title: Developmental pathways pervade stem cell responses to evolving extracellular matrices of 3D bioprinted microenvironments

city: Minneapolis

first: Brenda

last: Ogle

state: MN

address: 312 Church St. SE, 7-130 Nils Hasselmo Hall

department: Department of Biomedical Engineering

institute: University of Minnesota

summary: Developmental studies and 3D in vitro model systems show the production and engagement of extracellular matrix (ECM) often precedes stem cell differentiation.   Yet unclear is how the ECM triggers signaling events in sequence to accommodate multistep processes characteristic of differentiation. Here we employ transcriptome profiling and advanced imaging to delineate the specificity of ECM engagement to particular differentiation pathways and to determine whether specificity in this context is a function of long term ECM remodeling.  To this end, human mesenchymal stem cells (hMSCs) were cultured in 3D bioprinted matrices created from ECM proteins and associated controls.  We found exogenous ECM provided in 3D microenvironments at early time points impacts on the composition of microenvironments at later time points and that each evolving 3D microenvironment is uniquely poised to promote stem cell differentiation. Moreover, 2D cultures undergo minimal ECM remodeling and are ill-equipped to stimulate pathways associated with development.

overall_design: 3D environments composed ofbovine serum albumin, collagen I, fibronectin, and laminin was bioprinted using multiphoton-excited photochemistry. Human mesenchymal stem cell transcriptome modification due to interaction with 3D environments examined via RNA seq.

first: Quyen

last: Tran

first: Visar

last: Ajeti

first: Brian

last: Freeman

first: Paul

last: Campagnola


title: Colon lamina propria myeloid cell subpopulations versus intratumoral counterparts

status: Public on Jan 02 2018

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

type: Expression profiling by high throughput sequencing

summary: Monocytes, neutrophils and tissue resident macropahges of colon lamina propia are compared to their intratumoral counterparts found in colon adenomas

overall_design: Different myeloid subpopulations were isolated from healthy colon lamina propria and colon adenomas, sorted by flow cytometry and processed for RNA.

first: Christiane

last: Ruedl


title: Loss of microRNA-128 promotes cardiomyocyte proliferation and heart regeneration [RNA-seq]

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

country: USA

institute: University of Cincinnati

summary: To identify the potential microRNAs (miRNAs) involved in the regulation of cardiomyocyte (CM) proliferation during homeostasis and injury, RNA sequencing (RNA-seq) in mouse cardiac ventricles was performed on postnatal day 1, 7, and 28 (P1, P7, and P28). Significant upregulation of MiR-128 was found in P7 hearts as compared to P1. To further specify the effect of miR-128 in the heart, RNA-Seq was performed in control mice (Ctrl) and miR-128 overexpression mice (miR-128OE) on P7. These data provide novel insights into the mechanisms by which adult CMs exit the cell cycle arrest and is fundamental for therapeutic manipulation to stimulate endogenous CM proliferate in cardiac regeneration.

overall_design: RNA-seq profilig of heart tissues from wild type mice on postanatal day 1, 7, and 28 (P1, P7, and P28), RNA-seq of hearts from control (Ctrl) and miR-128 overexpression transgenic mice (miR-128OE) at P7.

first: Wei

last: Huang

first: Yuliang

last: Feng

first: Yigang

last: Wang


title: IRF4 modulates CD8 T cell sensitivity to IL-2 family cytokines

status: Public on Jan 01 2018

city: Xiamen

first: Yingjia

last: Shen

state: Fujian

address: A316 Jingquan Building

department: Ecology

country: China

institute: Xiamen University

summary: The purpose of this study is to identify expression differences between wild type CD8 T cells vs IRF4 knock out CD8 T cells.

overall_design: mRNA profiles were examed by Illumina Hiseq 2500 platform. Four samples were sequenced with two samples from wild type CD8 T cells and two samples from IRF4 knock-out CD8 T cells.

first: Jie

last: Sun

first: Guangjun

last: Zhang


title: Concerted metabolic shifts give new insights into the syntrophic mechanism between propionate-fermenting Pelotomaculum thermopropionicum and hydrogenotrophic Methanocella conradii

city: Marburg

first: Pengfei

last: liu

department: Department of Biogeochemistry

country: Germany

institute: Max-Planck-Institute for terrestrial microbiology

summary:
Purpose: To understand the adaptive mechanisms of Methanocellales  to low H2 and syntrophic growth.
Methods: We analyzed the transcriptomes of M. conradii and P. thermopropionicum under monoculture and syntrophic coculture conditions by strand specific mRNA sequencing using Illumina Hiseq 2000. Four biological replicates were sequenced.  The sequence reads that passed quality filters were analyzed by Burrows–Wheeler Aligner (BWA) followed by HTSeq and DESeq2. qRT–PCR validation was performed using SYBR Green assays
Results: The results showed that M. conradii and P. thermopropionicum interacted closely and synchronized their gene transcription during the syntrophic growth. In coculture, M. conradii and P. thermopropionicum significantly enhanced the transcription of genes related to energy conservation processes, including methanogenesis, propionate degradation and electron bifurcation. By contrast, the genes coding for biosynthesis steps were downregulated in both M. conradii and P. thermopropionicum during the syntrophic growth. The physiology experiment showed that formate but not H2 inhibited syntrophic oxidation of propionate. Accordingly, formate dehydrogenase-encoding genes in both M. conradii and P. thermopropionicum were markedly upregulated, indicating that formate plays an important role in the interspecies electron transfer between M. conradii and P. thermopropionicum in coculture.
Conclusions: our study provides abundant transcriptome data indicating the adaptations of Methanocella spp. to H2 limitation and suggests that flavin based electron bifurcations are critical to the syntrophic growth in both M. conradii and P. thermopropionicum.

sample_organism:
Pelotomaculum thermopropionicum
Methanocella conradii

overall_design: M. conradii and P. thermopropionicum under monoculture and syntrophic coculture conditions by strand specific mRNA sequencing using Illumina Hiseq 2000, four biological replicates were sequenced.

last: Liu

first: Yahai

last: Lu


title: The small RNA RyhB is a regulator of cytochrome expression in Shewanella oneidensis

city: Lausanne

first: Karin

middle: Lederballe

last: Meibom

state: Vaud

address: EPFL ENAC IIE EML  CE 1 543 (Centre Est)  Station 6

country: Switzerland

institute: EPFL

summary: Study of the roles played by Fur and RyhB in Shewanella oneidensis

overall_design: Potential RyhB targets were identified by RNAseq of wild-type and mutant strains and a RyhB-overexpressing strain

middle: L

first: Elena

middle: M

last: Cabello

first: Rizlan

last: Bernier-Latmani


title: Identification of PKA-dependent signaling network using CRISPR-Cas9 coupled with quantitative transcriptomics, proteomics and phosphoproteomics

city: Baltimore

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

institute: Johns Hopkins University School of Medicine

summary:
Purpose: PKA plays a crucial role in vasopressin signaling of renal collecting duct cells. To understand regulation of mRNA expression mediated by vasopressin/PKA signaling, mRNA expression was profiled  by RNA-Seq  in double knockout cells (both PKA catalytic genes) generated from mouse cortical collecting duct mpkCCD cell line versus control lines with intact PKA expression.
Methods: PKA double knockout (dKO) cell lines were generated from mouse cortical collecting duct mpkCCDc11 cells by CRISPR/Cas-9 genome editing method. For mRNA profiling using RNA-Seq analysis, three biological replicates of control (not mutated in PKA two catalytic subunits) cell lines and PKA double knockout cell lines were used. The reads uniquely mapped on GENCODE mouse gene set were analyzed with HOMER (v4.8) and edgeR (v3.10.5).
Results and conclusion: About 40-50 million sequence reads per sample were sucessfully mapped in the mouse genome (GENCODE, GPCm38.p5). Among total transcripts of the mouse genome, 10,190 transcripts (cutoff: Counts Per Million > 4 by edgeR) were considered as genes expressed in the cell lines. In differential expression analysis by standard edgeR analysis, 354 transcripts were differentially expressed between control cell lines and PKA dKO cell lines (FDR < 0.05). We also identified nine genes that  were markedly decreased in PKA dKO cell lines (log2 PKA dKO/Control < -2, FDR < 0.05) including aquaporin-2 (Aqp2) and two genes that were markedly increased in PKA dKO cell lines (log2 PKA dKO/Control > 2, FDR < 0.05). These results suggest PKA signaling is important for  regulation of expression of a very limited number of genes in vasopressin-responsive renal collecting duct cells.

overall_design: Total mRNA profiling of three control cell lines and three PKA double knockout cell lines generated from mpkCCDc11 cell line were carried out by standard RNA-Seq protocols with deep sequencing on an Illumina HiSeq 3000.

first: K

last: Isobe

first: H

first: V

last: Raghuram

first: C

last: Yang

first: J'Neka

last: Claxton

first: Pablo

last: Sandoval

first: Mark

middle: A

last: Knepper


title: RNA-seq of Injured Nerve in Schwann cell conditional knockout of Eed

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

summary: The goal of the experiment was to determine the role of the polycomb repressive complex 2 in the nerve injury response in peripheral nerve. A Schwann cell specific knockout of the Eed subunit of PRC2 was generated to compare with wild type mice in sham and injured mice at 1d and 14d timepoints after nerve injury.

overall_design: For each condition, three independent biological replicates were prepared (with the exception of the 14 d Eed ckO sample, which had only two replicates).

first: Ki

last: Ma


title: Gene-Expression Based Measure of Chronic Stress Exposure

city: Stony Brook

first: David

last: McKinnon

state: NY

address: Nichols Rd

department: Neurobiology and Behavior

institute: Stony Brook University

summary: Analysis of mRNA expression in the adrenal glands of rats from two different models of chronic stress: chronic shock (CS) and chronic variable stress (CVS)

overall_design: Analysis of mRNA expression in two different models of chronic stress

first: Barbara

last: Rosati


title: Transient Notch Activation Induces Long-term Gene Expression Changes Leading to Sick Sinus Syndrome in Mice

city: Saint Louis

first: Bo

last: Zhang

state: Missouri

address: 4515 McKinley Research Bldg 03212

department: Developmental Biology

institute: Washington University School of Medicine

summary: We are reporting RNA-seq data from doxycycline induced myocyte specific Notch signaling (iNICD) in adult right atrium compared to littermate controls.

overall_design: RNA was extracted from 6 different righta atrial samples for controls and iNICD

first: Catherine

last: Lipovsky

first: Stacey

last: Rentschler


title: Transcriptome of melanoma cell lines resistant to inhibition of the MAPK pathway.

city: San Francisco

first: Susana

last: Ortiz-Urda

state: CA

address: 2340 Sutter Street, N461

department: Dermatology

institute: University of California, San Francisco

summary: ABSTRACT: Despite major advances in targeted melanoma therapies, drug resistance limits their efficacy. Long noncoding RNAs (lncRNAs) are transcriptome elements that do not encode proteins but are important regulatory molecules. LncRNAs have been implemented in cancer development and response to different therapeutics and are thus potential treatment targets; however, the majority of their functions and molecular interactions remain unexplored. In this study we identify a cytoplasmic intergenic lincRNA (MIRAT), differentially expressed in drug-resistant melanoma samples. MIRAT is upregulated in early drug tolerance to MAPK inhibition and modulates MAPK signaling by binding to the MEK scaffold protein IQGAP1. Collectively, our results present MIRAT’s direct modulatory effect on the MAPK pathway and highlight the relevance of cytoplasmic lncRNA’s as potential targets for drug resistant cancer.

overall_design: RNA-seq data from parental cell lines and their cell clones that are resistant to the MEK inhibitor Trametinib or BRAF inhibitor PLX-4720 (suffix RM; Resistant to MAPK inhibitor)

first: Marin

last: Vujic

first: Martina

last: Sanlorenzo

first: Igor

first: Rosaura

last: Esteve-Puig

first: Kevin

last: Lai


title: Structural basis for DNMT3A-mediated de novo DNA methylation

city: Birmingham

first: Rui

last: Lu

state: AL

address: 1824 6th Ave S

institute: Univ of Alabama at Birmingham

type: Methylation profiling by genome tiling array

type: Methylation profiling by high throughput sequencing

summary: DNA methylation by de novo DNA methyltransferases 3A (DNMT3A) and 3B (DNMT3B) is essential for genome regulation and development. Dysregulation of this process is implicated in various diseases, notably cancer. However, the mechanisms underlying DNMT3 substrate recognition and enzymatic specificity remain elusive. Here we report a 2.65-Å crystal structure of the DNMT3A-DNMT3L-DNA complex where two DNMT3A monomers simultaneously attack two CpG dinucleotides, with the target sites separated by fourteen base pairs within the same DNA duplex. The DNMT3A-DNA interaction involves a target recognition domain (TRD), a catalytic loop and DNMT3A homodimeric interface. A TRD residue Arg836 makes crucial contact with CpG, ensuring DNMT3A enzymatic preference towards CpG sites in cells. Hematological cancer-associated somatic mutations at the substrate-binding sites decrease DNMT3A activity, induce CpG hypomethylation and promote transformation of hematopoietic cells. Together, our study reveals the mechanistic basis for DNMT3A-mediated DNA methylation and establishes its etiologic link to human disease.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Universal alternative splicing of noncoding exons

city: Darlinghurst

first: Ira

middle: William

last: Deveson

state: NSW

address: 384 Victoria St

country: Australia

institute: The Garvan Institute

summary: The human transcriptome is so large, diverse and dynamic that, even after a decade of investigation by RNA sequencing (RNA-Seq), we are yet to resolve its true dimensions. RNA-Seq suffers from an expression-dependent bias that impedes discovery of low-abundance transcripts and has prevented a complete census of gene expression. Here we performed targeted single-molecule and short-read RNA-Seq to survey the transcriptional landscape of a single human chromosome (Hsa21) at unprecedented resolution. Our analysis reaches the lower limits of the transcriptome and identifies a fundamental distinction between the architecture of protein-coding and noncoding gene content. Unlike their coding counterparts, noncoding exons undergo universal alternative splicing to produce a seemingly limitless variety of isoforms. Targeted RNA-Seq analysis of syntenic regions of the mouse genome shows that few noncoding exons are shared between human and mouse. Despite this divergence, human alternative splicing profiles are recapitulated on Hsa21 in mouse cells, indicative of regulation by a local splicing code that is more strongly conserved than the noncoding isoforms themselves. We propose that noncoding exons are functionally modular, with combinatorial alternative splicing generating an enormous repertoire of potential regulatory RNAs and a rich transcriptional reservoir for gene evolution.

overall_design: Duplicate or triplcate tissue samples from adult human, mouse or Tc1 mouse (carries human chromosome 21), anaylsed by RNA CaptureSeq targeted to Chr21 and syntentic regions of the mouse genome

middle: W


title: Structural basis for DNMT3A-mediated de novo DNA methylation (eRRBS)

overall_design: Dnmt1, Dnmt3a and Dnmt3b triple knockout (TKO) mouse embryonic stem cells were stably expressed with wild-type or R836A mutant DNMT3A. Genomic DNA was extracted and analyzed by eRRBS.

first: Gang

middle: G

last: Wang


title: The role of the TGF-β/DBL-1 pathway in shaping the C. elegans gut microbiota

city: Berkeley

first: Maureen

last: Berg

address: 3040 Valley Life Sciences Building # 3140

institute: UC Berkeley

summary: Comparison of gene expression profiles of Caenorhabditis elegans fed a complex microbiota (either a synthetic community or in soil) or a standard Escherichia coli diet. We find that immune and digestion genes are up-regulated in C. elegans that were fed a complex microbiota.

overall_design: C. elegans were fed a complex microbiota (either a synthetic community or in soil) or a standard E. coli diet.

first: Michael

last: Shapira


title: Uhrf1 is indispensable for normal limb growth by regulating chondrocyte differentiation through specific gene expression

city: Shinagawa-ku

first: KATSUHIDE

last: IGARASHI

state: Tokyo

department: Life Science Tokyo Advanced Research center (L-StaR)

country: Japan

institute: Hoshi University School of Pharmacy and Pharmaceutical Science

summary: Transcriptional regulation can be tightly orchestrated by epigenetic regulators. Among these, ubiquitin-like with PHD and RING finger domains 1 (Uhrf1) is reported to have diverse epigenetic functions, including regulation of DNA methylation. However, the physiological functions of Uhrf1 in skeletal tissues remain unclear. Here we show that limb mesenchymal cell-specific Uhrf1 conditional knockout mice (Uhrf1ΔLimb/ΔLimb) exhibit remarkably shortened long bones that have morphological deformities due to dysregulated chondrocyte differentiation as well as proliferation. RNA-seq performed on primary cultured chondrocytes obtained from Uhrf1ΔLimb/ΔLimb mice demonstrates abnormal acceleration of chondrocyte differentiation. In addition, integrative analyses using RNA-seq and MBD-seq reveal that Uhrf1 deficiency cause decreased genome-wide DNA methylation status and reduction in the promoters of specific genes such as Hspb1, which affects chondrocyte differentiation. These results indicate that Uhrf1 governs cell-type specific transcriptional regulation through genome-wide DNA methylation alteration and regulates consequent cell differentiation and skeletal maturation.

overall_design: DNA methylation profiles of primary chondrocytes obtained from Control and cKO mice were analyzed using MBD2 mediated methylated DNA enrichment followed by next generation sequencing (MBD-seq) with Illumina MiSeq.

first: Yuuki

last: Imai

first: Michiko

last: Yamashita

first: Maky

last: Ideta-Otsuka

first: Katsuhide

last: Igarashi


title: Expression profiles of lncRNAs and mRNAs in KGN/shPWRN2 cell lines

city: Shanghai

first: Xin

last: Huang

state: Shanghai

address: No.2699 Gaoke east road

department: Reproductive Medicine Centre

institute: Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: In this study, to identify the target genes of PWRN2, we first constructed lentivirus shRNA vectors to infect the KGN cell lines to gain three KGN/shPWRN2 cell lines with down-regulated PWRN2 expression levels. Then, the expression profiles of mRNAs and lncRNAs in KGN/shPWRN2 cells were determined by microarray. The results revealed thousands of lncRNAs and mRNAs expressed in KGN/shPWRN2. The expression of 176 lncRNAs significantly changed in KGN/shPWRN2 cell lines relative to control NC cell lines. Among these, 118 were up-regulated, whereas 58 were down-regulated. A total of 131 mRNAs significantly changed in expression: 84 were upregulated, and 47 were downregulated (fold change≥2.0, P value<0.05). We further do some bioinformatic analysis for the data. Our results will provide some new information to help us understand the molecular roles of PWRN2.

overall_design: (1) For the lncRNA and mRNA expression profiles in KGN/shPWRN2 cell lines, three KGN cell lines treated with LV-PWRN2-homo-502, LV-PWRN2-homo-1574, LV-PWRN2-homo-1261, respectively,  were as test group, while three KGN cell lines treated with LV-NC were as control group. (2) For microarray analysis, KGN/shPWRN2 with down-regulated (FC< 0.5) PWRN2 mRNA levels was selected as test group (3 KGN/shPWRN2 cell lines) and the corresponding NC cells (3 KGN cell lines with negative control) were as control groups. (3) The GO and KEGG pathways analyses were performed to predict the molecular function of the differentially expressed genes. (4) Combined to our two previously microarray data of PCOS (miRNAs array, lncRNA+mRNA array), we searched the candidate mRNA and miRNAs which related with PWRN2 and construct of PWRN2-mediated lncRNA-mRNA ceRNA network. (5) qRT-PCR validation of components of the PWRN2-mediated lncRNA-mRNA ceRNA network.


title: Gene Network Dysregulation in Dorsolateral Prefrontal Cortex Neurons of Humans with Cocaine Use Disorder

city: New York

first: Efrain

last: Ribeiro

state: New York

address: 1425 Madison Ave, Icahn bldg. Rm 10-24

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: total RNA-sequencing on dlPFC neurons from 19 human cocaine addicts (1-19) and 17 healthy controls (21-40)

overall_design: Total RNA-seq on FACs isolated neuronal nuclei from human post-mortem dorsolateral prefrontal cortex

first: Eric

middle: J

last: Nestler

first: Joseph

middle: S

last: Scarpa

first: Deborah

middle: C

last: Mash


title: Hexavalent chromium disrupts chromatin organization and accessibility to CTCF sites in promoters of differentially expressed genes [ATAC-seq]

first: Mario

last: Medvedovic

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Hexavalent chromium compounds are well-established respiratory carcinogens utilized in industrial processes. While inhalation exposure constitutes an occupational risk affecting mostly chromium workers, environmental exposure from drinking water is a widespread gastrointestinal carcinogen, affecting millions of people throughout the world. Cr(VI) is genotoxic, by forming protein-Cr-DNA adducts and silencing tumor suppressor genes, but its mechanism of action at the molecular level is poorly understood. We have used FAIRE to show that Cr(VI) elicits broad changes in chromatin accessibility resulting from disruption of the binding of transcription factors CTCF and AP-1 to their cognate sites in chromatin.  Here, we have used two complementary approaches to test the hypothesis that chromium perturbs chromatin organization and dynamics. DANPOS2 analyses of MNase.seq data identified several chromatin alterations induced by Cr(VI) affecting nucleosome architecture, including occupancy changes at specific genome locations; position shifts of 10 nucleotides or more; and fuzziness, or changes in signal amplitude. Using ATAC to analyze changes in chromatin accessibility, we found that Cr(VI) opened differentially accessible chromatin domains in a dose-dependent manner. These domains were enriched for the previously identified binding motifs for CTCF and AP-1, many located in promoters of differentially expressed genes. Cr(VI)-enriched CTCF sites were confirmed by ChIP.seq and, when compared with ENCODE-validated CTCF site datasets from mouse liver, correlated with evolutionarily conserved similar sites occupied in vivo. Our results show that Cr(VI) exposure promotes broad changes in chromatin accessibility and suggest that the subsequent dysregulation of transcription may result from the disruption of CTCF binding and nucleosome spacing, suggesting that transcription regulatory mechanisms are primary Cr(VI) targets.

overall_design: Examination of 2 different chromium dosage in mouse models by different sequencing technology (ATAC-seq, ChiP-seq, MNase-Seq)

first: Andrew

last: VonHandorf

first: Francisco

last: Sánchez-Martín

first: Jacek

last: Biesiada

first: Xiang

last: Zhang

first: Alvaro

last: Puga


title: Discovery of Jasmin Virus H

city: Edmonton

first: Juan

last: Jovel

state: Alberta

address: 7-142 KATZ Group Centre for Pharmacy & Health Research

country: Canada

institute: University of Alberta

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNA libraries were constructed from total RNA from Jasminum sambac plants exhibiting virus-like symptoms. After sequencing, small RNAs were assembled into contigs with MetaVelvet and assembled contigs were aligned against the NR database of NCBI using BLASTx. Top hits that reported a virus as subject were considered putative viral sequences. Based on such alignments, the whole genome of a virus, we tentatively name Jasmine Virus H was recovered and cloned. Two more small RNA libraries were made in a confirmatory experiment. One from Jasminum sambac and another one from Nicotiana benthamiana plants infected with the newly-cloned virus. The small RNA libraries were aligned against the full-length sequence of Jasmine Virus H to determine the spacial distribution of virus-derived small RNAs along the virus genome.

overall_design: Symptomatic leaves were collected in the field and used for virus discovery and isolation as described in the summary. Collection was repeated once and the small RNAs libraries repeated. In addition an infectious clone was produced and used to infect Nicotiana benhtamina plants, from which total RNA was extracted and viral small RNAs characterized again. All libraries were sequenced in an Illumina HiSeq 2500 instrument.

first: Yanhong

last: Han


title: Conditional p120ctn deletion in pancreatic ductal cells

city: Worcester

first: Jason

middle: R

last: Pitarresi

state: MA

address: 364 Plantation Street

institute: University of Massachusetts Chan Medical School

summary: These experiments aimed to determine the global gene expression patterns in p120WT, p120HET, and p120NULL cells in the context on oncogenic mutant KrasG12D

overall_design: p120ctn was deleted using in vitro lentiviral Cre recombinase in pancreatic ductal cells isolated from LSL-KrasG12D;Ctnnd1wt/wt (KC-p120ctnWT), LSL-KrasG12D;Ctnnd1fl/wt (KC-p120ctnHET) , and LSL-KrasG12D;Ctnnd1fl/fl (KC-p120ctnNULL) mice.

first: Anil

middle: K

last: Rustgi


title: miRNAseq in sertoli cells infected with ZIKV

summary: Because zika virus is sexually transmitted, with sought to investigate how ZIKV infection affect the transcriptome of sertoli cells, which are nurse cells

overall_design: Sertoli cells were either mock-inoculated or inoculated with Zika virus. Samples were collected at 48 hpi, all samples are in triplicates. RNAseq libraries were constructed according to recommendations of Illumina.


title: Alternative intronic polyadenylation influences cancer metastasis and response to therapy [CLIP-seq]

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

summary: CLIP-seq analysis of TIA1 protein in 4T1 invasive mammary tumor cells

overall_design: Examination of 3 replicates in CLIP-seq analysis

first: Stéphan

last: Vagner

first: Martin

last: Dutertre

first: Galina

last: Boldina

first: Maricarmen

last: Vallejos

first: Mandy

last: Cadix

first: Pierre

last: Gestraud

first: Aurélie

last: Teissandier


title: Nat14 is a novel essential regulator of neurogenesis by regulating cytoskeletal remodeling

city: Mainz

first: Abhijeet

last: Pataskar

address: Ackermannweg 4

institute: Institute of Molecular Biology

summary: Neuronal development involves massive reorganization of cytoskeletal proteins via posttranslational modifications that facilitates morphological remodeling underlying cell-fate changes. Tubulin acetylation has been shown to be essential in several contexts of cellular motility including neuronal migration during cortical development. However, the repertoire of proteins involved in tubulin acetylation remains poorly known. Here, using global gene expression profiles for a range of cell types representing the three embryonic lineages, we identify the acetyltransferase Nat14 as a novel factor specifically induced during cortical development. We find that the loss of Nat14 in neural progenitors blocks neuronal differentiation. Furthermore, such cells retain their progenitor state as reflected by their gene expression signatures and cellular properties. We next show that the cause of these effects are the lack of timely acetylation of tubulin during cortical development with which Nat14 directly physically associates. Cortical cells depleted for Nat14 also fail to migrate towards upper cortical layers that display high levels of acetylated tubulin. In addition, Nat14 was further essential for cellular migration in vitro. Altogether, our study establishes Nat14 as a novel regulator of cortical development by regulating tubulin acetylation dynamics during neurogenesis.

overall_design: Using IUE neuronal progenitors were electroporated at E.14.5 with control shRNA (NTC) or shRNA against Nat14 (shNat14) and embryos were sacrifized at E18.5. GFP positive cells were sorted and subjected to RNA isolation and library preparation and differentially expressed genes were anaylsed.

first: Angela

last: Garding

first: Vilma

last: Rraklli

first: Magdalena

last: Madej

first: Sudhir

last: Thakurela

first: Johan

last: Holmberg

first: Vijay

last: Tiwari


title: Alternative intronic polyadenylation influences cancer metastasis and response to therapy

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


title: Effect of Praziquantel on the Differential Expression of Mouse Hepatic Genes and Parasite ATP Binding Cassette Transporter Gene Family Members During Schistosoma mansoni Infection

city: Albuquerque

first: Charles

last: Cunningham

state: New Mexico

address: 1 University of New Mexico

department: Biology

institute: University of New Mexico

summary: Schistosomiasis is a disease caused by parasitic worms that significantly impacts on the lives of approximately 250 million people. During infection, female parasites release thousands of eggs, a significant number of which become trapped in the liver. The entrapment of the eggs triggers immune and inflammatory responses that in turn cause many of the health problems associated with the disease. In this study we analyzed the gene expression profiles of livers from mice infected with the human parasite Schistosoma mansoni over multiple time points, beginning when the parasites start to lay eggs. Mice were treated with a lethal dose of the anti-schistosomal drug praziquantel, and we identified a number of different genes and pathways that are central to immune and inflammatory responses that are active even in the absence of egg deposition. Praziquantel is the only drug available to treat schistosomiasis, however it is ineffective against juvenile parasites during the early stages of mammalian infection. We also show that the development of drug resistance may be due to the improved efficacy of the juvenile parasite to actively excrete the drug. These results provide insights into the effect of praziquantel on the host response to infection as well as ability of juvenile parasites to overcome the lethal effect of the drug.

overall_design: Liver mRNA profiles of mice 32, 35, 39, and 46-days post Schistosoma mansoni infection were generated by deep sequencing, in triplicate, using Illumina HiSeq.

first: Melissa

last: Sanchez


title: Alternative intronic polyadenylation influences cancer metastasis and response to therapy [3'-seq]

first: Nicolas

last: Servant

summary: We explored the impact of alternative polyadenylation regulation during tumor cell spreading.

overall_design: To identify differences in IPA usage associated in tumor cell spreading, we performed 4 pair-wise comparisons (in duplicates) between non-metastatic (67NR, 168FARN) and metastatic cell lines (4T07, 4T1), and between mock- and U1-ASO-transfected 4T1 cells.


title: Splicing defects in RNA export receptor mutants

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Comparison of splicing defects in Wild type and xpo1-1 mex67-5

first: Heike

last: Krebber

first: Daniel

last: Becker


title: Genome-wide transcriptional changes under oxidative stress in iron-starved Aspergillus fumigatus cultures

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

summary: Aspergillus fumigatus has to cope with a combination of several stress types in the human body, and the interplay between the different stress responses can significantly influence the survival of this human pathogen during the invasion of the host organism. In this study, we examined how the H2O2 induced oxidative stress response depends on iron availability. Surprisingly, the applied H2O2 treatment, which induced only a negligible stress response in iron fed cultures, deleteriously affected the fungus under iron starvation and the majority of observed transcriptome-level stress responses were characteristic only for the combined H2O2-iron starvation stress treatments. Our data suggest that the survival of the fungus highly depended on fragile balances, e.g. between siderophore and ergosterol productions or between economization on iron and production of essential iron containing proteins. The applied stress conditions also affected several processes related to virulence or drug susceptibility including secondary metabolism, zinc acquisition or antifungal drug transport. Our data clearly demonstrate that studying stress responses under single stress treatments is not sufficient at all to understand how fungal pathogens survive in a complex habitat and support the view that the evolutionary success of A. fumigatus as an opportunistic human pathogen is not the mere consequence of the productions of certain virulence factors. Importantly, this fungal pathogen is able to mount and coordinate high-complexity and outstandingly efficient responses to multiple and superpositioning stresses in various harsh habitats like the human body.

overall_design: Control (untreated), hydrogen-peroxide treated, iron-starved as well as hydrogen-peroxide treated and iron-starved A. fumigatus cultures were studied in three independent experiments (3x4 RNAseq data sets).

first: Tamás

first: Vivien

last: Kurucz

first: Károly

last: Antal

first: István

last: Pócsi


title: Extensive Functional Redundancy of Mammalian Enhancers

first: Diane

last: Dickel

address: 1 Cyclotron Road

institute: Lawrence Berkeley National Laboratory


title: Extensive Functional Redundancy of Mammalian Enhancers [ChIP-seq]

summary: Analysis of the epigenomic landscape in limbs of homozygous limb enhancer knockout mice

overall_design: Examination of the H3K27ac histone modifications in dissected forelimbs of limb enhancer knockout and wild-type embryos at embryonic day 11.5.

first: Yoko

last: Yuzawa

first: Marco

last: Osterwalder


title: Identification of Transcripts Involved in Neural Tube Closure Using RNA-sequencing

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

summary: The transcriptome of zebrafish embryos treated with a Nodal signaling inhibitor at sphere stage, which causes neural tube defects, is compared to those treated at 30% epiboly, which does not.

overall_design: Transcriptomic analysis of differential gene expression of key developmental pathways under differing inhibitory treatments.

first: Lexy

last: Kindt

first: Jennifer

middle: O

last: Liang

first: Alicia

last: Coughlin

first: Tianna

last: Perosino


title: BMI1 stress-related functions contribute to the redox-dependent fate of adult cardiac progenitors

city: Madrid

first: Monica

last: Franch

address: Darwin 3

department: BioinfoGP

country: Spain

institute: National Center for Biotechnology-CSIC

summary: The accumulation of reactive oxygen species (ROS) is linked to several cardiovascular pathologies; it is also associated with cell cycle exit by nenonatal cardiomyocytes, a key limiting factor in the regenerative capacity of the adult mammalian heart.  BMI1 is a component of the polycomb complex 1, which is linked to adult multipotent progenitors, and is also an important partner in DNA repair and redox regulation.  Here we show that high BMI1 expression is associated with a cardiac Sca1+ progenitor subpopulation with low ROS levels.  In homeostasis, BMI1 represses cell-fate genes, including a cardiogenic differentiation program.  Persistent oxidative damage nonetheless modified BMI1 activity in vivo, by derepressing canonical target genes in favor of their antioxidant and anticlastogenic functions.  This derepression induced cardiac progenitor proliferation and differentiation, and thus increased its contribution to mature cardiac progeny.  This redox-mediated mechanism is not restricted to damage situations, and we report ROS-associated differentiation of cardiac progenitors in steady state.  These findings demonstrate how redox status influences the adult cardiac progenitor response, and identifies a redox-mediated BMI1 function with potential implications in adult cardiac turnover.

overall_design: Examination of two different proteins (BMI1 and H2AK119ub) with two different treatments (Homeostasis and Damage) in Cardiac cells enriched in Sca1+CD45- from 6-8 weeks-old mice.

first: Diego

last: Herrero

first: María

last: Tomé

first: Susana

last: Cañón

first: Francisco

last: Cruz

first: Rosa

last: Carmona

first: Eva

last: Fuster

first: Enrique

last: Roche

first: Antonio

last: Bernad


title: Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species

city: Buenos Aires

first: Julieta

last: Mateos

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

summary: Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effects on transcription of FLOWERING LOCUS C (FLC) and PERPETUAL FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requirement in the Brassicaceae species Arabidopsis thaliana and Arabis alpina, respectively. We found that only 17% of their BSs were conserved in both species and that these contained a CArG-box that is recognised by MADS-box TFs. The CArG-box consensus at conserved BSs was extended compared to the core motif. By contrast, species-specific BSs usually lacked the CArG-box in the other species. Flowering-time genes were highly overrepresented among conserved targets and their CArG-boxes were widely conserved among Brassicaceae species. Cold-regulated genes (COR) were also overrepresented among targets, but the cognate BSs and the identity of the regulated genes were different in each species. In cold, COR gene transcript levels were increased in flc and pep1-1 mutants compared to wild-type and this correlated with reduced growth in pep1-1. Therefore FLC orthologs regulate a set of conserved target genes mainly involved in reproductive development and were later independently recruited to modulate stress responses in different Brassicaceae lineages. Analysis of TF BSs in these lineages thus distinguishes widely conserved targets representing the core function of the TF from those that were recruited later in evolution.

overall_design: leaves and apices mRNA profiles of 10-day old wild type (WT) and pep1-1 mutant of arabis alpina (accession pajares) were generated by deep sequencing, in triplicate


title: Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species.

city: Cologne

address: Carl-von-Linné-Weg 10

department: Department of Plant Developmental Biology

institute: Max Planck Institute for Plant Breeding Research

summary: Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effects on transcription of FLOWERING LOCUS C (FLC) and PERPETUAL FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requirement in the Brassicaceae species Arabidopsis thaliana and Arabis alpina, respectively. We found the BSs that were conserved in both species, and that these contained a CArG-box that is recognised by MADS-box TFs. The CArG-box consensus at conserved BSs was extended compared to the core motif. By contrast, species-specific BSs usually lacked the CArG-box in the other species. Flowering-time genes were highly overrepresented among conserved targets and their CArG-boxes were widely conserved among Brassicaceae species. Cold-regulated genes (COR) were also overrepresented among targets, but the cognate BSs and the identity of the regulated genes were different in each species. In cold, COR gene transcript levels were increased in flc and pep1-1 mutants compared to wild-type and this correlated with reduced growth in pep1-1. Therefore FLC orthologs regulate a set of conserved target genes mainly involved in reproductive development and were later independently recruited to modulate stress responses in different Brassicaceae lineages. Analysis of TF BSs in these lineages thus distinguishes widely conserved targets representing the core function of the TF from those that were recruited later in evolution.

sample_organism:
Arabidopsis thaliana
Arabis alpina

platform_organism:
Arabidopsis thaliana
Arabis alpina

overall_design: Investigation of FLC and FLC ortholog PEP1 in Arabidopsis thaliana and Arabis alpina.

first: Vicky

last: Tilmes

first: Pedro

last: Madrigal

first: George

last: Coupland


title: Transcriptome of SE, CBP20 and CBP80 mutants

city: Oldenburg

first: Sascha

last: Laubinger

address: Carl-von-Ossietzky-Str. 9-11

institute: University of Oldenburg

summary: This dataset includes the transcriptomes of plants bearing mutations  in genes enconding for three related Arabidopsis proteins: SERRATE (SE), CAP-BINDING PROTEIN 20 (CBP20) and  CAP-BINDING PROTEIN 80 (CBP80). The transcriptomes were obtained by mRNA sequencing. Comparison of the RNA accumulation patterns will enable the idenfication of common patterns and uncover possible common functions of SE, CBP20 and CBP80 in regulating gene expression.

overall_design: mRNA sequencing was carried out from four different plant genetypes: WT, se, cbp20 and cbp80 mutants. The aim is to compare the transcriptome of each mutant to a common WT control. Samples were prepared in triplicates form different pools of plants. WT1 is compared with se1, cbp201 and cbp801, and the same is true for replicate 2 and 3.

first: Claudia

last: Martinho

first: Corinna

last: Speth

first: Emese

middle: X

last: Szabo


title: Transcriptome-wide landscape of subcellular mRNA redistribution in cell stress

city: Ithaca

first: Hojoong

last: Kwak

address: 516 Campus Rd Biotechnology Bldg

department: Molecular Biology and Genetics

institute: Cornell University

summary: In cell stress, mRNA in the cytoplasm is sequestered to the insoluble ribonucleoprotein (RNP) compartments containing stress granules. These RNP granules are known to be involved in the control of mRNA processing and decay, but it has been elusive whether the mRNA redistribution in cell stress is universal or specific to a subset of transcripts. Here we provide a transcriptome-wide profiles of the RNP granules in cell stress and show that mRNA accumulation in stress granule differentially affects individual  transcripts. mRNA species accumulated in stress granules are largely conserved across distinct stress types, such as in endoplasmic reticulum stress, heat shock and arsenic stress. Many mRNA species involved in cell survival and proliferation are more dynamically redistributed, suggesting that mRNA sequestration can be a specific response mechanism through which cells can reshape the landscape of their transcriptome and affect the cell fate determination in stress conditions .

overall_design: 24 samples are analyzed, which include 3 replicates for control (DMSO) cytoplasmic fraction, 3 replicates of control (DMSO) RNP granule fraction, 3 replicates of Thapsigargin treated cytoplasmic fraction, 3 replicates of Thapsigargin treated RNP granule fraction, 2 replicates of control (H2O) cytoplasmic fraction, 2 replicates of control (H2O) RNP granule fractions, 2 replicates of heat shock (HS) treated cytoplsmic fraction (HS), 2 replicates of heat shock (HS) treated RNP granule fraction, 2 replicates of arsenite treated cytoplasmic fraction, and 2 replicates of arsenite treated RNP granule fraction.

first: Sim

last: Namkoong

first: Jun

middle: H

last: Lee


title: Extensive Functional Redundancy of Mammalian Enhancers [RNA-seq]

city: Berkeley

first: Diane

last: Dickel

summary: Analysis of the transcriptional changes in the limb resulting from the loss Gli3 limb enhancers

overall_design: Forelimbs were dissected from wild-type, single and double and enhancer-null embryos and processed for RNA-seq analysis.

first: Yoko

last: Yuzawa

first: Marco

last: Osterwalder


title: Fra-2 negatively regulates postnatal alveolar septation by modulating myofibroblast function

city: San Francisco

first: Kazuyuki

last: Tsujino

address: 1550-4th Street

department: Medicine

institute: University of California, San Francisco

summary:
Purpose: Compare the transciptome between lung myofibroblasts that contituatively express Fra-2 to control lung myofibroblasts to determine genes that may contribute to regulation of secondary alveolar septation
Methods:  mRNa sequences from lung myofibroblasts isolated from mutant mice that contituatively express Fra-2 in α-SMA expressing cells (sma-Fra2) were compared to control mice.  n=4 in each group
Results:  43,432 transcripts wre analyzed and 361 genes were differentially expressed in the smaFra2 mice compared to wild type control.  Functional analysis was performed using the Database for Annotation, Visualization and Integrated Discovery.  Changes in genes from lung myofibroblasts in smaFra2 mice: genes involved with extracellular matrix and cell adhesion were upregulated; Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 (Enpp2) and LPA receptor1 (LPA1) were downregulated.
Coclusion:  The secondary alveolar septation defect in smaFra2 mice could be explaned by Fra-2 mediated changes in extracellular matrix and cell adhesion in developing lung myofibroblasts.

overall_design: Genome-wide sequencing of lung myofiblasts that constituatively express Fra-2

first: Joshua

last: Pollack

first: Andrea

last: Barczak

first: Dean

last: Sheppard


title: ChIP-seq analysis of EZH1, H3K4me3 and H3K27me3 in 5F cells

city: Boston

first: Melissa

last: Kinney

address: 1 Blackfan Circle

institute: Boston Children's Hospital

summary: Blood develops in distinct stages. Haematopoietic progenitors in the embryo manifest restricted differentiation potential relative to definitive haematopoietic stem cells in adult bone marrow, which support lifelong multilineage haematopoiesis. To identify regulators of embryonic haematopoiesis, we screened chromatin modifiers and identified the Polycomb group protein EZH1 as a barrier to multilineage potential from pluripotent stem cells (PSCs). EZH1 was directly bound to bivalently poised, yet restricted, HSC and lymphoid genes in primitive progenitors; knockdown enabled robust generation of multilineage progenitors. Moreover, EZH1 haploinsufficiency promoted the generation of HSCs with long-term, multilineage and self-renewal potential from sites of embryonic haematopoiesis in vivo. Together, this work identifies EZH1 as a key epigenetic barrier to definitive haematopoiesis during embryonic development, and highlights the utility of chromatin modifiers as cell engineering targets to enhance blood differentiation from PSCs.

overall_design: ChIP-seq was performed to determine the chromatin occupancy of FLAG-biotin-tagged EZH1, H3K4me3 and H3K27me3 in 5F cells in the presence or absence of EZH1 knockdown (shEZH1)..

first: Linda

last: Vo

first: Xin

last: Liu

first: Yuannyu

last: Zhang

first: Jian

last: Xu

last: Daley


title: EZH1 as a key epigenetic barrier to definitive haematopoiesis during embryonic development

overall_design: Refer to individual Series


title: Expression level comparison under dividing and quiescent states in human primary fibroblasts

city: Rochester

first: Sina

last: Ghaemmaghami

state: NEW YORK

address: Hutchison Hall

department: Biology Department

institute: University of Rochester

summary: To identify genes with different expression levels in dividing and quiescent cells, mRNA-sequencing was done in both conditions for human primary fibroblasts (HCA2-hTert).

overall_design: mRNA profiles of dividing and quiescent cells were generated by deep sequencing, in triplicate, using Illumina highseq 2500.

first: Tian


title: Ionizing radiations potentiate high fat diet-induced insulin resistance and reprogram skeletal muscle and adipose progenitor cells

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: Exposure to ionizing radiation increases the risk of chronic metabolic disorders such as insulin resistance and type 2 diabetes later in life. We hypothesized that irradiation reprograms the epigenome of metabolic progenitor cells, which could account for impaired metabolism after cancer treatment. C57Bl/6 mice were treated with a single dose of irradiation and subjected to high fat diet (HFD). RNA Sequencing and Reduced Representation Bisulfite Sequencing were used to create transcriptomic and epigenomic profiles of preadipocytes and skeletal muscle satellite cells collected from irradiated mice. Mice subjected to total body irradiation showed alterations in glucose metabolism and, when challenged with HFD, marked hyperinsulinemia. Insulin signaling was chronically disrupted in skeletal muscle and adipose progenitor cells collected from irradiated mice and differentiated in culture. Epigenomic profiling of skeletal muscle and adipose progenitor cells from irradiated animals revealed substantial DNA methylation changes, notably for genes regulating the cell cycle, glucose/lipid metabolism and expression of epigenetic modifiers. Our results show that total body irradiation alters intracellular signaling and epigenetic pathways regulating cell proliferation and differentiation of skeletal muscle and adipose progenitor cells, and provide a possible mechanism by which irradiation used in cancer treatment increases the risk for metabolic disease later in life.

overall_design: Reduced representation bisulfite sequencing (RRBS), RNA-Seq and Methyl-CpG-binding domain sequencing (MBD-Seq) of SVF and satellite cells, on CHOW or HFD and untreated or irradiated

first: Vibe

last: Nylander

first: Emil

last: Andersen

first: Odile

last: Fabre

first: Christian

last: Garde

first: Morten

last: Rasmussen

first: Kiymet

last: Citirikkaya

first: Josephine

last: Baek

first: Gitte

last: Christensen

first: Marianne

last: Aznar

first: Lena

last: Specht

first: David

last: Simar

first: Romain

last: Barres


title: ACF1 regulates nucleosome spacing in Drosophila euchromatin [Mnase-seq embryos]

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

summary: The nature of chromatin as regular succession of nucleosomes has gained iconic status. The average nucleosome repeat length (NRL) determined by classical means serves as index for bulk chromatin of a given specimen. However, this value is dominated by regular heterochromatin since nucleosomal arrays are often not regular at individual single copy sequences. To obtain a measure for nucleosome regularity in euchromatin we subjected nucleosome dyad profiles to autocorrelation and spectral density analyses. This revealed variation in nucleosome regularity and NRL at different types of euchromatin and yielded a comprehensive catalog of regular phased nucleosome arrays (PNA). The absence of the nucleosome sliding factor ACF1 correlated with global loss of regularity in euchromatin and increased NRL and compromised phasing at a novel type of PNA. Our approach is generally applicable to characterize hallmarks of euchromatin organization.

overall_design: MNase-Seq in Drosophila melanogaster embryos wildtype and mutant for ACF1

first: Dhawal

last: Jain

first: Sandro

last: Baldi

first: Angelika

last: Zabel

first: Marion

last: Scheibe

first: Falk

last: Butter

first: Peter

middle: B

last: Becker


title: RNA-seq analysis of EZH1 knockdown in 5F cells, or EZH1 heterozygous and homozygous knockout YS and AGM cells

first: Melissa

last: Kinney

overall_design: RNA-seq was performed to determine gene expression changes in EZH1 deficient 5F cells or in mouse yolk sac (YS) and AGM cells.

first: Linda

last: Vo

first: Xin

last: Liu

first: Yuannyu

last: Zhang

first: Jian

last: Xu

first: George

last: Daley


title: ACF1 regulates nucleosome spacing in Drosophila euchromatin [ChIP-seq]

overall_design: ChIP-Seq in Drosophila melanogaster embryos


title: ACF1 regulates nucleosome spacing in Drosophila euchromatin

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


title: ACF1 regulates nucleosome spacing in Drosophila euchromatin [MNase-seq BG3]

overall_design: MNAse-Seq in Drosophila melanogaster BG3 cells under various RNAi knockdown conditions.


title: Metabolic exhaustion of T cells in chronic infection is mediated by inhibitory receptor PD-1 and T cell receptor dependent transcription factor IRF4

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

institute: Monash University

summary: During chronic stimulation T cells acquire an exhausted phenotype characterized by expression of multiple inhibitory receptors and down-modulation of effector function. While this is required for the protection of the organism from excessive immunopathology, it also prevents successful immunity against persistent viruses or tumor cells. Here we demonstrate that CD8+ T cell exhaustion is characterized by a progressive decline in cellular metabolism. Exhausted T cells exhibit reduced metabolic reserve, impaired fatty acid oxidation and production of mitochondrial reactive oxygen species (ROS). Blockade of inhibitory PD-1/PD-L1 signaling rescued mitochondrial biogenesis, oxidative phosphorylation and ROS production, which was required for efficient restoration of cellular expansion and effector function. Expression of inhibitory receptors and impaired metabolic function was fuled by high amounts of IRF4, BATF and NFAT, which formed a TCR-responsive transcriptional circuit that sustained the transcriptional network responsible for T cell exhaustion.

overall_design: Transcriptional profiling of T cells in mice with chronic and acute infections using RNA sequencing

first: Kevin

last: Man

first: Yang

last: liao

first: Axel

last: Kallies


title: Mode of action analysis: Distinct Staphylococcus aureus transcriptome changes upon antivirulence lactone treatment

city: Garching

first: Jan

last: Vomacka

address: Lichtenbergstraße 4

department: Department of Chemistry

institute: Technische Universität München

summary: To elucidate the antivirulent lactone U1 mode of action, next generation sequencing was applied to analyze the transcriptome of NCTC 8325 cells treated with either compound or DMSO as control.

overall_design: Two biological replicates for compound treated and also two biological replicates for DMSO treated Staphylococcus aureus cultures were analysed.

first: Bianca

last: Schwanhäußer

first: Katrin

last: Lorenz-Baath


title: Transcriptomic analysis of atphb3 mutant.

city: Jinan

first: Xiangpei

last: Kong

address: 27 Shanda South Road

institute: Shandong University

summary: To identify genes that are regulated by AtPHB3, we used RNA-seq to assess gene expression in atphb3 and wild type roots.

overall_design: Examination of  primary root root  of Col and atphb3 mutant  under normal condition

first: Zhaojun

last: Ding


city: Houston

first: srikanth

last: appikonda

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary: Gene expression profiles of rescue with wild type or SUMO double mutant TRIM24 after shRNA mediated knockdown of TRIM24 in MCF7 cell line

overall_design: Gene expression profiles of rescue with wild type TRIM24 and SUMO double mutant, 3 replicate each

first: Srikanth

last: Appikonda

first: Parantu

last: Shah

first: Michelle

last: Barton


title: Spatial-temporal order of regulation in tomato early fruit development

city: Beijing

first: Xia

last: Cui

address: 12 Zhongguancun Nandajie

institute: Chinese Academy of Agricultural Sciences

summary: Early fruit development is crucial for crop production in tomato. After fertilization, the ovary undergoes a cell division and a cell expansion stages before maturation. Although the roles of regulatory signals such as hormone and carbohydrate during early fruit development have been studied, the spatial distribution and the sequential initiation of these regulatory signals is still poorly understood. Using the cultivated tomato “Moneymaker” as materials, we analyzed the transcriptome of the ovule and the ovary wall dissected from the different stages of the early developing fruits. These datasets provide us the whole picture about the spatial and temporal signal distribution of fruit formation which has not been studied in such a detailed manner. Our results suggest that the hormone signal was initiated in both ovule and ovary wall after fertilization. After that, the different signals were activated in ovule and ovary wall due to their distinct developmental processes. By analyzing the global expression profiling of hormone related genes, we found that the auxin might be synthesized in both ovule and ovary wall after fertilization. The expression pattern of sugar related genes revealed the different carbohydrate metabolism events occurred in ovule and ovary wall. At last, we identified a gene showed tissue and stage specific expression pattern and localized in previously reported fruit weight locus which might be selected during tomato breeding.

overall_design: RNA-seq of ovule and ovary wall/pericarp tissues in four stages of tomato early developing fruits

first: Shuaibin


title: Basal-A Triple Negative Breast Cancer Cells Selectively Rely on RNA Splicing for Survival

first: Rory

last: Kirchner

address: 677 Huntington Ave

department: Department of Biostatistics

institute: Harvard T.H. Chan School of Public Health

summary: Development of targeted therapies for triple-negative breast cancer (TNBC) has failed at least in part because of the heterogeneity of these poor prognosis cancers. To identify common dependencies of basal-like TNBCs, we performed a targeted siRNA lethality screen in 7 human breast cancer cell lines focusing on 154 previously identified dependency genes of one basal-A TNBC line. Thirty genes were shared basal-A TNBC dependencies. Genes for proteins involved in RNA splicing, in particular those associated with the U4/U6.U5 tri-snRNP complex (e.g. PRPF8, PRPF38A), were prominent shared dependencies. Spliceosome genes were commonly up-regulated in primary basal-like TNBCs. Knockdown of PRPF8 or PRPF38A led to widespread intronic retention, expression of immune system genes and aberrant splicing of transcripts involved in protein translation, proteasome function, mitosis and apoptosis, including the TNBC dependency gene MCL1. These transcripts were susceptible to inhibition of RNA splicing more generally, since they were similarly affected by the RNA splicing inhibitor drug E7107. In particular, E7107 caused splicing of MCL1 to its pro-apoptotic splicing variant in multiple cell lines, killed MCL1-dependent basal-A cells in vitro, and suppressed the growth of 2 basal-A cell-lines and 1 of 2 patient-derived basal-like TNBC xenografts in vivo. Thus, TNBCs critically rely on RNA splicing  and could be susceptible to RNA splicing inhibitors.

overall_design:
Two datasets:

1) 5 control samples, 5 PRPF8 knockdown and 5 PRPF38 knockdown samples

2) 4 control samples, 4 E7107 treated samples

first: Stefanie

last: Chan

first: Sridhar

last: Praveen

first: Ying

last: Lock

first: Zach

last: Herbert

first: Silvia

last: Buonamici

first: Peter

last: Smith

first: Judy

last: Lieberman

first: Fabio

last: Petrocca


title: Regeneration in the Ctenophore Mnemiopsis leidyi: A Transcriptomic Analysis

city: St. Augustine

first: Rachel

last: Sanford

state: FL

address: 9505 Oceanshore Blvd

institute: University of Florida

summary: Ctenophores’ amazing capacity of regeneration has fascinated biologists for centuries. The morphological features of ctenophore regeneration have been documented, but the molecular and cellular components behind this phenomenon have remained a mystery. Here, next generation sequencing technologies and transcriptomic analysis are used to investigate the regeneration dynamics in the ctenophore Mnemiopsis leidyi. The resulting data identify multiple signaling pathways that might be involved in ctenophore regeneration. These include evolutionarily conserved pathways, such as Ca2+-dependent and MAP-kinase signaling pathways, that are up regulated during regeneration, as well as genes involved in energetics and cytoskeleton function. The data also show evidence for involvement of dozens of ctenophore specific secretory molecules, their receptors and processing components that are important signal messengers in regeneration. A unique subset of transcription factors were also found to be involved in regeneration which may be upstream regulators of those signaling pathways. In summary, our data indicate that the strategies which ctenophores employ to regenerate use a unique combination of evolutionarily conserved and ctenophore specific signaling components. These data provide novel insights into the mechanisms of regeneration in the earliest branching taxa in Metazoa.

overall_design: Transciptomic evalutation of control tissue vs regenerating tissue at 30 minutes, 1 hour and 2 hours after regeneration. This tested both in total RNA and nascent RNA.

first: Andrea

last: Kohn

first: Leonid

last: Moroz


title: Transcriptome datasets of big-fruit tomato MM, cherry tomato CC and wild tomato PP

summary: Six stages of flower and fruit materials from S. lycopersicum var. Moneymaker (MM), S. lycopersicum var. cerasiforme LA1310 (CC) and Solanum pimpinellifolium PI365967 (PP) including 5DPA, 20DPA, mature green, break stage and red ripen fruits and -2DPA flower

sample_organism:
Solanum lycopersicum
Solanum pimpinellifolium
Solanum lycopersicum var. cerasiforme

overall_design: RNA from six tissues from each species was extracted and mixed together to construct the libraries and perform RNA-seq

last: Zhang


title: Methylmercury (MeHg) induced Transgenerational Inheritance of Brain Transcriptome in Zebrafish (Danio rerio)

city: Milwaukee

first: Michael

last: Carvan III

state: WI

address: 600 E. Greenfield Ave.

department: School of Freshwater Sciences

institute: University of Wisconsin-Milwaukee


title: Methylmercury (MeHg) induced Transgenerational Inheritance of Retinal Transcriptome in Zebrafish (Danio rerio) [retina]

summary: Methylmercury (MeHg) is a ubiquitous environmental toxicant that is often detected in the tissues of fish-eating species. It has been well established that prenatal exposure to MeHg can lead to widespread brain damage and impaired neurological development resulting in defects ranging from severe cerebral palsy and cognitive deficits to impaired motor and sensory function. A wide range of environmental toxicants have been shown to induce transgenerational inheritance of diseases via changes in DNA methylation—a well-known epigenetic modification. Our previous research has demonstrated that developmental MeHg exposure may yield transgenerational inheritance of neurological dysfunction in adult F3-lineage zebrafish via quantitative neurobehavioral assays that evaluated the visual startle response, retinal electrophysiology, and locomotor function. The objective of the current study was to examine the correlation between neurobehavioral phenotypes and the transcriptome activity in the brain and retina of F3 zebrafish by RNA sequencing (RNAseq). Transcriptomic analyses of F3 generation MeHg-treated zebrafish (compared to control) revealed significant gene dysregulation in both the brain and retina. There were 1648 and 138 differentially expressed genes in the retina and brain, respectively (FDR <0.05). Thirty-five genes were commonly dysregulated in both organs. Gene set enrichment analysis revealed significantly enriched pathways including: neurodevelopment, visual functions, phototransduction, and motor movement. Moreover, commonly dysregulated genes were associated with circadian rhythm and metabolic pathways, as well as arginine and proline metabolism. To our knowledge, this is the first evidence of a transgenerational transcriptome induced by ancestral developmental exposure to MeHg in any species.  If the transgenerational phenotypes, transcriptome, homologous biomarkers, or similar molecular pathways hold true for human populations, our findings have significant impact on global public health in terms of identifying the susceptible populations using biomarkers and preventing  transgenerational inheritance of MeHg-induced neurobehavioral deficits.

overall_design: Eggs of EK strain zebrafish were exposed to methylmercury (0.0 and 0.03μM with ethanol as the vehicle) for 24 hours, then raised normally. This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage. The F2 and F3 generations were never exposed to exogenous MeHg. The retinas were collected from F3 generation fish of each lineage. 12 samples of total RNA isolated from adult zebrafish retina were analyzed. There were 6 biological replicates for vehicle control (0 µM MeHg) and exposure (0.03 µM MeHg) groups.

first: Thomas

last: Kalluvila

last: Carvan

first: Rebekah

last: Klingler

first: Marcus

last: Walz


title: Methylmercury (MeHg) induced Transgenerational Inheritance of Brain Transcriptome in Zebrafish (Danio rerio) [brain]

overall_design: Eggs of EK strain zebrafish were exposed to methylmercury (0.0 and 0.03μM with ethanol as the vehicle) for 24 hours, then raised normally. This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage. The F2 and F3 generations were never exposed to exogenous MeHg. The brain were collected from F3 generation fish of each lineage. 12 samples of total RNA isolated from adult zebrafish brain were analyzed. There were 6 biological replicates for vehicle control (0 µM MeHg) and exposure (0.03 µM MeHg) groups.


title: Female Reproductive Impacts of Dietary Methylmercury in Yellow Perch (Perca flavescens) and Zebrafish (Danio rerio)

address: 600 E. Greenfield

summary: This study sought to evaluate the effects of dietary MeHg exposure on adult female yellow perch (Perca flavescens) and zebrafish (Danio rerio) reproduction by relating controlled exposures with subsequent reproductive effects. Yellow perch were used in the study for their socioeconomic and ecological importance within the Great Lakes basin, and the use of zebrafish allowed for a detailed analysis of the molecular effects of MeHg. MeHg exposures at environmentally relevant levels were done in zebrafish for a full life cycle, mimicking a realistic exposure scenario, and in adult yellow perch for twenty weeks, capturing early seasonal ovarian development. In zebrafish, several genes involved in reproductive processes were shown to be dysregulated by RNA-seq and QPCR, but no significant phenotypic or physiological changes were observed with ovarian staging, fecundity, or embryo mortality. Yellow perch did not appear to be affected by MeHg, either at a molecular level, as assessed by QPCR of eight genes in the pituitary, liver, and ovary tissue, or a physiological level, as seen with ovarian somatic index, circulating estradiol, and ovarian staging. Lack of impact in yellow perch limits the usefulness of zebrafish as a model and suggests that the reproductive sensitivity to environmentally relevant levels of MeHg differs between yellow perch and zebrafish.

overall_design: 12 samples of total RNA isolated from adult zebrafish ovaries were analyzed. Each exposure group (1, 3, and 10 ppm MeHg) had three replicates, as did the vehicle control. Each sample was comprised of pooled total RNA of up to 6 individual fish.

first: Abigail

last: DeBofsky


title: RNA profiling for mouse B cells by drug treatment

city: Shenyang

first: Guoxin

last: Liang

state: Liaoning

address: No.155 Nanjing North street

department: AIDS research center

institute: China Medical University

summary: We used genome-wide transcriptome analysis to profile the mRNA, long noncoding RNA (lncRNA)  expression of mouse splenic B cells which were treated with JQ1+ (80nM), Flavopiridol (30nM) and Control for 3 days.

overall_design: CD43+ negative isolated mouse splenic B cells (CD43-)  were teated with Trizol for RNA preparation.

first: Jianbo

last: Sun

first: Uttiya

last: Basu


title: ATAC-seq analysis in 5F cells and AGM cells with EZH1 depletion

first: Melissa

last: Kinney

overall_design: ATAC-seq was performed to determine the chromatin accessibility in 5F cells transduced with shRNAs for luciferase (control) or EZH1, or in Ezh1 WT, HET or KO embryonic day (E)10.5 AGM cells.

first: Linda

last: Vo

first: Xin

last: Liu

first: Yuannyu

first: Jian

last: Xu

first: George

last: Daley


title: Transcriptome analysis using customized AZ microarray on tomato Flower Abscission zone of transgeneic line TAPG::antisense TPRPgene

city: Bet-Dagan

first: Srivignesh

last: Sundaresan

state: Israel

address: P.O.Box 6, Bet- Dagan

department: Post Harvest Technology

country: Israel

institute: Agricultural Research Organisation, The volcani center, Israel

summary: To extend our previous knowledge from our gene expression studies on Flower pedicel Abscission zone using Affymetrix microarray chip we have employed whole transcriptome analysis by NGS as a discovery platform to identify and add the transcripts to pre-existing database. We designed the Customized AZ Microarray chip with the transcripts obtained from NGS (includes novel transcripts), pre existing Agilent probes, and some additional transcripts from previous databases. we developed transgenic lines by antisense silenciencing the genes, which are expressed in the AZ  to study the functional role in abscission process. In the current stuty we silenced TPRP gene by antisense technology under abscisson promoter (TAPG::antsisense TPRP). The flower pedicel AZ tissue tissue was sampled at six time points (0, 4, 8, 12, 16 and 20 h), following flower removal, and analyzed for their gene expression profiles using the customized AZ microarray.

first: Shimon

last: Meir

first: Sonia

last: Philosoph-Hadas


title: A Direct and Accelerated Platform for Analyzing Reprogramming by Defined factors

city: Guangzhou

first: Lihui

last: Lin

state: Guangdong

address: No.190, Kaiyuan Street

department: Stem cell

institute: Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science

summary: Somatic cells can be reverted back to a pluripotent state by nuclear transfer, cell fusion, and defined factors, representing three distinct approaches to reprogram cell fate. Unlike cell fusion, reprogramming by nuclear transfer or defined factors gives rise to cells that contribute to the development of a live animal in mouse, thus making a quasi-direct comparison possible Combining optimized culture conditions and modified reprogramming factors, we report here that mouse fibroblasts can be reprogrammed by defined factors into cells capable of contributing to chimera formation and germline transmission in as short as 96 hours, comparable to the time required for the formation of inner cell mass in cloned embryos by nuclear transfer. Gene expression profiling analysis shows that this accelerated reprogramming process in fact corresponds well with previously reported longer ones with similar molecular signatures. Additionally we find a new set of genes activated as the reprogramming cells acquire chimera competency. In a broader sense, this platform may be adopted for applications such as high throughput screenings for reprogramming mediators both chemical and biological, as well as omics-related mechanistic investigations.

overall_design: We examined transcriptome transition during somatic cells reprogramming using two reprogramming systems, OSK system and OvSvK system (Ov is Oct4-vp16 and Sv is Sox2-vp16). We can get reprogrammed cells capable of contributing to chimera formation and germline transmission in 4 day using OvSvK system and 7 day in OSK system, so, we got samples at D0,  D1, D2, D3, D4 after OvSvK transfection and performed RNA-seq, similarly, we sequenced the samples at D0, D1, D3, D5, D7 in OSK system. Furthermore, we also sequenced several control samples, such as GFP samples at different time points of reprogramming. At the same time,  we examined the effect of several  elements on transcriptome during reprogramming, including Vitamin C, bGFG, GSK3 inhibitor(CHIR-99021  and LiCl).

first: Duanqing

last: Pei


title: Analysis of small RNA through the cell cycle in HeLa

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Small RNA profiles through the cell cycle in HeLa [small RNA-seq]

summary: Dicer plays a key role in RNA silencing. By processing pre-miRNAs and dsRNAs, Dicer generates miRNAs and siRNAs that act as post-transcriptional regulators of gene expression. Dicer is also implicated in heterochromatin formation and toxic RNA degradation.  Here we report that Dicer is controlled in cell cycle. The Dicer protein level drastically rises at late G1 phase and falls at early S phase.  Interestingly, the protein stability of Dicer is decreased specifically at early S phase. MG132, an inhibitor of proteasome, increases Dicer protein level, suggesting that the stability of Dicer is controlled via ubiquitination-dependent proteasome pathway.

overall_design: All samples were first synchronized to early S phase by thymidine double block, then RNA were extracted from the cells after 8, 10, 14, 16, 18 or 20 hours from releasing the cell cycle progression.

first: Jung

last: Lee

first: Inha

last: Heo

first: Jongeun

last: Park

first: V

middle: N

last: Kim


title: Authentic single cell RNA-Seq by measuring the transcriptome of an individual cell twice

first: YangLu

last: Yang

state: Beijing

address: Beijing Xicheng District Yongan Road NO.95

institute: Beijing Friendship Hospital, Capital Medical University

summary: We developed a novel single-cell RNA-Seq technique that can directly measure the technical noises for each individual gene by splitting a single cell into two equal halves and measuring their transcriptomes separately (Measure a single cell twice by RNA-Seq, MAST-Seq).The MAST-Seq protocol was developed from the single cell RNA-Seq technique we previously developed (Tang et al. 2010). We first lysated the cell to release the RNA from the cell, then reverse transcripted the mRNA into cDNA, added polyA to the 3' end of cDNA, synthesized the second strand of cDNA used designed primer, and at last PCR amplified the double strand cDNA to get enough amount of DNA to construct the cDNA libraries.

overall_design: 10 single mouse ES cells, 4 half of single mouse ES cells, 4 quarter of single mouse ES cells, 8 eighth of single mouse ES cells, 4 quarter of 2 single mouse ES cells, 4 quarter of 2 single MEF cells,5 single mouse inner cell mass cells, 5 mouse trophectoderm cells, 4 half of single zygotes, 12 half of single 2-cell embryo blastomeres, 24 half of single 4-cell embryo blastomeres, 8 eighth of 8-cell embryo and 64 half of single 8-cell embryo blastomeres, in total 156 samples.

first: Lu

first: Zhaochun

last: Ma

first: Chen

last: Cao

first: Xinglong

last: Wu

first: Raymond

first: Boqiang

last: Hu

first: Aaron

last: Streets

last: Wen

first: Yanyi

last: Huang

first: Kaiqin

last: Lao

first: Fuchou

last: Tang


title: Expression data from engorged Haemaphysalis flava ticks (ET) salivary gland and semi-engorged Haemaphysalis flava ticks (SET) salivary gland (SGs)

city: Changsha City

first: Tian-Yin

last: Cheng

state: Hunan province

address: Furong District

department: College of Veterinary Medicine

institute: Hunan Agricultural University

summary: To characterize the differentially expressed genes between engorged ticks and semi-engorged ticks

overall_design: A total of 100 salivary glands of all collected Haemaphysalis flava ticks (50 engorged ticks and 50 semi-engorged ticks) were dissected.

first: Xing-Li

last: Xu


title: Identification of PRMT5-dependent genes in ESA+CD24lowCD44+ MCF7 cells

status: Public on Dec 31 2017

city: Birmingham

first: Kelly

last: Chiang

address: Vincent Drive

department: Institute of Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

summary: PRMT5 has been associated with poor prognosis in breast cancer. Here, we identify genes which are dependent on PRMT5 expression in MCF7 ESA+CD24lowCD44+ breast cancer stem cells by RNA-seq

overall_design: RNA-seq profiling of ESA+CD24lowCD44+ cells from MCF7 shCTRL or shPRMT5 cell lines. Three independent ESA+CD24lowCD44+ cell populations from MCF7 shCTRL or shPRMT5 cells were isolated by flow cytometry.

first: Clare

last: Davies


title: Gene expression alteration associated with early embryonic MeHg exposure in zebrafish (Danio rerio)

first: Francisco

middle: Xavier

last: Mora Zamorano

address: 600 E Greenfield Ave

institute: University of Wisconsin - Milwaukee

summary: Methylmercury (MeHg) is an environmental neurotoxicant known to cause adverse effects in fish, such as locomotor abnormalities, visual deficits or teratogenesis. However, very few studies have investigated the effects of environmentally realistic MeHg exposures on the gene expression of fish embryos. Since the primary source of MeHg exposure in wild fish is through the diet, this study analyzed differential gene expression in zebrafish embryos from parents that had been subjected to environmentally relevant dietary MeHg exposures (0, 1, 3, and 10ppm) throughout their whole life cycle.

overall_design: Parental generations of zebrafish were exposed to environmentally realistic MeHg dietary regimes (0, 1, 3, and 10ppm) throughout their whole life cycles. Upon reaching adulthood, their offspring was analyzed for gene expression alteration.

last: Mora

first: Michael

last: Carvan

first: Rebekah

last: Klingler

first: Marcus

middle: E

last: Walz


title: Transcriptomic response to adult hypothalamic deletion of Snord116

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

summary: Snord116 deletion mouse models recapitulate aspects of the Prader-Willi Syndrome.  In this study, we examine the gene expression changes in the mediobasal hypothalamus for mice which have an adult onset deletion of Snord116 in the mediobasal hypothalamus.

overall_design: Snord116 floxed mice were stereotaxically injected in the mediobasal hypothalamus with adeno-associated viruses (AAVs) expressing Cre or GFP.  RNA sequencing was performed on laser-captured hypothalamic regions where Cre was expressed as well as in matching regions from GFP injected controls.  AAV-Cre treated animals were also classed based on their body weight phenotype as obese or non-obese.

first: Joseph

last: Polex-Wolf

middle: Y

first: Anthony

middle: P

last: Coll

first: Stephen

last: O'Rahilly

first: Giles

last: Yeo


title: microRNA-triggered transposon small RNAs mediate genome dosage response (mir845 sRNA-Seq)

city: Versailles

first: Filipe

last: Borges

address: Route de St-Cyr (RD10)

institute: Institut Jean-Pierre Bourgin - INRAE

summary: Chromosome dosage plays a significant role in reproductive isolation and speciation in both plants and animals, but underlying mechanisms are largely obscure. Transposable elements can promote hybridity through maternal small RNA, and have been postulated to regulate dosage response via neighboring imprinted genes. Here, we show that a highly conserved microRNA in plants, miR845, targets the tRNAMet primer-binding site (PBS) of LTR-retrotransposons in Arabidopsis pollen, and triggers the accumulation of 21 to 22-nucleotide small RNA in a dose dependent fashion via RNA polymerase IV. We show that these epigenetically activated small-interfering RNAs (easiRNAs) mediate hybridization barriers between diploid seed parents and tetraploid pollen parents  (“the triploid block”), and that natural variation for miR845 may account for “endosperm balance” allowing formation of triploid seeds. Targeting the PBS with small RNA is a common mechanism for transposon control in mammals and plants, and provides a uniquely sensitive means to monitor chromosome dosage and imprinting in the developing seed.

overall_design: Small RNA sequencing of Arabidopsis pollen

first: Claudia

last: Köhler


title: The CCCH-type zinc finger transcription factor Zc3h8 protects hepatocytes from degeneration by repressing the inflammatory response in zebrafish.

city: Chongqing

first: Qingliang

last: ZOU

address: Tiansheng road

institute: Southwest university

summary: Transcriptional profile of hepatocytes during the cq5 mutant liver degeneration (middle stage-5.5 dpf, and later stage-7.5 dpf).

overall_design: Examination of gene expression at two different stages for mutant (sample group) and wild-type (control group).

last: Zou

first: Jianbo

last: He

first: Lingfei

last: Luo


title: microRNA-triggered transposon small RNAs mediate genome dosage response (Bisulfite-Seq)

overall_design: Bisulfite sequencing of Arabidopsis pollen nuclei

first: Robert

middle: A

last: Martienssen


title: Transcriptional analysis of ZIKV-infected Ifnar-/- and Ifnar+/- placentas  and IFN-beta (IFN-b) or IFN-lambda (IFN-l) treated human mid-gestation chorionic villus explants

city: New Haven

first: Akiko

last: Iwasaki

state: CT

address: 1 Gilbert St

institute: Yale

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


title: RNA sequencing analysis of PINCH mutant sciatic nerves

city: Porto

middle: (Porto

last: Portugal)

address: Rua Alfredo Allen, 208

country: Portugal

institute: Instituto de Biologia Molecular e Celular (IBMC)/I3S

summary: During peripheral nervous system (PNS) development, Schwann cells (SC) depend on interactions between extracellular matrix proteins, integrins and growth factor signal transduction pathways for survival, sorting and wrapping of axon segments to form myelin. Together with integrin-linked-kinase and parvins, PINCH (Particularly-interesting-new-cystidin-hystidin-rich protein) forms a heterotrimeric complex referred to as the IPP complex, which functions as a signaling hub connecting integrins with various signaling pathways. Using SC-specific conditional gene targeting in mice, gene expression profiling by RNAseq, and other methodologies, we demonstrate distinct functional roles for PINCH1 and PINCH2 in SC.

overall_design: Total RNA was prepared from nerves collected from control, PINCH1 mutant and PINCH2 mutant (three biological replicates each).  Each biological replicate consisted in a pool of four SN, from 1 male and 1 female to avoid gender-related differences). All procedures involving mice were in strict accordance to the guidelines approved by the Portuguese Veterinary Office (DGAV) and EU directives.

first: Joana

last: Paes-de-Faria

first: João

last: Relvas


title: Analysis of transcriptional differences after IFN-beta (IFN-b) or IFN-lambda (IFN-l) treated human mid-gestation chorionic villus explants

summary:
Purpose: Treatment of midgestation chorionic villus explants with recombinant IFN-b leads to morphological changes including formation of syncitial knots. However, treatment of explants with IFN-l, which is constitutively expressed by syncytiotrophoblasts, is not sufficient to cause these same changes. To understand the different transcriptional changes induced by IFN-b and IFN-l and underlying cause of these morphological changes, we performed RNAsequencing after these different treatments.
Methods: Chorionic villi of 18-21 gestation week placentas were dissected. Explants were cultured in DMEM F/12 with 1000 U recombinant IFN-b or 1000U recombinant IFN-l for 24 hours. RNA was then isolated from explants, and RNAsequencing was performed to assess transcriptional changes.
Results/ Conclusions: IFN-b but not IFN-l induces interferon stimulated genes (ISGs) in mid gestation chorionic villus explants.

overall_design: MRNA proflies from 3 untreated, 3 IFN-b treated (1000IU), and 3 IFN-l treated (1000IU) were generated using an llumina HiSeq2500.

first: Carolyn

last: Coyne

first: Nitin

last: Arora

first: Laura

last: Yockey


title: RNA-seq of Solanum lycopersicum cv. M82 and S. pennellii introgression line 3-5 day old root tip tissue

city: Davis

first: Siobhan

middle: M

last: Brady

state: CA

address: 1 Shields Ave

department: Plant Biology

institute: UC Davis

summary: The goal of this study was to perform RNA-seq expression analysis on Solanum lycopersicum cv. M82 X S. pennellii introgression lines, deriving expression Quantitative Trait Loci which were analyzed together with pre-existing genomic and phenotypic data to define genes and regulatory pathways controlling tomato root development and observed natural variation.  We completed the RNAseq expression profiling analysis and developed a tool to display this information graphically in collaboration with Nicholas Provart at the University of Toronto: http://bar.utoronto.ca/efp_tomato/cgi-bin/efpWeb.cgi?dataSource=ILs_Root_Tip_Brady_Lab To identify candidate genes and pathways we focussed on one root growth trait, root growth angle, and identified two statistically significant genomic regions within tomato root growth angle QTL containing two candidate genes that likely control the gravitropic setpoint angle (CDC73 and PAP27), both of which are conserved between Arabidopsis and tomato, and which we tested using transgenic lines of the Arabidopsis orthologs.  A possible regulatory role for suberin in root growth angle control was also identified.

sample_organism: Solanum lycopersicum x Solanum pennellii

overall_design: Seedlings of S. lycopersicum (cv. M82), S. pennellii (LA0716), and 75 introgression lines between those parents were grown according to (Ron et al., 2013). Plates were placed vertically in a rack in a randomized block design and the experiments were carried out in a growth chamber with a 16:8 light:dark cycle at 22ºC and 50-75% humidity with a light intensity of 100μE. The germination date was monitored for each seed. Immediately prior to harvesting root tissue for RNA-seq, each replicate of each genotype had between 2 and 5 plates, all of which were scanned with a Epson Perfection V700 photo flatbed scanner into 24-bit RGB TIF image files at 300 dpi. Images were analyzed with the imageJ program (Rasband 1997-2014) and custom macros. Based on germination date and scan date, seedling age in days after germination was determined, and primary roots of seedlings that were 3 or 4 days post-germination were traced with the imageJ polyline tool, following the root centerline from the top of the root (at start of hairs and change from green to white) to the tip. The coordinates of the polylines were recorded by the macros in data tables saved as files, along with metadata including genotype, plate ID, plating date, germination day of each seedling, plate harvest date, measurer, and two flags for each root: “collide” was true if the root contacted or crossed another root, and “along” was true if the root contacted another root and grew along it for any distance. The polylines in the vetted data were analyzed to measure root length and angle using multiple traits (Figure 1A). Additional data was calculated from the metadata: root age (days from germination to harvest), “germination age” (days from plating to germination), “plating age” (days from plating to harvest), and biological replicate number (based on plating date; replicates were named REP2 through REP5, and later replicates for fixing genotype errors were named REPN2 through REPN5 and REPX1 through REPX6). Plates were opened only once, at harvest time, to ensure the same growth conditions for all seedlings. Sampling occurred mid-afternoon. Ten segments (1cm) of the root tip from each genotype replicate were cut and immediately placed into a labeled 2ml tube containing silica beads and immersed in liquid nitrogen. Samples were stored at −80ºC until library preparation. Four replicates of each of the 77 genotypes were grown. Between 7 and 14 root tips, 3 to 4 days post-germination, were collected and libraries were created using a modified Kumar et. al. protocol. Library enrichment was done using 12 cycles. Each library was barcoded, using a unique bar code for each IL, but the same barcode for all replicates of an IL.  The libraries of each replicate were pooled, and the four pools were purified with Ampure beads. The library pooling was tested using a Bioanalyzer. Each pool was sequenced in 50 bp single-end format on a total of 5 lanes of a HiSeq 2000 platform (Illumina Inc. San Diego, CA, USA).  Two replicates were lost during library creation, S. pennellii #3 and IL7-5 #3.

first: Ted

middle: W

last: Toal


title: Haploinsufficiency for SIX2 increases nephron progenitor proliferation leading to elevated branching and nephron number

city: Parkville

first: Belinda

last: Phipson

address: 1G Royal Parade

department: Bioinformatics

institute: WEHI

summary: The regulation of final nephron number in the kidney is poorly understood. However, cessation of nephron formation occurs when the self-renewing nephron progenitor population commits to differentiation. Transcription factors within this progenitor population, such as SIX2, are assumed to control expression of genes promoting self-renewal such that homozygous Six2 deletion results in premature commitment and an early halt to kidney development. In contrast, Six2 heterozygotes were assumed to be unaffected. Using quantitative morphometry, we demonstrate here a paradoxical 18% increase in ureteric branching and final nephron number in Six2 heterozygotes, despite evidence for reduced levels of SIX2 protein and transcript. This is accompanied by a clear shift in nephron progenitor identity with a distinct subset of progenitor genes, including Cited1 and Meox1, downregulated, while others were unaffected. The net result was an increase in nephron progenitor proliferation, as assessed by elevated EDU labelling, an increase in MYC protein and transcriptional upregulation of MYC target genes. Reducing proliferation by introducing Six2 heterozygosity onto the Fgf20-/- background resulted in premature differentiation of the progenitor population. Overall, this data demonstrates a unique dose response of the nephron progenitors to the level of SIX2 protein in which the role of SIX2 in progenitor proliferation versus self-renewal is separable.

overall_design: Gene expression profiling of 33 embryonic whole kidney samples for Six2 wild type, heterozygous and knock out mice at 11.5 and 15.5 dpc.


title: Alterations of microRNAs throughout the malignant evolution of cutaneous squamous cell carcinoma

city: Jerusalem

first: Iddo

middle: Z.

last: Ben-Dov

address: Ein Kerem

department: Nephrology and Hypertension

institute: Hadassah Medical Center

summary: Skin carcinogenesis is known to be a multi-step process with several stages along its malignant evolution. We hypothesized that transformation of normal epidermis to cutaneous squamous cell carcinoma (cSCC) is causally linked to alterations in miRNA expression. For this end we decided to evaluate their alterations in the pathologic states ending in cSCC. Total RNA was extracted from FFPE biopsies of five stages along the malignant evolution of keratinocytes towards cSCC: Normal epidermis, severe solar elastosis (SE), actinic keratosis (KIN1-2), advanced actinic keratosis, (KIN3) and well differentiated cSCC. Next generation small RNA sequencing was performed. We found that 18 miRNAs are over expressed and 28 miRNAs are under expressed in cSCC compared to normal epidermis. miR-424, miR-320, miR- 222 and miR-15a showed the highest fold change among the over expressed miRNAs. And miR-100, miR-101 and miR-497 showed the highest fold change among the under expressed miRNAs. Heat map of hierarchical clustering analysis of significantly changed miRNAs and principle component analysis disclosed that the most prominent change in miRNAs expression occurred in the switch from “early” stages; normal epidermis, solar elastosis and early actinic keratosis to the “late” stages of epidermal carcinogenesis; late actinic keratosis and cSCC. We found several miRNAs with "stage specific" alterations while others display a clear “gradual”, either progressive increase or decrease in expression along the malignant evolution of keratinocytes. The observed alterations focused in miRNAs involved in the regulation of AKT/mTOR or in those involved in epithelial to mesenchymal transition. We chose to concentrate on the evaluation of the molecular role of miR- 497. We found that it induces reversion of epithelial to mesenchymal transition. We proved that SERPINE-1 is its biochemical target. The present study allows us to further study the pathways which are regulated by miRNAs along the malignant evolution of keratinocytes towards cSCC.

overall_design: Comparisons were made with regards to miRNA content between total RNA extracted from paraffin samples on the spectrum between normal skin and cSCC, and additional cell line RNA reference.

first: Adi

last: Mizrahi

first: Aviv

last: Barzilai

first: Devorah

last: Gur-Wahnon

middle: Z

first: Yechezkel

last: Sidi

first: Dror

last: Avni


title: Transcriptomic response to 24-hour food deprivation in four hypothalamic nuclei in Snord116 deletion mice

first: Brian

last: Lam

summary: Mice with a congenital Snord116 deletion model aspects of the Prader-Willi Syndrome.  In this study, we examine the gene expression changes in four hypothalamic nuclei across 24-hour food deprived versus ad libitum fed mice.

overall_design: Using mice with paternal deletion of the Snord116 cluster, we laser-captured microdissected four hypothalamic nuclei for RNA sequencing: the ventromedial hypothalamus (VMH), arcuate nucleus (ARC), dorsomedial hypothalamus (DMH) and paraventricular nucleus (PVN).  Samples were taken from male mice in either the fed or 24-hour fasted state.

first: Joseph

last: Polex-Wolf

first: Anthony

last: Coll

first: Stephen

last: O'Rahilly

first: Giles

middle: S

last: Yeo


title: Gene expression profile of differentially recognized Mtb-epitopes as a function of disease history

city: La Jolla

first: Cecilia

middle: Lindestam

last: Arlehamn

address: 9420 Athena Circle

department: Division of Vaccine Discovery

institute: La Jolla Institute for Allergy & Immunology (LJI)

summary:
Purpose: The goals of this study are to compare two types of Mtb epitope-specific transcriptome profiling (RNA-seq) in individuals with latent TB infection.
Methods: Epitope-specific T cells were isolated by IFNg capture assay or activation induced marker assay (CD25, OX40). Total RNA was purified using miRNAeasy micro kit from Qiagen and amplified using Smart-seq2 protocol. Nextera CT sequencing libraries were prepared and samples were sequenced using HiSeq2500 from Illumina. The sequence reads that passed quality filters were mapped against the hg19 reference using TopHat. Differentially expressed genes between the two epitope sets were identified by Bioconductor package DESeq2, pairwise comparisons and Benjamimi-Hochberg-adjusted p values.
Results: Quantile normalized gene expression values and pairwise comparisons between the epitope-specific memory T cells revealed 9 differentially expressed genes (adjusted p<0.05) for IFNg capture and 1 differentially expressed gene for activation induced marker assay.

overall_design: Comparison of T cells specific for 2 types of differentially recognized Mtb epitope sets using RNA-seq

last: Lindestam Arlehamn

first: Zheng

last: Fu