: Moriarity


title: Epigenetic Reprogramming of Androgen Receptor by Histone H4 Tyr88-phosphorylation Promotes Castration Resistance

status: Public on Mar 01 2017

city: Ann Arbor

first: Rohit

last: Malik

state: MI

address: 1400 E Medical Center Dr.

department: Pathology

institute: University of Michigan

summary: Androgen receptor (AR) is critical for the progression of prostate cancer to the castration resistant (CRPC) state. Despite initial response, AR antagonists are ineffective long term in stifling AR activity due to their inability to repress expression of the AR or its splice variant, AR-V7. Here, we report that ACK1 tyrosine kinase, frequently deregulated in CRPCs, phosphorylates histone H4 at tyrosine 88, upstream of the AR transcription start site. WDR5/MLL2 complex reads the H4Y88 marks and modifies H3 in trans to deposit the transcriptionally activating H3K4 trimethyl marks, promoting AR transcription. Reversal of the pY88-H4 epigenetic marks by ACK1 small molecule inhibitor, (R)-9bMS, sensitized naïve and enzalutamide-resistant cancer cells, repressed AR and AR-V7 levels to mitigate in vivo CRPC tumor growth. Thus, a feed-forward ACK1-H4-WDR5/MLL2-AR/AR-V7 epigenetic circuit drives CRPC and is necessary for maintenance of the malignant state.

overall_design: Two-condition experiment, DMSO versus inhibitor treated cells. 5 prostate cancer cell lines, LNCaP-C4-2B, VCaP, LAPC4, PC3 and DU145. Cells were treated with 3.5 uM of inhibitor for 24 hours.

first: Nupam

last: Mahajan

first: Kiran

first: Chandan

middle: K

last: Sinha

first: Sudhanshu

last: Shukla


title: Effects of Belinostat and Dexamethasone treatment of A549 gene expression

status: Public on Mar 16 2017

first: Steven

last: Timmermans

address: Technologiepark 71

institute: VIB-UGent

summary: Glucocorticoid resistance (GCR), i.e. unresponsiveness to the beneficial anti-inflammatory activities of the glucocorticoid receptor (GR), poses a serious problem in the treatment of inflammatory diseases. One possible solution to try and overcome GCR, is to identify molecules that prevent or revert GCR by hyper-stimulating the biological activity of the GR. To this purpose, we screened for compounds that potentiate the dexamethasone (Dex)-induced transcriptional activity of GR. To monitor GR transcriptional activity, the screen was performed using the lung epithelial cell line A549 in which a glucocorticoid responsive element (GRE) coupled to a luciferase reporter gene construct was stably integrated. Histone deacetylase inhibitors (HDACi) such as Vorinostat and Belinostat are two broad-spectrum HDACi that strongly increased the Dex-induced luciferase expression in our screening system. In sharp contrast herewith, results from a genome-wide transcriptome analysis of Dex-induced transcripts using RNAseq, revealed that Belinostat impairs the ability of GR to transactivate target genes. The stimulatory effect of Belinostat in the luciferase screen further depends on the nature of the reporter construct. In conclusion, a profound discrepancy was observed between HDACi effects on two different synthetic promoter-luciferase reporter systems. The favorable effect of HDACi on gene expression should be evaluated with care, when considering them as potential therapeutic agents.

overall_design: 12 samples total, 4 conditions with 3 biological replicates each

last: Dendoncker

first: Kelly

last: Van Looveren

first: Lode

last: De Cauwer

first: Karolien

last: De Bosscher

first: Claude

last: Libert


title: Data Exploration, Quality Control and Statistical Analysis of ChIP-exo/nexus Experiments

city: Madison

first: Rene

last: Welch

state: Wisconsin

address: 626 Johnson St.

department: Statistics

institute: University of Wisconsin-Madison

summary: ChIP-exo/nexus experiments present modifications on the commonly used ChIP-seq protocol for high resolution mapping of transcription factor binding sites. Although many aspects of the ChIP-exo data analysis are similar to those of ChIP-seq, these high throughput experiments pose a number of unique quality control and analysis challenges. We develop a statistical quality control pipeline and accompanying R package, ChIPexoQual, to enable exploration and analysis of ChIP-exo and related experiments. ChIPexoQual evaluates a number of key issues including strand imbalance, library complexity, and signal enrichment of data. Assessment of these features are facilitated through diagnostic plots and summary statistics calculated over regions of the genome with varying levels of coverage.  We evaluated our QC pipeline with both large collections of public ChIP-exo/nexus data and multiple, new ChIP-exo datasets from E. coli. ChIPexoQual analysis of these datasets resulted in guidelines for using these QC metrics across a wide range of sequencing depths and provided further insights for modelling ChIP-exo data. Finally, although ChIP-exo experiments have been compared to ChIP-seq experiments with single-end (SE) sequencing, we provide, for the first time, comparisons with paired-end (PE) ChIP-seq experiments. We illustrate that, at fixed sequencing depths, ChIP-exo provides higher sensitivity, specificity, and spatial resolution than PE ChIP-seq and both significantly outperform their SE ChIP-seq counterpart.

overall_design: Examination of sig70 factor in E. coli: 2 growth conditions, under two treatmnent and two replicates each.

first: Robert

last: Landick

first: Jeffrey

last: Grass

first: Keles

last: Sunduz

first: Welch

last: Rene

first: Chung

last: Dongjun


title: Streptococcus mutans differential gene expression in response to simulated microgravity

city: Gainesville

last: Rice

address: 1355 Museum Dr

department: Microbiology and Cell Science

institute: University of Florida

summary: Astronauts have been previously shown to exhibit decreased salivary lysozyme and increased dental calculus and gingival inflammation in response to space flight, host factors that could contribute to oral diseases such as caries and periodontitis. However, the specific physiological response of caries-causing bacteria such as Streptococcus mutans to space flight and/or ground-based simulated microgravity has not been extensively investigated. In this study, High Aspect Ratio Vessel (HARV) S. mutans simulated microgravity and normal gravity cultures were assessed for changes in metabolite and transcriptome profiles, H2O2 resistance, and competence in sucrose-containing biofilm media. Stationary phase S. mutans simulated microgravity cultures displayed increased killing by H2O2 compared to normal gravity control cultures, but competence was not affected. RNA-seq analysis revealed that expression of 153 genes was up-regulated ≥ 2-fold and 94 genes down-regulated ≥ 2-fold during simulated microgravity HARV growth. These included a number of genes located on extrachromosomal elements, as well as genes involved in carbohydrate metabolism, translation, and stress responses. Collectively, these results suggest that growth under microgravity analog conditions promotes changes in S. mutans gene expression and physiology that may translate to an altered cariogenic potential of this organism during space flight missions.

overall_design: Differential gene expression was compared between RNA from S. mutans grown in normal gravity HARVs (n=3 independent cultures) and RNA from  S. mutans grown in simulated microgravity HARVs (n=3 independent cultures)


title: Transcriptomic assessment of interactions between doublesex and its target genes across sexes and tissues in horned beetles

status: Public on Feb 28 2017

city: Bloomington

first: Cristina

last: Ledon-Rettig

state: IN

address: 915 E 3rd Street

department: Biology

institute: Indiana University

summary: Purpose: Sexual dimorphisms fuel significant intraspecific variation and evolutionary diversification. Yet the developmental-genetic mechanisms underlying sex-specific development remain poorly understood. We focused on the conserved sex-determination gene doublesex (dsx) and the mechanisms by which it mediates sex-specific development in a species of horned beetle by combining systemic dsx knockdown, high-throughput sequencing of diverse tissues, and a genome-wide analysis of Dsx binding sites. We find that Dsx regulates sex-biased expression predominantly in males, that Dsx's target repertoires are highly sex- and tissue-specific, and that Dsx can exercise its regulatory role via two distinct mechanisms: as a sex-specific modulator by regulating strictly sex-specific targets, or as a switch by regulating the same genes in males and females in opposite directions. More generally, our results suggest Dsx can rapidly acquire new target gene repertoires to accommodate evolutionarily novel traits, evidenced by the large and unique repertoire identified in head horns, a recent morphological innovation.

overall_design: Control and dsxRNAi individuals were collected within the first day after pupation. Six male and six female pupae from each group were sampled tissue for four distinct regions: the supraesophageal ganglion (brain), genitalia, thoracic horns, and head horns.

first: Eduardo

last: Zattara

first: Armin

last: Moczek


title: DNA methylation regulates intron retention via altered MeCP2-mediated splicing factor recruitment

city: Camperdown

first: Dadi

last: Gao

address: RPA, Missenden Road

institute: Centenary Institute

type: Methylation profiling by high throughput sequencing

summary: While intron retention (IR) is now recognized as a widespread and conserved mechanism of gene expression control, its regulation is poorly understood. Here, we identify significantly reduced DNA methylation levels near splice junctions flanking retained introns compared to non-retained introns in diverse primary cells and cell lines. Further, we identify increased IR following inhibition of DNA methylation indicating that reduced DNA methylation promotes IR. We demonstrate reduced occupancy of MeCP2 near the splice junctions of retained introns, mirroring the reduced DNA methylation at these sites. Accordingly, MeCP2 depletion in tissues/cells enhances IR. By analyzing the MeCP2 interactome, we demonstrate that decreased MeCP2 binding near splice junctions facilitates IR via reduced recruitment of the splicing factor, Tra2b, and increased RNA polymerase II stalling. Our study identifies a dynamic interplay between DNA methylation, MeCP2 and splicing factors including Tra2b in IR regulation and provides novel insights into the mechanisms governing splicing.

overall_design: For methylome analysis, genomic DNA was extracted from FACS-purified primary mouse promyelocytes and granulocytes using the Purelink Genomic DNA kit (Thermo Fisher Scientific).  DNA methylation at cytosine residues was assayed using MethylC-seq Whole Genome Bisulfite Sequencing (WGBS) at Macrogen. The DNA was fragmented  to 300–500 bp via sonication using a  Covaris S2 system (Covaris).  End repair was performed with the End-It DNA End-Repair Kit (Epicenter). Paired-end universal library adaptors (Illumina) were ligated to the sonicated DNA according to the manufacturer’s instructions. Ligated products were purified with AMPure XP beads (Beckman, Brea, CA, USA). Adaptor-ligated DNA was bisulfite-treated using the EpiTect Bisulfite Kit (QIAGEN) as per the manufacturer’s instructions. PCR-amplification was performed using PfuTurboCx Hotstart DNA polymerase (Agilent, Santa Clara, CA, USA) with the following PCR conditions (2 min at 95 °C, 4 cycles of 15 s at 98 °C, 30 s at 60 °C, 4 min at 72 °C and then 10 min at 72 °C). The subsequent  products were purified using the MinElute gel purification kit (QIAGEN). Sequencing was performed on an Hi-seq 2000 (Illumina).           For MeCP2 Chip-seq, chromatin immunoprecipitation was performed using the Magna ChIP HiSens kit (Milipore 17-10460) following the manufacturer's instructions. Sample concentration and size distribution of immunoprecipitated DNA were measured with Qubit dsDNA HS Assay Kits (Invitrogen) and High Sensitivity DNA Analysis KIt (Agilent Technologies), respectively. Approximately 20 ng of the input and ChIP DNA samples were sent to Macrogen for ChIP-seq library preparation and sequencing on an Illumina Hiseq2000.

first: Justin

last: Wong

first: Trung

last: Nguyen

first: Chau-To

last: Kwok

first: Michelle

last: van Geldermalsen

first: Rob

last: Middleton

first: Natalia

last: Pinello

first: Annora

last: Thoeng

first: Rajini

last: Nagarajah

first: Jeff

last: Holst

first: William

last: Ritchie

first: John

last: Rasko


title: Histone/protein deacetylase 11 targeting promotes Foxp3+ Treg function

status: Public on Feb 24 2017

city: Philadelphia

first: Wayne

middle: W

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

summary: Current interest in Foxp3+ T-regulatory (Treg) cells as therapeutic targets in transplantation is largely focused on their harvesting pre-transplant, expansion and infusion post-transplantation. An alternate strategy of pharmacologic modulation of Treg function using histone/protein deacetylase inhibitors (HDACi) may allow more titrable and longer-term dosing. However, the effects of broadly acting HDACi vary, such that HDAC isoform-selective targeting is likely required. We report data from mice with constitutive or conditional deletion of HDAC11 within Foxp3+ Treg cells, and their use, along with small molecule HDAC11 inhibitors, in allograft models. Global HDAC11 deletion had no effect on health or development, and compared to WT controls, Foxp3+ Tregs lacking HDAC11 showed increased suppressive function, and increased expression of Foxp3 and TGF-beta. Likewise, compared to WT recipients, conditional deletion of HDAC11 within Tregs led to long-term survival of fully MHC-mismatched cardiac allografts, and prevented development of transplant arteriosclerosis in an MHC class II-mismatched allograft model. The translational significance of HDAC11 targeting was shown by the ability of an HDAC11i to promote long-term allograft allografts in fully MHC-disparate strains. These data are powerful stimuli for the further development and testing of HDAC11-selective pharmacologic inhibitors, and may ultimately provide new therapies for transplantation and autoimmune diseases.

overall_design: RNA from three independent samples of magnetically separated CD4+CD25+ Treg of fl-HDAC11/Foxp3cre mice, compared to wild type (C57BL6) control

first: Jianbing

last: Huang

first: Liqing

last: Wang

first: Rongxiang

last: Han

first: Satinder

last: Dahiya

first: Arabinda

last: Samanta

first: Ulf

middle: H

last: Beier

first: Tricia

last: Bhatti

first: Joel

last: Bergman

first: Alan

last: Kozikowski

first: Edward

last: Seto


title: Chicken Hepatic Response to Chronic Heat Stress Using Integrated Transcriptome and Metabolome Analysis

status: Public on Feb 21 2017

city: Newark

first: Carl

last: Schmidt

state: DE

address: 601 Sincock Ln

institute: University of Delaware

summary: The liver plays a central role in metabolism and is important in maintaining homeostasis throughout the body. This study integrated transcriptomic and metabolomic data to understand how the liver responds under chronic heat stress. Chickens from a rapidly growing broiler line were heat stressed for 8 hours per day for one week and liver samples were collected at 28 days post hatch. Transcriptome analysis reveals changes in genes responsible for cell cycle regulation, DNA replication, and DNA repair along with immune function. Integrating the metabolome and transcriptome data highlighted multiple pathways affected by heat stress including glucose, amino acid, and lipid metabolism along with glutathione production and beta- oxidation.

overall_design: Ross 708 broiler chickens were raised from day of hatch to day 28, on the University of Delaware farm. Birds were placed into two separate houses, one thermoneutral house and one experimental (heat stress) house. Both houses were kept at 23 hours of light and 1 hour of dark and birds were placed on litter and given feed (meeting all NRC requirements) and water with ad libitum access.  Both houses were kept at 35 degrees celsius for the first week and the temperature was decreased 5 degrees celsius each week until 25 degrees celsius. The thermoneutral hosue was maintained at 25 degrees celsius for the remainder of the study. Starting on day 21, the experimental house began a cyclical heat stress scheme with 8 hours per day of increased temperatures (35 - 37 degrees celsius) through completion of the trial at day 28 where necropsies were performed and tissue samples collected.

first: S

last: Jastrebski

first: C


title: TMPRSS2:ERG gene fusion variants induce TGF-β signaling and epithelial to mesenchymal transition in human prostate cancer cells

city: Heidelberg

first: Leonie

last: Ratz

address: Im Neuenheimer Feld 460

department: Cancer Genome Research

institute: DKFZ

summary: TMPRSS2:ERG (T/E) gene fusions are detectable in approximately 50% of all prostate cancer cases and can be considered as biomarkers for molecular subtypes. Several T/E variants have been identified and expression of specific fusion mRNAs was associated with adverse clinicopathologic parameters. However, the underlying molecular processes induced by distinct T/E variants still remain unclear. We therefore aimed to characterize the molecular and cellular profile and specific transcriptional modulation induced by different T/E gene fusion variants.

overall_design: A modified LNCaP cell model was used that stably overexpresses the T/E variants III and VI in a doxycycline-inducible (Tet-On) promoter system. Gene expression was induced with doxycylin for 72h. Expression profiles were compared to induced or uninduced empty vector control. Total RNA was obtained in triplicates for each variant clone and empty vector clone.

first: Mark

last: Laible

first: Lukasz

middle: A

last: Kacprzyk

first: Stephanie

middle: M

last: Wittig-Blaich

first: Yanis

last: Tolstov

first: Stefan

last: Duensing

first: Peter

last: Altevogt

first: Sabine

last: Klauck

first: Holger

last: Sültmann


title: Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton

status: Public on Feb 15 2017

city: Braunschweig

first: Jannik

last: Donner

address: Inhoffenstr. 7

institute: Helmholtz-Center for Infection Research

summary: Carolacton is a novel biofilm inhibitor that kills biofilm cells of Streptococcus mutans and inhibits growth of the clinically relevant and human pathogenic bacterium Streptococcus pneumoniae TIGR4 in nanomolar concentrations. Interestingly, Carolacton also inhibits Escherichia coli with a defective outer membrane protein TolC . The cellular target of Carolacton is still unknown. Here, we adressed the differential transcription of cellular RNAs when E.coli TolC was grown in the presence of Carolacton. This was done to identify transcriptional regulatory networks that are directly affected by treatment of the strain with Carolacton. In order to gain insights into the primary transcriptional response, early time-points were chosen for sampling, which should not reflect secondary responses (e.g. due to differences in growth phase, nutrient depletion etc.).

overall_design: For each of the four examined time-points (0, 5, 15, 30), two biological replicates of Carolacton-treated and untreated samples were collected.

first: Michael

last: Reck


title: Defining stem cell dynamics and migration during wound healing in mouse skin epidermis (D4 post-wound)

city: Bruxelles

first: Cedric

last: Blanpain

address: route de Lennik, 808

institute: Université Libre De Bruxelles

summary: Wound healing is essential to repair the skin after injury. In the epidermis, distinct stem cells (SCs) populations contribute to wound healing. However, how SCs balance proliferation, differentiation and migration to repair a wound remains poorly understood. Here we show the cellular and molecular mechanisms that regulate wound healing in mouse tail epidermis. Using a combination of proliferation kinetics experiments and molecular profiling, we identify the gene signatures associated with proliferation, differentiation and migration in different regions surrounding the wound. Functional experiments show that SC proliferation, migration and differentiation can be uncoupled during wound healing. Lineage tracing and quantitative clonal analysis reveal that, following wounding, progenitors divide more rapidly, but conserve their homeostatic mode of division, leading to their rapid depletion whereas SCs become active, giving rise to new progenitors that expand and repair the wound. These results have important implications for tissue regeneration, acute and chronic wound disorders.

overall_design: To micro dissect the different regions surrounding the wound, at D4 post wound, one punch of 4mm in diameter was done, around the wound 3mm in diameter, to remove the leading edge zone and a punch of 6mm of diameter was used to remove the proliferative hub. Another piece of skin was taken, as control, from a region far from the wounded area. The 4mm punched samples where then FACS sorted for the positive expression of ITGA5, the 6mm punched samples where then FACS sorted for negative expression of ITGA5. The three replicates samples at each time point were a pull of 5 CD1 mice. For each sample, 300 basal cells were FACS sorted and used for RNA extraction and hybridization on Affymetrix microarrays.

first: Mariaceleste

last: Aragona

first: Sophie

last: Dekoninck


title: Defining stem cell dynamics and migration during wound healing in mouse skin epidermis

overall_design: To micro dissect the different regions surrounding the wound, at D4 and D7 post wound, one punch of 4mm in diameter was done, around the wound 3mm in diameter, to remove the leading edge zone and a punch of 6mm of diameter was used to remove the proliferative hub. Another piece of skin was taken, as control, from a region far from the wounded area. The two replicates samples at each time point were a pull of 5 CD1 mice. For each sample, 300 basal cells were FACS sorted and used for RNA extraction and hybridization on Affymetrix microarrays.


title: Species-Specific Developmental Timing is Maintained by Pluripotent Stem Cells Ex Utero

status: Public on Feb 10 2017

first: Christopher

last: Barry

state: WI

address: 330 N. Orchard St.

department: Regenerative Biology

institute: Morgridge Institute for Research

summary: We performed whole transcriptome RNA sequencing experiments on two sets of differentiation time course starting from human ES cells (EGFP-H1) and mouse EGFP-EpiS cells: (1) in vitro neural differentiation, and (2) teratoma formation

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In vitro differentiation time courses were sampled every day for the first 8 days, then every other day over 3 weeks for mouse cells and 6 weeks for human cells (day 28 was missed).  Mouse teratomas were sampled on days 1, 2, 4, 8, 9, 10, 11, 14, 16 ,18, and 21; human teratomas on days 2, 8, 10, 11, 14, 16, 18, 21, 23, 28, 36, and 42

first: Matthew

last: Schmitz

first: Peng

last: Jiang

last: Schwartz

first: Bret

last: Duffin

first: Scott

last: Swanson

first: Rhonda

last: Bacher

first: Jennifer

last: Bolin

first: Angela

middle: L

last: Elwell

first: Brian

last: McIntosh

first: Ron

last: Stewart

first: James

last: Thomson


title: Oncoscan for subclonal analysis in a lobular breast cancer with classical and solid growth pattern mimicking a solid-papillary carcinoma

status: Public on Feb 09 2017

city: Hannover

first: Doris

last: Steinemann

address: Carl-Neuberg-Straße 1

department: Human Genetics

institute: Medizinische Hochschule Hannover

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Affymetrix Oncoscan arrays were performed according to the manufacturer's directions on DNA extracted from FFPE-breast cancer tissues.

overall_design: Copy number analysis using Affymetrix Oncoscan arrays was performed for 3 parts of the tumor

first: Jana

last: van Luttikhuizen

first: Matthias

last: Christgen

first: Hans

last: Kreipe


title: Identification of genes regulated by REST in developing hearts

status: Public on Feb 13 2017

city: Bronx

first: Deyou

last: Zheng

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: Selective suppression of cardiac gene expression by RE-1 silencing transcription factor (REST) in embryonic stage is essential for cardiogenesis and function; however, the underlying mechanism remains unclear. In this study, we show that REST  suppression of cardiac genes during development is temporarily regulated through non-CpG methylation at REST binding sites. Gene expression analyses revealed that the expression of Hcn2 (hyperpolarization-activated cyclic nucleotide-gated ion channel 2), a REST-targeted gene, was developmentally upregulated, while DNMT3B level and REST expression was downregulated. Concurrently, bisulﬁte sequencing and chromatin immunoprecipitation (ChIP) analyses showed that non-CpG methylation of the REST site located in the Hcn2 intron 1 and its co-occupancy by REST and DNMT3B were diminished at E?. Further in vitro inhibition and in vivo myocardial deletion of Rest and Dnmt3b uncovered that non-CpG methylation of the REST site by DNMT3B promoted REST binding to suppress Hcn2 transcription in the embryonic stage. Moreover, using an integrated approach of transcriptomic analysis, ChIP assay, and bisulfate sequencing, we showed that the same mechanism regulated the expression of ~30% REST targeted genes. The expression of these genes was developmentally upregulated as Hcn2. Together, our results suggest that non-CpG methylation at a subset of transcription factor binding sites may regulate cardiac gene program critical for heart development and its dysregulation may contribute to heart disease.

overall_design: we performed RNA-seq analysis of E12.5 wild type (WT) and Rest KO ventricles to identify REST targets. Each group included three biological replicates, by pooling from 4 hearts for each replicate

first: Donghong

last: Zhang

first: Bingruo

last: Wu

first: Ping

last: Wang

first: Yidong

first: Pengfei

last: Lu

first: Tamilla

last: Nechiporuk

first: Thomas

last: Floss

first: Bin

last: Zhou


title: Novel Pathways Revealed in Bursa of Fabricius Transcriptome in Response to Extraintestinal Pathogenic Escherichia coli (ExPEC) Infection

city: Beijing

first: hongyan

last: sun

address: Poultry genetic group, College of Animal Science and Technology, China Agricultural Univeristy, Yuanmingyuan West Rd. No. 2, Haidian District, Beijing, China

institute: Iowa State University

summary:
Purpose: This study is to more comprehensively understand the genome-wide host response to avian pathogen E. coli (APEC).
Methods: Four-week-old male broiler chickens were infected with APEC O1 or given saline as a control. Bursas were collected at 1 and 5 days post-infection (dpi). Infected birds were classified based upon lesions in liver, pericardium and air sacs as having mild or severe pathology, representing resistant and susceptible phenotypes, respectively. Twenty-two individual bursa RNA libraries were sequenced, each yielding an average of 27 million single-end, 100-bp reads.
Results: There were 2469 novel genes in a total of 16,603 detected. Large numbers of significantly differentially expressed (DE) genes were enriched in susceptible versus resistant birds and in susceptible versus non-infected birds at 5 dpi, as well as in 5 dpi versus 1 dpi susceptible birds. The DE genes represented signal transduction, immune response, and cell growth and death pathways.
Conclusions: These data provide considerable insight into potential mechanisms of resistance to ExPEC infection, thus paving the way to develop strategies for ExPEC prevention and treatment, as well as enhancing innate resistance by genetic selection in animals.

overall_design: Bursa mRNA profiles of six treatment groups were generated by deep sequencing, in four replicates, using Illumina HiSeq 2000.

first: Hongyan

last: Sun

first: Susan

last: Lamont


title: The Hippo pathway effector YAP is an essential regulator of submandibular gland ductal progenitor patterning

status: Public on May 24 2017

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: To investigate the roles of YAP in the submandibular gland (SMG) epithelium, we compared the gene expression profiles of E15.5 SMGs isolated from Yap-loxP/loxP or Yap-loxP/loxP;Shh-Cre (i.e. Cre recombinase from the Shh promoter) embryos.

overall_design: We collected RNA from E15.5 SMGs isolated from Yap-loxP/loxP and Yap-loxP/loxP;Shh-Cre litter mate mice. Embryonic SMGs from three separate timed matings were used for this experiment.

first: Xaralabos

last: Varelas

first: Aleksander

last: Szymaniak


title: Potential roles of DNA methylation in the initiation and establishment of replicative senescence revealed by array-based methylome and transcriptome analyses

status: Public on Feb 12 2017

city: Setagaya-ku

first: Mizuho

last: Sakaki

state: Tokyo

department: Maternal-Fetal Biology

country: Japan

institute: National Research Institute for Child Health and Development

summary: Cellular senescence is classified into two groups; replicative and premature senescence. The gene expression and epigenetic changes differ between two groups of senescence, replicative and premature senescence, and cell types.  Normal human diploid fibroblast TIG-3 cells have often been used in cellular senescence research, however, their epigenetic profiles are not fully understood. To elucidate how cellular senescence is epigenetically regulated in TIG-3 cells, we analyzed the gene expression and DNA methylation profiles of three types of senescent cells, namely, replicative senescent, ras-induced senescent (RIS), and non-permissive temperature-induced senescent SVts8 cells, using gene expression and methylation microarrays. The expression of genes involved in the cell cycle and immune response was commonly either down- or up-regulated in the three types of senescent cells, respectively. The sequential alteration of the DNA methylation level in a time-dependent manner was observed in replicatively senescent cells, but not in premature senescent cells. The integrated analysis of gene expression and methylation in replicatively senescent cells demonstrated that the expression of 759 genes involved in the cell cycle and immune response was associated with methylation. Furthermore, hypomethylation occurred in non-CpG island regions (open sea) of the genes exhibiting increased expression as well as non-CpG island promoters of the genes related to the immune response. Several miRNAs regulated through DNA methylation were found to affect the expression of their target genes. Taken together, these results indicate that DNA methylation contributes to the introduction and establishment of replicative senescence partly by regulating gene expression.

overall_design: We examined the gene expression and epigenetic difference following senescence among three different types of senescent cells, replicative senescent, RAS-induced senescent (RIS) and senescent SVts8 cells, derived from Normal human diploid fibroblast TIG-3 cells. Gene expression, miRNA expression and genome-wide DNA methylation profiles were obtained using SurePrint G3 Human GE microarray 8×60K Ver. 2.0 (Agilent), Human miRNA V21.0 microarray (Agilent) and Infinium HumanMethylation27/450 BeadChip (Illumina), respectively.

first: Yukiko

last: Ebihara

first: Kohji

last: Okamura

first: Kazuhiko

last: Nakabayashi

first: Arisa

last: Igarashi

first: Kenji

last: Matsumoto

first: Kenichiro

last: Hata

first: Yoshiro

last: Kobayashi

first: Kayoko

last: Maehara


title: Depot dependent effects of dexamethasone on gene expression in human omental and abdominal subcutaneous adipose tissues from obese women.

summary:
We used microarrays to identify transcripts regulated by dexamethasone in omental (Om) and abdominal subcutaneous (Abdsc) adipose tissues of severely obese females obtained during elective surgeries.
Minced tissue was treated with Dexamethasone in organ culture for 7 days as previously described (Lee et al, Am J Physiol Endocrinol Metab. 2011 Mar;300(3):E571-80).

overall_design: 3 samples of Abdsc cultures and Om from the same individual was cultured in the presence of 0.7 nM insulin plus 0,1,10 or 1000 nM Dexamethasone.  Adipose tissue from subject A was similtaneously cultured with 200 nM cortisol.  Sample A is from one subject, Sample B and C are pooled from two different subjects each.

last: Fried

first: Mi-Jeong

last: Lee

first: Richard

last: Pickering


title: Gene expression profiles of Schistosoma japonicum in four developmental stages

first: Shuai

last: Liu

address: Dong Dan San Tiao 9, Beijing, China

institute: Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: In the complex lifecycle of schistosomes, four developmental stages are closely associated with their definitive hosts: cercaria (infective stage), schistosomula and adult worm (parasitic stages), egg (pathogenic- and pathophoresis-stage). We have examined the gene expression profiles of Schistosoma japonicum in the four developmental stages. Genes with different expression patterns were identified and the information obtained will help indentify new anti-schistosomal intervention targets in the future.

overall_design: Three biological replicates each of  eggs, cercariae, hepatic schistosomula, adult worm pairs, separated adult male and female worms were used. Two technical replicates each of eggs, cercariae, hepatic schistosomula, separated adult male and female worms were also included. A  12 x 135K array was designed and manufactured by NimbleGen for expression analysis.

first: Pengfei

last: Cai

first: Xianyu

last: Piao

last: Hou

first: Qijun

last: Chen


title: Inhibition of BET protein BRD4 activity synergizes with cisplatin in ovarian cancer by targeting ALDH activity through an ALDH1A1 super-enhancer and the associated enhancer RNA

status: Public on Feb 05 2017

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: The emergence of tumor cells with certain stem-like characteristics such as high aldehyde dehydrogenase (ALDH) activity contributes to chemotherapy resistance.  Here we report that inhibition of the BET protein BRD4 potentiates the tumor suppressive effects of cisplatin by targeting ALDH activity.  The clinically applicable small molecule BET inhibitor JQ1 synergized with cisplatin by suppressing the growth of epithelial ovarian cancer cells both in vitro and in vivo.  This correlated with the suppression of ALDH activity and ALDH1A1 gene expression.  BRD4 regulates ALDH1A1 gene transcription through a super-enhancer and expression of its associated enhancer RNA.  Thus, targeting the BET protein BRD4 using clinical applicable small molecule inhibitors such as JQ1 is a promising strategy to enhance cisplatin response.

overall_design: DMSO and JQ1 treated cells were assayed by BRD4 CHIP-seq and RNA-seq

first: Yuhki

last: Yokoyama

first: Rugang

last: Zhang


title: Gene expression data from the sham and irradiated lungs of three murine strains with well-characterized phenotypic variation in pulmonary radiation response.

status: Public on Feb 08 2017

city: Baltimore

first: Yuji

state: MD

address: 660 W. Redwood Street

institute: University of Maryland

summary:
Intrinsic variations in the development of lung injury among patients undergoing radiotherapy for tumors in the thoracic region suggest there are one or more genes that influence the development and severity of radiation pneumonitis and/or fibrosis.
We hypothesized well-characterized murine strain differences in pulmonary response to radiation may offer a novel method to extract the specific genes and/or pathways participating in the development of pneumonitis and/or fibrosis.

overall_design: Gene expression profiling with microarrays was performed on lung tissue harvested 24 h after sham (0 Gy) or single dose (12.5 or 15 Gy) whole thorax lung irradiation from mice with well characterized phenotypes of radiation pneumonitis and/or fibrosis.

first: Isabel

last: Jackson

first: Soren

last: Bentzen

first: Zeljko

last: Vujaskovic


title: Identification of candidate regulators of powdery mildew resistance in cucumber using comparative RNA-sequencing based transcriptome analysis

status: Public on Jan 31 2017

city: Yangzhou

first: Xuewen

last: Xu

state: Jiangsu

address: 48 wenhui east road

institute: Yangzhou University

summary: To investigate the candidate genes governing Pm5.1 and their effects on powdery resistance, the RNA-sequencing based transcriptomes of the powdery mildew resistant segment substitution line SSL508-28 and recurrent parent D8 were compared 48 h after inoculation with the PM pathogen.

overall_design: mRNA levels of the leaves of SSL508-28 and D8 after 48 h of powdery mildew inoculation, along with uninfected control leaves from each, was generated by deep sequencing, in triplicate, using Illumina Hiseq2500

first: Xuehao