title: Transcriptome of diurnal wild-type neutrophils and neutrophils deficient in cxcr2, cxcr4 and arntl

summary: Our study aims to analyze time-dependent changes in neutrophil phenotype, compare them with included neutrophil-specific mutants, and indentify common signatures among the 5 groups

overall_design: Blood neutrophils from wild-type and mutants were isolated based on Ly6G staining, then standard RNA extraction procedures were performed. Wild-type samples were extracted at ZT5 and ZT13, all other samples at ZT5.


title: Genetic compensation is triggered by mutant mRNA degradation

status: Public on Jan 17 2019

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

type: Expression profiling by high throughput sequencing

summary: Genetic compensation by transcriptional modulation of related gene(s) (also known as transcriptional adaptation) has been reported in numerous systems1-3; however, whether and how such a response can be activated in the absence of protein feedback loops is unknown.  Here, we develop and analyze several models of transcriptional adaptation in zebrafish and mouse that we show are not caused by loss of protein function.  We find that the increase in transcript levels is due to enhanced transcription, and observe a correlation between the levels of mutant mRNA decay and transcriptional upregulation of related genes.  To assess the role of mutant mRNA degradation in triggering transcriptional adaptation, we use genetic and pharmacological approaches and find that mRNA degradation is indeed required for this process.  Notably, uncapped RNAs, themselves subjected to rapid degradation, can also induce transcriptional adaptation.  Next, we generate alleles that fail to transcribe the mutated gene and find that they do not show transcriptional adaptation, and exhibit more severe phenotypes than those observed in alleles displaying mutant mRNA decay.  Transcriptome analysis of these different alleles reveals the upregulation of hundreds of genes with enrichment for those showing sequence similarity with the mutated gene's mRNA, suggesting a model whereby mRNA degradation products induce the response via sequence similarity.  These results expand the role of the mRNA surveillance machinery in buffering against mutations by triggering the transcriptional upregulation of related genes.  Besides implications for our understanding of disease-causing mutations, our findings will help design mutant alleles with minimal transcriptional adaptation-derived compensation.

overall_design: Examination of transcriptional adaptation based on 3 genes in 3 cell types. Actb was assessed in ESCs as a K.O. and full locus deletion and compared versus wild type (2 replicates each).  Actg1 was assessed in MEFs as a K.O. and full locus deletion and compared versus wild type (2 replicates each). Kindlin 2 was assessed in MKFs as a K.O. and and compared versus floxed (2 replicates each).

first: Mohamed

middle: A

last: El-Brolosy

first: Andrea

last: Rossi

first: Zacharias

last: Kontarakis

first: Stefan

last: Günther

first: Nana

last: Fukuda

first: Carter

last: Takacs

first: Shih-Lei

last: Lai

first: Ryuichi

first: Claudia

last: Gerri

first: Khrievono

last: Kikhi

first: Antonio

middle: J

last: Giraldez

first: Didier

middle: Y

last: Stainier


title: A Molecular signature for Delayed Graft Function [BS-Seq]

status: Public on Jan 18 2019

city: Glasgow

first: Paul

last: Shiels

address: Level 3, Wolfson Wohl Cancer Research Centre

department: Wolfson Wohl Translational Research Centre

country: United Kingdom

institute: University of Glasgow

type: Methylation profiling by high throughput sequencing

summary: Purpose: The aim of this study was to identify a molecular signature for extreme DGF in a retrospective analysis of paired renal allograft biopsies obtained at two time points: pre-implantation during preparatory phase (pre-perfusion biopsies, b) and after reperfusion when circulation was restored (post-perfusion biopsies , b1).

overall_design: RNA-seq and whole genome bisulfite sequencing in paired human renal allograft biopsies

middle: G

first: Dagmara

last: McGuinness

first: Suhaib

last: Mohammed

first: Laura

last: Monaghan


title: A Molecular signature for Delayed Graft Function [RNA-Seq]


title: Circular RNA profiling reveals the different distribution/characteristic and possible transport mechanism among the subcellular fractions

status: Public on Jan 16 2019

city: Beijing

first: Fei

last: Chen

address: NO.1 Beichen West Road, Chaoyang District

country: China

institute: Beijing Institute of Genomics

summary: We systemically investigated the circRNA profiles among the subcellular fractions of HepG2 cell, including nucleus, cytoplasm, mitochondria, ribosome, cytosol and exosome. Our studies reveals the wide distribution of circRNAs among the subcellular fractions except the mitochondria. Further comparative analysis indicate the differential subcellular distributions in expression, length, GC content, classification, alternative circularization and function of the parental genes. Through analyzing the binding motifs distribution of the transport-related RBPs among the subcellular circRNAs, we found that the different subcellular distribution characteristics of circRNAs might be resulted from the RBP-mediated selective transportation. It also implies that the circRNAs may follow the same transportation mechanism as linear RNAs: the RBPs specially recognize, bind to and transport the RNAs with the corresponding binding motifs, regardless of circular or linear RNAs. Our researches not only facilitate better understanding of the life history and molecular behavior of circRNA in cell, but also contribute to the exploration for new biological functions of circRNA.

overall_design: Examined seven fractions of HepG2 (cell, nucleus, cytoplasm, ribsome, cytosol, exosome, mitochodria) and each has two repeats


title: ATAC-seq analysis of Kindlin-2 and Rela K.O. mouse fibroblasts

city: bad nauheim

address: ludwigtr. 43

institute: MPI for heart and lung research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The goal of this study was to observe changes in chromatin accessibility between Kindlin-2 and Rela K.O. mouse fibroblasts with their wild-type counterparts.  We performed ATAC-seq which allowed us to identify regions with enhanced chromatin accessibility in the K.O. cells compared to their wild-type counterparts.

overall_design: Examination of chromatin accessibilty changes between Kindlin-2 and Rela K.O. mouse fibroblasts with their wild-type counterparts (2 biological replicates each)

first: Mohamed


title: A Molecular signature for Delayed Graft Function

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

overall_design: Refer to individual Series


title: The long non-coding RNA MALAT1 contributes to the pathogenesis of multiple sclerosis through alternative splicing and backsplicing regulation

status: Public on Jan 15 2019

city: Pieve Emanuele

first: Giulia

last: Cardamone

address: via Rita Levi Montalcini 4

country: Italy

institute: Humanitas University

summary: Since we found an upregulation of the long non coding RNA MALAT1 in Multiple Sclerosis (MS) patients, we decided to explore the global effect of MALAT1 modulation on transcriptome. We hence performed high-coverage RNA-seq experiments of MALAT1 knockdown in Jurkat E6-1 T cells to analyze gene expression, alternative splicing (AS), and backsplicing profiles. We found 107 differentially expressed genes, 1114 dysregulated AS events, and 49 circular RNAs that were modulated by MALAT1. These results highlighted the role of MALAT1  in splicing and backsplicing regulation.

overall_design: Jurkat E6-1 cells were incubated with 500 nM GapmeR targeting MALAT1 (kd) or 500 nM GapmeR negative control (mock)

first: Elvezia

last: Paraboschi

first: Rosanna

last: Asselta

last: Soldà

first: Stefano

last: Duga


title: Contrasting roles of the RSC and ISW1/CHD1 chromatin remodelers in RNA polymerase II elongation and termination

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

country: USA

institute: National Institutes of Health

summary: We addressed the roles of four remodeling machines (ISW1, ISW2, CHD1 and RSC) in specifying the chromatin organization.

overall_design: Comparison of budding yeast nucleosome positions obtained using micrococcal nuclease digestion followed by paired-end sequencing (MNase-seq). We sequenced nucleosomes from isogenic strains with the essential RSC8 gene linked to a GAL promoter and isw1Δ, isw2Δ or chd1Δ mutations in all combinations. We measured gene activity by ChIP-seq for the Rpb3 subunit of RNA polymerase II.

first: Josefina

last: Ocampo

middle: V

first: Peter

middle: R

last: Eriksson

first: David

last: Clark


title: Flipping the switch on Sex-lethal expression: Sister of Sex-lethal antagonizes Sxl-dependent alternative splicing to maintain a male-specific gene expression pattern in Drosophila

city: Regensburg

first: Gerhard

last: Lehmann

address: Universitaetsstrasse 31

department: Biochemistry 1

institute: University of Regensburg


title: G1/S cyclin-CDKs promote cell-cycle transcription by relieving the inhibition of a pulse-generating transcription factor network

status: Public on Jan 31 2019

city: Durham

first: Steven

middle: B

last: Haase

state: NC

department: Biology

institute: Duke University

type:
Expression profiling by array
Third-party reanalysis

summary: Transcript dynamics in the S. cerevisiae BF264-15D strains with genetically perturbed TFN or CDK-APC/C components. We compared the extents to which the programs of cell-cycle transcription were initiated during various cell-cycle arrests.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design:
Early G1 cells were obtained by centrifugal elutriation or α-factor arrest and then released at 30°C or 37°C at time point 0 for time-series microarray. Results of biological replicates are included.

This series contains a re-analysis of all samples in GSE8799 and GSE32974. The data matrix with all 378 samples (270 new samples and 108 re-analyzed samples) is available on the series record. All 378 samples were normalized together using dChip implementation with default parameters from the affy package (1.32.1) within R/Bioconductor.

first: Chun-Yi

last: Cho

first: Christina

middle: M

last: Kelliher


title: Flipping the switch on Sex-lethal expression: Sister of Sex-lethal antagonizes Sxl-dependent alternative splicing to maintain a male-specific gene expression pattern in Drosophila (RIP-Seq)

summary: In Drosophila female development is governed by a single RNA-binding protein, Sex lethal (Sxl), that controls the expression of key factors involved in dosage compensation, germline homeostasis and the establishment of female morphology and behaviour. Functional Sxl protein is only synthesized in female flies. Its expression is established in the pre-cellular, female embryo by an X-chromosome counting mechanism and maintained by a positive feedback loop with Sxl controlling alternative splicing of its own transcript. In male flies this feedback loop is not activated, keeping Sxl expression in the ‘off’ state. But what protects males against accidental triggering of the self-sustaining feedback loop and Sxl protein production snowballing out of control?  Here we identify Sister of sex lethal (Ssx) as a protein that antagonizes Sxl in autoregulatory splicing by competition for the same RNA elements. Male flies mutant for ssx exhibit a low level of productive Sxl mRNA splicing and in cultured Drosophila cells, Sxl-induced changes in alternative splicing can be reverted by the expression of Ssx. In sum, this demonstrates that Ssx helps to establish a stable, male-specific gene expression pattern by protecting male flies against triggering Sxl expression.

overall_design: Identification of Drosophila Sister of Sex-lethal (Ssx) bound RNAs

first: Rebecca

last: Moschall

first: Oliver

last: Rossbach

first: Lars

last: Kullmann

first: Norbert

last: Eichner

first: Daniela

last: Strauss

first: Nicholas

last: Strieder

first: Gunter

last: Meister

first: Michael

last: Krahn

first: Jan

last: Medenbach


title: Flipping the switch on Sex-lethal expression: Sister of Sex-lethal antagonizes Sxl-dependent alternative splicing to maintain a male-specific gene expression pattern in Drosophila (iCLIP)

overall_design: Examination of Drosophila Sister of Sex-lethal (Ssx) RNA binding sites


title: Impact of depeltion of CG5694/ova on transcription in Drosophila ovaries [miRNA- and RNA-seq]

status: Public on Jan 14 2019

first: huanwei

last: huang

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

institute: NIBS

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose:  To analysis Ova impact on transcription in Drosophila ovaries by mRNA-seq and small RNA-seq
Methods: mRNA-seq and small RNA-seq of RNA extracted from Drosophila ovaries
Results: Ova has no obvious impact on protein coding genes expression or piRNA biogenesis.

overall_design:
Isolation of total mRNA  from w1118(Ctrl) and germline-specific nosGAL4 driven ova RNAi ovaries, followed by deep sequencing analysis. Purification of total RNA from w1118(Ctrl) and germline-specific nosGAL4 driven ova RNAi ovaries using PEG8000 protocol.
We extracted the small RNA according to proper size ( Seperation of 18-30 nt small RNA according to appropriate RNA markers), followed deep sequencing. We normalized the total reads number of small RNA from w1118(ctrl) and ova RNAi samples. After filtering the tRNA,  snRNA, and miRNA, we got the small RNAs mapping to the repeat regions in Drosophila genome. For wild-type, it is usually a small peak at 21 nt representing endo-siRNAs and the rest peaks at 25 nt represented piRNAs. As it remains essentially unchanged in both w1118 and ova RNAi samples for both small RNA size distribution and abandunce (data provided in the smallRNA.txt), we conclude that Ova is not required for piRNA biogenesis.

first: Fu

last: Yang

first: Rongwen

last: Xi


title: Analysis of gene expression profiles from alloreactive TCR-Tg CD8 T cells during activation and induction of tolerance

city: Worcester

first: Dr Yvonne

last: Edwards

state: MA

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary: RNA-seq was used to evaluate transcriptional changes in alloreactive TCR-Tg CD8 T cells during activation and tolerance induction. CBA mice were exposed to a low dose whole body irradiation and then injected with bone marrow from TCR-Tg KB5 mice to generate synchimeric mice. The KB5 TCR recognizes alloantigens from H2b MHC molecules, specifically Kb, that are expressed by C57BL/6 mice. The injection of bone marrow from KB5 mice into CBA mice enables the development of small and traceable population of TCR-Tg KB5 CD8 T cells. A clonotypic antibody specific for the KB5 TCR allows these cells to be monitored and sorted from the periphery of synchimeric mice by flow cytometry. KB5 CD8 T cells were purified by sorting cells from synchimeric mice under the following conditions: 1) not exposed to alloantigens and in a naïve state, 2) exposed to H2b antigens from C57BL/6 mice to activate the KB5 CD8 T cells, 3) exposed to H2b antigens in the presence of anti-CD154 that blocks costimulatory signals and induces transplantation tolerance, or 4) treated with alloantigens, anti-CD154 and LPS, that induces an inflammatory response and abrogates the induction of tolerance. KB5 CD8 T cells were FACS purified to a level of greater than 95%, RNA was recovered from the purified cells and RNA-seq was performed on triplicate samples from 3 independent experiments. Overall, the analyses revealed expression changes for a number of genes that regulate immune responses and inflammation, cell proliferation and immune cell homing.

overall_design: Determine the changes in gene expression profiles that are induced during constimulation blockade.

last: Brehm

first: Sonal

last: Jangalwe

first: Roger

last: Davis

first: Norman

last: Kennedy


title: Genome-wide analysis of RNA Pol II CTD modifications in resonse to lysine deacetylase inhibition

status: Public on Jan 12 2019

city: San Francisco

first: Melanie

last: Ott

state: CA

address: 1650 Owens Street, 5th Floor

department: Virology and Immunology

institute: Gladstone Institutes

summary: To investigate the role of RNA Pol II CTD acetylation we performed comprehensive deacetylase inhibition using common small-molecule inhibitors and performed ChIP-seq from mouse cells using antibodies against RNA Polymerase II CTD modifications: (8WG16, unmodified heptads; K7ac, acetylated heptads; 4H8, S5-phosphorylated heptads). In addition, we tested the effect of knockdown of RPRD1B, a key transcription regulator that recruits RPAP2, a CTD S5-phosphatase.

overall_design: Examination of RNA Pol II CTD modifications in NIH3T3 cells in response to lysine-deacetylase inhibition across multiple biological replicates and conditions.

first: Ibraheem

last: Ali


title: miR-93-5p is a bona fide Oncodriver Targeting both Classical and Epigenetic Tumor Suppressive Pathways in Liver Cancer

city: Shanghai

first: Ke

middle: Ai

last: Wu

state: Shanghai

address: 138 Yixueyuan Road

department: Liver Cancer Institute

institute: Zhonghai Hospital

summary:
Purpose: The goals of this study are to compare the transcriptome profiling among LEPC-Control, LEPC-Biotin-miR-93-5p and LEPC-Biotin-miR-93-5p-Muttion group to elevate the enrichment mRNA by Biotin-miR-93-5p in LEPC cells.
Methods: LEPC-Control, LEPC-miR-93-5p and LEPC-miR-93-5p-MDX cells mRNA profiles were generated by deep sequencing, in triplicate, using Illumina Hiseq2500/Miseq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Results: we set the increase by ≥ 4 fold and transcripts at an FPKM ≥1 in LEPC cells as significance. By stepwise analysis, we identifies 615 high confident miR-93-5p-targted mature mRNA that is selectively enriched by biotin-miR-93-5p, but not biotin-miR-93-5p mutant, the miR-93-5p targetome we identified by HITS-CLSBP has 97.4% overlap with online predicted miR-93-5p mRNA targets.
Conclusions: Overexpression of miR-93-5p instigates the malignant transformation of LEPC by regulating multiple cancer-related pathways.

overall_design: LEPC-Control, biotin-LEPC-miR-93-5p and LEPC-miR-93-5p-Mutation group mRNA profiles and miRNA interacting mRNA profiles were generated by deep sequencing, using Illumina Hiseq2500; H3K4me3, H3K27me3 and H3K9me3 ChIP-seqs were did in scr and miR-93-5p overexpressed LEPC cell lines.

first: Jia

last: Fan

first: Yujiang

last: Shi


title: A gene expression study of the developing human eye

city: Cambridge

first: Aurora

last: Gomez-Duran

state: Cambridge

address: Welcome Trust/MRC Building

department: Department of Clinical Neurosciences

institute: Cambridge University

summary: There is a vast range of tools with which to study the cells and tissues of the human body, however the scarcity of human embryonic material as a resource for direct study means that there is still limited data on the specific expression patterns which exist during human development. While embryonic studies are common place in other mammalian organisms and these have contributed greatly to our knowledge, characterising the events which occur during human development specifically is crucial in order to extrapolate the differences which exist between humans and other organisms and understand the human situation more completely. Establishing and maintaining collections of human developmental tissue for direct study requires significant time and resources, and is not a viable option for all. For this reason the creation of an atlas defining the key events which occur during human eye development would be of great value to the field. Through the Human Developmental Biology Resource we have collected human developmental eye tissue from post conception week 4 to 19 and performed gene expression studies using RNA sequencing. This study begins to reveal the spatiotemporal gene expression patterns which occur during normal human eye ontogenesis and represents a benchmark for comparison with development, disease and cellular differentiation studies.

overall_design: 32 samples, which include 10 embryonic, 19 foetal and 3 adult samples

first: Majlinda

last: Lako

first: Carla

last: Mellough

first: Joseph

last: Collin

first: Roman

last: Bauer

first: Jannetta

last: Steyn


title: Knockdown of Brd4 or SEC affects the HMBA-induced global Pol II pausing release

city: Xiamen

first: Min

last: Liu

state: Fujian

address: Rm.214, Bldg. Chaoyang Huang, Xiamen University-Xiang'an Campus

department: School of Life Sciences

institute: Xiamen University

summary: To test whether Brd4 and SEC co-regulate the release of promoter-proximally paused Pol II, we performed Pol II ChIP-Seq to analyze the effect of depletion of Brd4 or SEC on HMBA-induced pause release in HCT116 cells.

overall_design: Total 6 ChIP-seq samples were sequenced. Samples with indicated shRNA(s) infection in HCT116 cells were treated with solvent or 10 mM HMBA for 2hr. Signal from input sample was considered as the background signal to be substracted from all ChIP-seq samples.The number of ChIP-seq reads from each ChIP-seq sample were normalized by the concentration of input DNA and then calculated Pol II pause ratio (TR).

first: Bin

last: Yu


title: Triggering of NOD2 receptor converts inflammatory Ly6Chigh into Ly6Clow monocytes with patrolling properties.

city: Montréal

first: Tarik

last: Moroy

state: Québec

address: 110 Avenue des Pins

country: Canada

institute: Institut de recherches cliniques de Montréal (IRCM)

summary: In the present study, we demonstrate that NOD2 receptor triggering by muramyl dipeptide converts blood inflammatory Ly6Chigh monocytes into patrolling Ly6Clow monocytes. Muramyl dipeptide administration to Nr4a1-/- mice, which lack Ly6Clow monocytes, and to Ly6Clow-depleted mice leads to the emergence of blood patrolling monocytes expressing phenotypic profile of typical Ly6Clow monocytes, including high expression of CX3CR1 and LFA1. Furthermore using intravital microscopy in live animal models of inflammatory diseases, we observed that converted Ly6Chigh monocytes are capable of patrolling the endothelium of blood vessels and their presence contributes to reduce the inflammatory response following muramyl dipeptide injection.

overall_design: We study the effects of NOD2 triggering by muramyldipeptide on the monocytes subtypes in C57Bl/6, NR4A1-/- and NOD2-/- mice.

first: Anne-Julie

last: Lessard

first: Manon

last: Lebel

first: Benoit

last: Egarnes

first: Paul

last: Préfontaine

first: Peter

last: Thériault

first: Arnaud

last: Droit

first: Alexandre

last: Brunet

first: Serge

last: Rivest

first: Jean

last: Gosselin


title: A forward genetic screen for modifiers of transgene silencing in the mouse identifies Inhibitor of Growth Family Member 5 (Ing5)

city: Adelaide

first: Luke

middle: Thomas

last: Isbel

state: South Australia

address: 4 North Terrace, AHMS, Lvl 9

country: Australia

institute: SAiGENCI

summary: Here we report the identification of a mutant allele of the Ing5 gene, also known as Inhibitor of Growth Family Member 5 and a member of the MOZ/MORF histone acetyltransferase complex. The mutation likely alters functionality of the Ing5 protein by inhibiting its ability to bind to its histone substrate, H3K4me3. We find that Ing5 acts as a suppressor of a multi-copy transgene reporter suggesting a complex role for Ing5 in regulating gene expression and show that Ing5 is required for normal embryonic development.

overall_design: Investigating the result of heterozygosity of an Ing5 mutation using RNA sequencing, in mouse liver.

first: Hanada

last: Ghazala

first: Harald

last: Oey

first: Brian

last: Smith

first: Alex

last: Spurling

first: Emma

last: Whitelaw

first: Lucia

last: Daxinger


title: Gene expression in melanoma cells following treatment with IFN-beta

status: Public on Jan 08 2019

city: Minato-ku

first: Yoshinori

last: Watanabe

state: Tokyo

address: 3-19-18, Nishi-shimbashi

country: Japan

institute: Jikei Hospital

summary: To further determine the candidate genes which expressed in four melanoma cells and melanocyte after treatment with IFN-β, total RNA was extracted from melanoma cells, which have different sensitivities to IFN-β,  and melanocyte after treatment with or without IFN-β at a concentration of 1,000 IU/ml for 48 h. For expression profiling, oligonucleotide microarray analysis was performed at Hokkaido System Science (Sapporo, Japan) using an Agilent Human Genomic microarray 8 × 60 K version 2.0 (Agilent Technologies, Santa Clara, CA). Then, we focused on two candidate genes, CXCL-10 and IL-24,  which are associated with the sensistibity of melanoma cells to IFN-β. We examined whether CXCL10 and IL-24 directly or indirectly cause sensitivitiy of melanoma to IFN-β.

overall_design: total RNA was extracted from melanoma cells (A375, RPMI-7951, SK-MEL-5, and SK-MEL-1) and primary melanocyte after treatment with or without IFN-β at a concentration of 1,000 IU/ml for 48 h.

first: Yoshimasa

last: Nobeyama


title: NOVA2 cTag-CLIP and Nova2-cKO RNA-seq in mouse brain

status: Public on Jan 09 2019

city: New York

first: Yuhki

last: Saito

state: NY

address: 1230 York avenue

institute: The Rockefeller University


title: NOVA2 cTag-CLIP

summary: Mouse cortex or cerebellum samples from E18.5 or P28 Nova2-cTag mouse crossed with a series of Cre driver mice were subjected to Nova2 cTag-CLIP to generate functional NOVA2-RNA maps from single neuronal populations in the mouse brain.

overall_design: Tissues were UV-irradiated and subjected to NOVA2 cTag-CLIP with mouse anti-GFP (Heiman et al., 2014), clones 19F7 and 19C8 (detailed desription in accompanying paper).

first: Robert

last: Darnell


title: Quantitative Analysis of negative control and overexpression-TRIB1 in PC3 and DU145 Transcriptomes

city: Guangzhou

first: Yifeng

last: Luo

state: Guangdong

address: 58 Zhongshan 2nd Road

department: Institute of Respiratory Diseases of Sun Yat-sen University

institute: The First Affiliated Hospital of Sun Yat-sen University

summary: The goals of this study is to find effect of overexpression-TRIB1 to prostate cancer cell (PC3 and DU145).

overall_design: Overexpressing-TRIB1 DU145 and PC3 cell lines were constructed. Detection of transcriptional changes in 2 cell lines.Repeat 2 times for each cell.Differently expressed genes (DEGs) were identified by cutoff with Ilog2(FoldChange)I> 1 and padj (Corrected Pvalue) < 0.05. KEGG\GO and PPIs analysis should be done.

first: Zezhen

last: Liu

first: Weide

last: Zhong


title: RNA-seq (Nova2-cKO, Nova2-KO, Nova2.Ptbp2-dKO)

summary: We sequenced RNA from adult mouse spinal cord and from cell sorted Nova2-cKO neurons (crossed with Emx1-Cre, Gad2-Cre, Pcp2-Cre driver mice) and from Nova2.Ptbp2-dKO to compare gene expression level, and alternative splicing events.

overall_design: Neuronal cell-type specific mRNA profiles by deep sequencing using Illumina Hiseq2500.


title: RNA-Seq analysis of skin of adult Mantella betsileo

status: Public on Jan 07 2019

city: Storrs

first: John

middle: Henri

last: Malone

state: CT

address: 181 Auditorum Road, Unit 3197

department: Institute of Systems Genomics and Department of Molecular and Cell Biology

institute: University of Connecticut

summary: RNA-Seq data from polyA+ selected RNA from the skin of Mantella betsileo.

overall_design: PolyA+ RNA was enriched from total RNA extracted from pooled dorsal and ventral skin samples harvested from five adult Mantella betsileo frogs that were bred in captivity. Sex of frogs was not determined.

first: Megan

middle: L

last: Civitello

first: Rob

last: Denton

middle: H

first: Michael

last: Zasloff


title: TL1A signaling enhances the differentiation of TH9 cells and TH9-driven mucosal pathologies via BATF and BATF3 signaling pathways

city: Los Angeles

first: Jie

last: Tang

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

summary: The TNF family member TL1A (TNFSF15) co-stimulates several T helper subsets and promotes T cell-dependent models of inflammatory diseases, including inflammatory bowel diseases (IBD) and allergic lung disease. TL1A polymorphisms confer susceptibility to IBD and have been associated with disease severity. In this study, we identified TL1A as a strong inducer of TH9 cell differentiation in vitro. Mechanistically, TL1A induced NF-B signaling and down-stream STAT6 activation and facilitated cooperative binding of BATF, BATF3, and IRF4 to the Il9 promoter. In vivo, utilizing an adoptive T cell transfer model we demonstrated that TL1A promoted IL-9-dependent, TH9 cell-induced intestinal and lung inflammation and blocking anti-IL-9 antibodies attenuated TL1A-driven mucosal inflammation. Our results demonstrate that TL1A promotes TH9 cell differentiation and function and define a role for IL-9 in TL1A-induced mucosal inflammation.

overall_design: 4 samples (2x2)

first: Masato

last: Tsuda

first: Vincent

last: Funari

first: Kathrin

middle: S

last: Michelsen


title: The dual function of the tumor suppressor Rbf in flight muscle development in DrosophilaThe dual function of the tumor suppressor Rbf in flight muscle development in Drosophila

status: Public on Jan 04 2019

city: Chicago

first: Maria

middle: Paula

last: Zappia

state: IL

address: 900 S Ashland Ave

department: Biochemistry and Molecular Genetics

institute: University of Illinos at Chicago

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

overall_design: Refer to individual Series


title: Global gene regulation in tomato plant (Solanum lycopersicum) responding to vector (Bactericera cockerelli) feeding and pathogen (‘Candidatus Liberibacter solanacearum’) infection

city: College Station

first: Ordom

middle: Brian

last: Huot

state: Texas

address: 2475 Texas A&M University

department: Entomology

institute: Texas A&M University

summary: ‘Candidatus Liberibacter solanacearum’ (Lso) has emerged as a major pathogen of crops worldwide. This bacterial pathogen is transmitted by Bactericera cockerelli, tomato psyllid, to solanaceous crops. In this study, the transcriptome profiles of Solanum lycopersicum exposed to B. cockerelli infestation and to Lso infection were evaluated at one, two and four weeks following colonization and/or infection. Plant transcriptional response to Lso-negative B. cockerelli was different than plant responses to Lso-positive B. cockerelli. The comparative transcriptomes of plant responses to Lso-negative B. cockerelli revealed the up-regulation of genes associated with plant defenses regardless of the time-point. In contrast, the plant general responses to Lso-positive B. cockerelli and Lso-infection were temporally different. Infected plants down-regulated defense genes at week one while delayed the up-regulation of the defense genes to week two and four, time points in which early signs of disease development were also detected in the transcriptional response. For example, infected plants up-regulated carbohydrate metabolism genes which could be linked to the disruption of sugar distribution usually associated with Lso infection. Also, infected plants down-regulated photosynthesis genes potentially resulting in plant chlorosis, another symptom associated with Lso infection. Overall, this study highlights that S. lycopersicum plants induced different sets of genes in response to different stages of B. cockerelli infestation and Lso infection. This is the first transcriptome study of tomato responses to B. cockerelli and Lso, a first step in the direction of finding plant defense genes to enhance plant resistance.

overall_design: Examination of plant transcriptional response to Lso-positive and Lso-negative Bactericera cockerelli over a course of four weeks

first: Julien

last: Levy

first: Cecilia

last: Tamborindeguy


title: Differential gene expression analysis of drought responsive sense and antisense genes in Populus

status: Public on Jan 06 2019

city: Houghton

first: Yinan

last: Yuan

state: MICHIGAN

address: UJ Noblet 100B, 1400 townsend drive

department: School of Forest Resources and Environmental Science

institute: Michigan Technological University

summary: In this study we employ a strand-specific RNA-seq appoach and stranded gene expression analysis tools to identify drought responsive antisense gene loci and sense-antisense gene pairs in Populus. we generated and sequenced 28 strand-specific cDNA libraries derived from either leaf or root tissues of Populus trichocarpa plants associaed with both short-term drought (24 hours of water stress of 40% of field capacity) and long-term drought ( 25 days of water stress of 40% of field capacity) . We mapped over 71 billion nucleotides to Populus genome. Our data demonstrates that with the current sequence depth ~ 19 % of Populus genome undergoes antisense transcription subjected to drought regulation. All in all we have identified that in root tissues 524 differentially expressed antisense genes and 247 drought-responsive SA gene pairs which are significantly regulated by drought (padj <0.05). Taken all data from both drought treatments, we have identified 1185 unique drought-responsive antisense gene loci and 606 drought-responsive SA gene pairs (padj <0.05).

overall_design: strand-specific RNA libraies are constructed from apex and mature leaves of plants invoved in short-term drought or apex, young leaves, mature leaves and root tissue of Populus plants involved in long-term drought.  RNA libraries are sequenced with illumina Hiseq 2500.


title: MicroRNA 130b-3p Regulates DENND1A Variant 2 Expression and Androgen Biosynthesis in Polycystic Ovary Syndrome (PCOS) Theca Cells

city: Hershey

first: Jan

last: McAllister

state: Pennsylvania

address: 500 University Dr

department: Pathology

institute: Penn State College of Medicine

summary: miR deep-sequencing using total RNA was collected from 4th passage theca cells from individual cultures of normal or PCOS theca cells treated with and without 20 micro forskolin for 16h

overall_design: miR deep-sequencing comparison between normal and PCOS theca cells

first: Jerome

middle: F

last: Strauss III


title: Transcriptional profile of larval notum and flight muscle in Rbf knockdown and WT Drosophila flies

summary: Our study focuses on understanding how Rbf impacts the formation of flight muscles in Drosophila. We analyzed by RNA-seq the transcriptional changes dependent on Rbf in proliferating adult muscle precursors and in mature flight muscles at two different stages of Drosophila development

overall_design: Total RNA was extracted at two different developmental stages: notum tissues from third instar larval wing discs, which contains adult muscle precursors, and the flight muscles of pharate flies. Total RNA libraries were made and followed by sequencing. The following two genotypes were compared at these two developmental stages: WT and Rbf-conditional knockdown using Mef2-Gal4 driver and UAS-Rbf-RNAi. Three replicates were done for notum tissue and two replicates for flight muscles

middle: P

first: Maxim

last: Frolov


title: An alternative CTCF isoform antagonizes canonical CTCF occupancy and changes chromatin architecture to promote apoptosis

city: Boston

first: Dipanjan

last: Chowdhury

address: 4 Blackfan Circle

institute: Dana-Farber Cancer Institute

summary: CTCF plays key roles in gene regulation, chromatin insulation, imprinting, X chromosome inactivation and organizing the higher-order chromatin architecture of mammalian genomes. Previous studies have mainly focused on the roles of the canonical CTCF isoform. Here, we explore the functions of an alternatively spliced human CTCF isoform in which exons 3 and 4 are skipped, producing a shorter isoform (CTCF-s). Functionally, we find that CTCF-s competes with the genome binding of canonical CTCF and binds a similar DNA sequence. CTCF-s binding disrupts CTCF/cohesin binding, alters CTCF-mediated chromatin looping and promotes the activation of IFI6 that leads to apoptosis. This effect is caused by an abnormal long-range interaction at the IFI6 enhancer and promoter. Taken together, this study reveals a non-canonical function for CTCF-s that antagonizes the genomic binding of canonical CTCF and cohesin, and that modulates chromatin looping and causes apoptosis by stimulating IFI6 expression.

overall_design: ChIP-seq of CTCF and CTCF-s and RNA-seq of Hela S3 cells with overexpression or knockdown of CTCF and CTCF-s. Also included are HiChIP-seq of control or CTCF-s overexpressing Hela S3 cells.

first: Kaimeng

last: Huang

first: Jiao

last: Li

first: Gongcheng

last: Hu

first: Hongjie

last: Yao


title: Breakdown of the Photosynthetic Apparatus in Chromochloris zofingiensis

status: Public on Jan 03 2019

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

summary: RNA-Seq of Chromochloris zofingiensis following the transition from photoautotrophic growth to heterotrophic growth on glucose.

overall_design:
Cultures of Chromochloris zofingiensis were grown diurnally (16 h light, 8 h dark) in 100 μmol photons m^−2 s^−1 medium light (ML)
in glucose-free media (glc-).  At t = 0, cultures were transferred to media supplemented with 10 mM glucose (glc+).
Samples were collected in quadruplicate at 0, 0.5, 1, 3, 6, and 12 h for glc- cultures and at 0.5, 1, 3, 6, and 12 h for glc+ cultures.
All samples were collected during the 16hr daylight period.

first: Melissa

last: Roth

middle: D


title: Biogenesis and Breakdown of the Photosynthetic Apparatus in Chromochloris zofingiensis


title: Analysis of RNA expression profiles identifies dysregulated vesicle trafficking pathways in Creutzfeldt-Jakob Disease

city: Bologna

first: Piero

last: Parchi

state: BO

address: Ospedale Bellaria, Via Altura 1/8

department: DIMES

institute: University of Bologna

summary: Functional genomics applied to the study of RNA expression profiles identified several abnormal molecular processes in experimental prion disease. However, only a few similar studies have been carried out to date in a naturally occurring human disease. To better characterize the transcriptional cascades associated with sporadic Creutzfeldt-Jakob disease (sCJD), the most common human prion disease, we investigated the global gene expression profile in the frontal cortices of 10 patients with sCJD and 10 non-neurological controls by microarray analysis. The comparison identified 333 highly differentially expressed genes (hDEGs) in sCJD. Functional enrichment Gene Ontology analysis revealed that hDEGs were mainly associated with synaptic transmission, including GABA (q-value=0.049) and glutamate (q-value=0.005) signalling, and the immune/inflammatory response. Furthermore, the analysis of cellular components performed on hDEGs showed a compromised regulation of vesicle-mediated transport with mainly up-regulated genes related to the endosome (q-value=0.01), lysosome (q-value=0.04), and extracellular exosome (q-value<0.01). A targeted analysis of the retromer core component VPS35 (Vacuolar protein sorting-associated protein 35) showed a down-regulation of its gene expression (p=0.006) and protein levels (p=0.002). Taken together these results confirm and expand previous microarray expression profile in CJD. Most significantly, they also demonstrate the involvement of the endosomal-lysosomal system. Since the latter is a common pathogenic pathway linking together diseases such as Alzheimer’s and Parkinson’s, it could be the focus of future studies aimed at identifying new therapeutic targets in neurodegenerative diseases.

overall_design: The study was approved by the Local Ethics Committee. Grey matter tissue samples were collected from the frontal cortex (middle frontal gyrus) of 10 sCJD brains (5 each from the two commonest disease subtypes, MM1 and VV2) and 10 controls (CTRL) without any history of neurological or psychiatric illnesses (CTRL). Sporadic CJD subjects and CTRL were matched for age (sCJD=66.9±8.2; CTRL=65.7±10.7) and sex (% of males, sCJD=40%; CTRL=50%). Tissue was obtained post-mortem according to a standard protocol. Tissue from the right hemisphere was rapidly frozen at -80° C while the left hemisphere was fixed in 10% formalin and processed by paraffin wax embedding. Total RNA was extracted from the frontal cortex of snap-frozen brain according to an optimized protocol [Durrenberger PF et al., 2012] using the RNeasy tissue lipid kit (Qiagen, Mannheim, Germany), and stored at -80C° until use. RNA concentration and purity were assessed by spectrophotometry (NanoDrop ND100, Thermo Fisher Scientific, Waltham, MA, USA). Total RNA quality was tested through capillary electrophoresis (Bioanalyzer 2100, Agilent Technologies, Santa Clara, CA, USA) and RNA was considered suitable when the integrity quality number (RIN) scored above eight. The RNA expression profile was analyzed using the Illumina whole-genome HumanRef8 v2 BeadChip (Illumina, California, USA). Briefly, RNA samples were processed for array analysis using the Illumina TotalPrepTM96 RNA Amplification Kit (Ambion, Inc., Austin, Texas, USA). Double-stranded complementary DNA (cDNA) was synthesized from 0.5 µg of total RNA. Using cDNA as template, complementary RNA was synthesized and labelled with biotin and then applied to the arrays using the whole-genome gene expression direct hybridization assay system (Illumina). The BeadChips were scanned with the Illumina BeadArray Reader. The data were extracted and processed by applying a quantile normalization using the Illumina Beadstudio 3.2 software (Illumina).

first: A

last: Bartoletti-Stella

first: P

last: Corrado

first: N

last: Mometto

first: S

last: Baiardi

first: PF

last: Durrenberger

first: T

last: Arzberger

first: R

last: Reynold

first: H

last: Kretzschmar

last: Capellari


title: Total comparative RNA sequencing of WT vs. ccr4-1 knockout Plasmodium yoelii

status: Public on Jan 02 2019

city: University Park

first: Scott

middle: E.

last: Lindner

address: W224 Millennium Science Complex

department: Biochemistry and Molecular Biology

institute: Penn State University

summary: The transmission of the malaria parasite between mosquitoes and mammals requires translational repression to ensure that only the proper proteins are expressed at the right time, while still allowing the parasite to prepare the mRNAs it will need for the next developmental stage. With relatively few known specific transcription factors (ApiAP2 family) that may specifically initiate gene transcription, Plasmodium parasites also regulate the stability and turnover of transcripts to provide more comprehensive gene regulation. The CAF1/CCR4/NOT complex has been shown in model organisms to be important for not only mRNA degradation, but also translational control through its deadenylases CAF1 and CCR4. However, few proteins that impose translational repression in Plasmodium sexual stages are known, and those that are characterized primarily affect female gametocytes. Therefore, we have characterized two deadenylases and have uncovered their roles in transmission. We have identified and characterized CCR4-1, which we show plays a role in activating male gametocytes, stabilizing transcripts in gametocytes, and regulating host-to-vector transmission. We find that when ccr4-1 is genetically deleted, there is a loss in the coordination of male gametocyte activation and a reduction in the ability of the parasite to productively infect the mosquito, which is independent of its effect upon male activation. Comparative RNA-seq shows that the deletion of ccr4-1 affects many transcripts that are translationally repressed in females, are related to male gamete function, and/or are important for early mosquito stage development. In contrast, we found that genetic deletion of the major deadenylase Caf1 is lethal. However, we observed that expression of only the N-terminal Caf1 domain is permissive, yet prevents proper complex assembly and phenocopies the ccr4-1 deletion. We therefore conclude that the general and transmission-specialized deadenylases of the CAF1/CCR4/NOT complex play critical and intertwined roles in parasite growth and transmission.

overall_design: Comparison of 6 replicates of wild type (PY17XNL) parasites with 4 replicates of ccr4-1 knockout parasites using RNA-sequencing.

first: Kevin

middle: J

last: Hart

first: Jenna

last: Oberstaller

first: Michael

last: Walker

first: Mark

last: Kennedy

first: Ian

last: Padykula

first: John

last: Adams

middle: E

first: Allen

last: Minns


title: Tuning water use efficiency and drought tolerance in wheat using ABA receptors

city: Yokohama

first: Masanori

last: Okamoto

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

institute: RIKEN

summary: Water availability is a key determinant of terrestrial plant productivity. Many climate models predict that water stress will increasingly challenge agricultural yields and exacerbate projected food deficits. To ensure food security and increase agricultural efficiency, crop water productivity must be increased. Research over past decades has established that the phytohormone abscisic acid (ABA) is a central regulator of water use and directly regulates stomatal opening and transpiration. In this study, we investigated whether the water productivity of wheat could be improved by increasing its ABA sensitivity. We show that overexpression of a wheat ABA receptor increases wheat ABA sensitivity, which significantly lowers a plant’s lifetime water consumption. Physiological analyses demonstrated that this water-saving trait is a consequence of reduced transpiration and a concomitant increase in photosynthetic activity, which together boost grain production per liter of water and protect productivity during water deficit. Our findings provide a general strategy for increasing water productivity that should be applicable to other crops because of the high conservation of the ABA signaling pathway.

overall_design: One representative transgenic line (TaPYLox) and its background non-transgenic cultivar (Null; cv. Fielder) were subjected to the analysis. The transcriptome was analyzed using three biological replicates of RNA samples from leaves of 40-day-old plants after exposure to one of three stress conditions. The three treatments were as follows: WWC, corresponding to normal conditions (soil water potential [SWP] > -110 kPa); ABA, namely, incubation for 24 h after spraying with 25 μM ABA; and drought, involving incubation for 24 h after withholding water to maintain SWP < -390 kPa. Each total RNA was isolated using the RNeasy® Plant Mini Kit (Qiagen) and evaluated for quality and quantity with an Agilent 2100 Bioanalyzer (Agilent Technologies) and the Agilent RNA 6000 Nano Kit (Agilent Technologies). Library preparation was performed according to the TruSeq RNA Sample Preparation v2 guide (Illumina). Sequencing on an Illumina HiSeq® 2500 system generated an average of 91.3 M paired-end reads (2 × 101 nt) per library.

first: Ryosuke

last: Mega

first: Fumitaka

last: Abe

first: June-Sik

last: Kim

first: Yuuri

last: Tsubo

first: Keisuke

last: Tanaka

first: Hisato

last: Kobayashi

first: Yoichi

last: Sakata

first: Kosuke

last: Hanada

first: Hisashi

last: Tsujimoto

first: Jun

last: Kikuchi

first: Sean

middle: R

last: Cutler


title: Biogenesis of the Photosynthetic Apparatus in Chromochloris zofingiensis

last: Gallaher

summary: RNA-Seq of Chromochloris zofingiensis following the transition from heterotrophic growth on glucose to photoautotrophic growth.

overall_design:
Cultures of Chromochloris zofingiensis were grown diurnally (16 h light, 8 h dark) in 100 μmol photons m^−2 s^−1 medium light (ML)
for 72 h in media supplemented with 20 mM glucose (glc+).  At t = 0, cultures were transferred to glucose-free media (glc-).
Samples were collected in quadruplicate at 0, 0.5, 1, 3, 6, and 12 h for glc+ cultures and at 0.5, 1, 3, 6, and 12 h for glc- cultures.
All samples were collected during the 16hr daylight period.

first: Melissa

last: Roth


title: Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the mouse brain

city: Beijing

first: Qin

last: Ma

address: NO.1 Beichen West Road, Chaoyang District

department: Chinese Academy of Sciences

institute: Beijing Institute of Genomics

summary: The study provides new insights into how 5mC/5hmC vary across different part of brain, and the association and distinct roles of 5mC/5hmC in regulating tissue identity and specification.

overall_design: Examination of hydroxymethylomes of mouse cortex, olfactory bulb and cerebellum tissues,as well as methylomes and allele-specific transcriptomes of the same tissues


title: Reversing Abnormal Neural Development by Inhibiting OLIG2 in Down Syndrome Human iPSC Brain Organoids and Neuronal Mouse Chimeras

status: Public on Jan 01 2019

city: Houston

first: Ying

last: Liu

address: 1825 Pressler

institute: UTHealth

summary: Down syndrome (DS), caused by triplication of human chromosome 21 (HSA21), is the most common genetic origin of intellectual disability. Despite the limited success of current pharmacological interventions, little has been achieved to reverse the abnormal brain developmental in DS. Here, using human induced pluripotent stem cell (hiPSC)-based brain organoid and in vivo human neuronal chimeric mouse brain models, we demonstrate that the HSA21 genes OLIG1 and OLIG2 exhibit distinct temporal expression patterns during neuronal differentiation. The population of OLIG2-expressing ventral forebrain neural progenitors is overabundant in DS, which results in excessive production of calretinin- and somatostatin-expressing GABAergic interneurons and causes impaired recognition memory in DS chimeric mice. Furthermore, we find that overexpression of OLIG2 in DS alters the expression of GABAergic neuron lineage-determining transcription factors such as DLX1 and LHX8. We further show that OLIG2 can directly bind to promoter regions of DLX1 and LHX8 to increase their expression, leading to lineage specification of interneurons. Importantly, knockdown of OLIG2 largely reverses the abnormal global gene expression profile of early stage DS neural progenitors, reduces inhibitory neuronal population in DS organoids and chimeric mouse brains, as well as improves behavioral performance of DS chimeric mice. Therefore, OLIG2 potentially is a target for developing prenatal personalized therapeutics for intellectual disability in subjects with DS

overall_design: Organoids (5-week old) generated from hiPSC lines derived from two DS patients (patient DS1 and DS3 and corresponding cell lines include DS1, control1, isogenic Tri-DS3 and Di-DS3, Tri-DS3+ContshRNA, and Tri-DS3+OLIG2shRNA hiPSCs) were used for RNA-sequencing. For each cell line, total 40-60 organoids collected from three batches of organoid cultures were pool together for RNA extraction and sample preparation. By pooling organoids, we increased the chances of identifying genes that were commonly up- or down-regulated in the three batches of cultures, whereas on the other hand, we decreased the chances of identifying genes that had varied expression levels in the three batches of cultures.

first: Jiang

last: Peng


title: The chromatin associated proteins HP1 behave as liver specific tumour suppressors in mice

city: montpellier

first: florence

last: cammas

address: 208 rue des apothicaires

country: France

institute: ircm

summary:
Purpose : In this study we observed that inactivation of the genes encoding for the chromatin associated proteins HP1 lead to a highly increased predisposition of mice to develop tumours within liver. The purpose of this analysis was to identify and characterize genes whose expression was altered early on within livers of the HP1 mutant mice that could explain the tumorigenesis phenotype observed in very old animals.
Results : this analysis revealed that only few genes (129 for HP1αKO, 84 for HP1αβliverKO and 87 for HP1αγliverKO) displayed differential expression between control and mutant animals [with a threshold of 1.5 fold difference and an adjusted pvalue≤0.05]. Besides several genes putatively involved in tumorigenesis, we found a significant enrichment in genes encoding several members of the family of transcriptional repressors KRAB-ZFP and presented data arguing that this increased expression resulted from their own loss of repressive activity because of the loss of interaction between their corepressor TRIM28 and HP1.
Conclusions: our study represents the first demonstration that HP1 behave as tumour suppressors within liver and provide a comprehensive analysis of the underlying molecular mechanisms suggesting that HP1 main function within liver is to allow an appropriately regulated activity of the KRAB-ZFP/TRIM28/HP1 axis essential for liver homeostasis.

overall_design: RNA profile of livers from 5 week old WT, HP1aKO, HP1abKO and HP1agKO mice were generated by Illumina RNA sequencing

first: Florence

middle: M

last: Cammas

first: Celine

last: Keime

first: Bernard

last: Jost


title: Cannabinoid attenuation of intestinal inflammation in chronic simian immunodeficiency virus (SIV)-infected rhesus macaques involves differential modulation of pro-inflammatory microRNA/gene expression and T-cell activation

city: San Antonio

first: Mahesh

last: Mohan

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

summary: We profiled and characterized mRNA expression in colon of 12 chronically SIV-infected rhesus macaques (RMs) receiving vehicle (n=7) or delta-9-tetrahydrocannabinol (THC) and 4 uninfected control macaques. Further analysis identified significant downregulation of genes associated with ion transport, epithelial barrier integrity/function, protection against oxidative injury, double stranded DNA damage repair and autophagy. Similarly, mRNA expression of genes associated with interferon response, anti-microbial defense, apoptosis, oxidative DNA damage, endoplasmic reticulum stress and inflammasome signaling were markedly upregulated.

overall_design: Colon tissue was harvested from 12 chronically SIV-infected (7 VEH-SIV and 5 THC-SIV) and 4 control Indian rhesus macaques. Intact colon tissue was lysed in Qiazol solution (Qiagen Inc) for total RNA extraction. Comparisons in gene expression were made between VEH-SIV and controls, THC-SIV and controls and VEH-SIV relative to THC-SIV macaques.


title: Fbxo32 mediated gene expression program underlies EMT and metastasis

city: Mainz

first: Abhijeet

last: Pataskar

address: Ackermannweg 4

institute: Institute of Molecular Biology

summary: The epithelial-mesenchymal transition (EMT) is a process by which cells lose their cell contacts and gain migratory and invasive properties. EMT is essential for numerous developmental processes including neural tube formation, in wound healing, organ fibrosis and cancer metastasis. Despite progress, the repertoire of factors involved in global transcriptional reprogramming underlying EMT remains unknown. Here we show that FBXO32, a member of the F-box protein family, is essential for phenotypic changes hallmark of EMT. Such dependency results from FBXO32-driven transcriptional reprogramming of critical EMT genes and involved changes in their chromatin state. Furthermore, we found that CTBP1, an established regulator of EMT, requires FBXO32 ubiquitination at Lysine 63 for its nuclear retention and gene regulatory function. FBXO32 is also highly amplified in a large panel of metastatic cancers and its knockdown severely impaired metastatic properties of cancer cells in vitro and in vivo. In addition, FBXO32 is also induced during neurogenesis and is essential for neuronal migration in vivo. Together, these findings uncover FBXO32-dependent gene regulatory circuitry that underlies EMT during development and disease.

overall_design: For all siRNA mediated knockdown experiments, cells were seeded at same starting density and transfected with ON-TARGET plus SMART pool siRNAs (i.e. a mixture of 4 siRNA provided as a single reagent) (Dharmacon) every second day. For siRNA transfections, Lipofectamine RNAiMax (Invitrogen, 13778-150) was used according to the manufacturer's instructions. For experiments during TGF-β-induced EMT, TGF-β-induction performed at the same time when siRNA was added to avoid indirect effect due to loss of function of protein.

first: Sanjeeb

middle: K

last: Sahu

first: Vijay

last: Tiwari


title: Comparing the Gene expression profile between Osteoblast and Odontoblast

city: New York

first: Mo

last: Chen

state: New York

address: 630 W168th Street

institute: Columbia University

summary: Comparing differentially expressed genes between osteoblast and odontoblast, to identify the signaling controling stem cell fate

overall_design: Donor matched cells isolated from 2 weeks old 2.3kb type I collagen promoter driven EGFP transgenic mice were isolated from dental pulp and calvarial bone. The cells were isolated by enzyme digestion and sorted out by GFP signal. Total RNA was extracted for microarray analysis

first: Jian

last: Zhou

first: Jeremy

last: Mao


title: Transcriptomic Analysis between Normal and High-intake Feeding Geese Provides Insight into Adipose Deposition and Susceptibility to Fatty Liver in Migratory Birds

city: Chengdu

first: Jiwen

last: Wang

state: Sichuan

address: 211 Humin Road, Wenjiang District

department: Department of Animal Science

institute: Sichuan Agricultural University

summary: Geese have a high tolerance of massive energy intake and exhibit little pathological development. We assessed phenotypes and transcriptomes of Tianfu geese to investigate the dynamic expression network behind goose adipogenesis. Goose liver exhibited higher fat accumulation than adipose tissues during fattening. We identified differentially expressed genes that function in several important lipid metabolism pathways, immune response, regulation of cancer, and differentially expressed long noncoding RNAs that might be involved in regulation of these pathways. We found that genes like BGE1 and SCD, which have key roles in glycolysis and synthesis of fatty acids, had higher fold change in liver than in adipose tissue. we suppose that the evolutionary split from mammals in adipogenesis is a result of adaptive evolution to long-distance migration.

overall_design: Twenty 126-day-old Tianfu meat geese were randomly assigned to two group (N=10). One group was designed to simulate the high-intake feeding, while the other group was normally fed. The feeding trial was 19 days in total. The high-intake feeding group was given increased amount of dietary across the feeding process. The weight for each goose was recorded every 3 days during the feeding process, and all geese were sacrificed at the end of 19 days. Tissues including liver, abdominal adipose, subcutaneous adipose, heart, breast muscle, leg muscle, duodenum, gizzard, gadular stomach, spleen and bursa of fabricius. Weight for each tissue was recorded and liver, abdonimal adipose as well as subcutaneous adipose were performed red oil staining. Lipid content in liver was quantified by Soxhlet extraction. We chose 3 replicates from each tissue and treatment (in total of 18) and sent them to perform total RNA-seq and subjected the data to further analysis.

first: Guosong

first: Long

last: Jin

first: Mingzhou

last: Li


title: Host Gene Expression in Nasal and Blood Samples for the Diagnosis of Viral Respiratory Infection

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: Assessment of host gene expression is an emerging tool for the diagnosis of human infections. We compared nasal and blood samples for evaluation of the host transcriptomic response in children with acute respiratory syncytial virus (RSV), symptomatic and asymptomatic picornavirus (PV) infection, and virus-negative asymptomatic controls (Ctrls). RNA was extracted from nasal and blood samples and analyzed by microarray. Despite generally lower quality of nasal RNA, the number of genes detected in each sample type was equivalent.  Nasal gene expression signal derived mainly from epithelial cells but also included a leukocyte contribution that was higher in samples from symptomatic children. The number of genes with increased expression in virus-infected children was comparable in nasal and blood samples, while nasal samples also had large numbers of genes with decreased expression, including many genes associated with ciliary function and assembly. Compared to symptomatic children, those with asymptomatic PV had fewer genes with increased or decreased expression in both sample types. Genes with increased expression in comparisons of symptomatic children versus Ctrls included genes associated with components of innate immunity and apoptosis. Children with RSV but not PV also had increased expression of genes related to the cell cycle. Using nested leave-one-pair-out cross-validation and supervised principal components analysis, we defined sets of genes whose expression patterns accurately classified subjects, with high area-under-the-curve values in receiver operating characteristic analysis. Our results support use of nasal samples to augment pathogen-based tests to diagnose viral respiratory infection.

overall_design: RNAs were extracted from whole blood and nasal swabs from 26 subjects, including 9 symptomatic cases who were infected with picornaviruses (sPV), 5 asymptomatic cases infected with picornaviruses (asPV), 6 symptomatic cases infected with respiratory syncytial virus (RSV) (2 cases had no blood specimens available), and 6 asymptomatic cases with no virus infection.

first: Gregory

middle: A

last: Storch

first: Thomas

last: Mariani


title: Cannabinoid attenuation of intestinal inflammation in chronic SIV-infected rhesus macaques involves differential modulation of pro-inflammatory microRNA/gene expression and T-cell activation

type:
Expression profiling by array
Expression profiling by RT-PCR

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

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Refer to individual Series


title: MicroRNA profiling of colon tissue samples following chronic Delta-9-Tetrahydrocannabinol (THC) treatment to chronically SIV-infected rhesus macaques

summary: The study describes miRNA expression in colon tissue following delta 9 tetrahydrocannabinol (Δ9-THC) administration to chronically SIV-infected rhesus macaques. To identify the underlying molecular mechanisms underlying its anti-inflammatory effects, we simultaneously profiled miRNA and mRNA expression in colon of chronically simian immunodeficiency virus (SIV)-infected rhesus macaques (RMs) administered either vehicle (VEH/SIV; n=9) or Δ9- tetrahydrocannabinol (THC; THC/SIV; n=8). Relative to controls, differentially expressed miRNAs were ~2 fold higher in VEH/SIV than THC/SIV RMs. Proinflammatory miR-130a, miR-222 and miR-29b, Lipopolysaccharide-responsive miR-146b-5p and SIV-induced miR-190b were significantly upregulated in VEH/SIV RMs. Compared to VEH/SIV RMs, 10 miRNAs were significantly upregulated in THC-SIV RMs, among which miR-204 was confirmed to directly target MMP8, an extracellular matrix-degrading collagenase that was significantly downregulated in THC/SIV RMs. Moreover, THC/SIV RMs failed to upregulate proinflammatory miR-21, miR-141 and miR-222 and alpha/beta defensins, suggesting attenuated intestinal inflammation. Further, THC/SIV RMs showed higher expression of tight junction proteins (occludin, claudin-3), anti-inflammatory MUC13, keratin-8 (stress protection), PROM1 (epithelial proliferation) and anti-HIV CCL5. Trichrome mason staining detected significant collagen deposition (fibrosis) in the paracortex and B cell follicular zones of axillary lymph nodes from all VEH/SIV but none of the THC/SIV RMs, thus demonstrating the ability of THC to prevent lymph node fibrosis, a serious irreversible consequence of HIV induced chronic inflammation. Furthermore, using flow cytometry, we showed that THC suppressed intestinal T cell proliferation/activation (Ki67/HLADR) and exhaustion (PD1) and increased the percentages of anti-inflammatory CD163+ macrophages. Finally, while THC did not affect CD4+ T cell levels, it significantly reduced CD8+ T cell percentages in blood at 150 and 180 days post SIV infection. These translational findings strongly support a role for differential miRNA/gene induction and T cell activation in THC-mediated suppression of intestinal inflammation in HIV/SIV and potentially other chronic inflammatory diseases of the intestine.

overall_design: Twenty-three age- and weight-matched male Indian rhesus macaques were randomly divided into 3 groups. Group 1 (n=6) remained uninfected. Group 2 (Vehicle only; VEH/SIV, n=9) animals received twice daily intramuscular injections of vehicle and were infected intravenously with 100TCID50 of SIVmac251. Group-3 THC/SIV (n=8) animals received twice daily injections of Δ9-THC and were infected with SIV. Colon tissue was collected at necropsy, ~180 days post SIV infection. ~100 ng of total RNA was first reverse transcribed and preamplified according to the manufacturer’s recommendation. MicroRNA expression profiling was performed using TaqMan ®OpenArray® Human microRNA panels. Data analysis was performed using ExpressionSuite® software. The results from the ExpressionSuite software analysis containing five columns (well, sample, detector, task and CT values) were saved as a tab-delimited text file which was later imported and analyzed using the Omics Office StatMiner qPCR analysis software, TIBCO Spotfire, (Perkin Elmer, Waltham, MA). Omics Office StatMiner Software utilizes the comparative Cτ (ΔΔCτ) method to rapidly and accurately quantify relative gene expression across many genes and samples. miRNA expression data were normalized using the global normalization method and analyzed using the non-parametric Wilcoxon’s rank sum test. Comparisons were made between uninfected and both treatment groups (VEH/SIV and THC/SIV). To determine the effect of chronic THC treatment during SIV infection, comparisons were also made between VEH/SIV and THC/SIV.


title: Genomic occupancy profile of Rbf and Dp in flight muscles of WT Drosophila pharate

city: Chicago

first: Maria

last: Zappia

address: 900 S Ashland Ave

institute: University of Illinos at Chicago

summary: Our study focuses on understanding the genomic occupancy profile of Rbf and Dp in flight muscles of D. melanogaster. We analyzed Rbf and Dp occupancy by ChIP-seq using Rbf and Dp antibodies in dissected flight muscles of pharate flies (WT)

overall_design: ChIP with Rbf and Dp antibodies followed by sequencing. Two independent biological samples per antibody were processed

first: Maxim

middle: V

last: Frolov

first: Abul

middle: B

last: Islam


title: A coronin 1-dependent signaling axis in T cells essential for allograft rejection

city: Basel

first: Geoffrey

last: Fucile

address: Klingelbergstrasse 50/70

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

summary: The goal of this analysis was to assess the similarity in transcriptomes between WT and Coro1-/- across regulatory and conventional T cells.

overall_design: mRNA profiles of wild-type and Coronin1A knockout from murine regulatory (trg) and conventional (con) T cells were generated by deep sequencing, in triplicate, using Illumina TruSeq stranded mRNA sample kit.

first: Jean

last: Pieters


title: RNA Sequencing Facilitates Quantitative Analysis of Wild Type and HRD1-/- liver Transcriptomes

city: Memphis

first: John

last: Crispino

state: Tennessee

address: 262 DANNY THOMAS PL

institute: St. Jude Children's Research

summary: Screen the differential genes of Wild Type and HRD1-/- liver under fasted and refed condition

overall_design: Hepatic mRNA profiles of 12 weeks old wild type (WT) and HRD1 KO mice were generated by deep sequencing, in duplicate.

first: Deyu

last: Fang

first: Juncheng

last: Wei


title: Novel RNA partners of the Mei2 RNA binding protein during early meiosis in Schizosaccharomyces pombe

first: Kaustav

last: Mukherjee

address: 1 Gustave Levy Place

institute: Mount Sinai Medical Center

summary: We used CLIP-Seq to determine the RNAs bound specifically to RNA binding protein Mei2 in early meiosis in fission yeast. We added a TAP tag to the C-terminal ends of two meiotic RNA binding proteins, Mei2 and Msa1. We used an untagged fission yeast strain as a negative control. These strains were nitrogen starved and allowed to progress into meiosis, after which they were harvested, lyzed and crosslinking immunoprecipitaion was performed. The RNAs purified after CLIP were sequenced

overall_design: We determined the RNAs bound to immunoprecipitated Mei2-TAP and Msa1-TAP

first: Bruce

last: Futcher

first: Janet

last: Leatherwood


title: RNAseq TX1072 WT and HDAC3KO

city: Paris

first: Aurélie

last: Bousard

address: 26, rue d'Ulm

institute: Institut Curie

summary: During development, changes in gene transcription are accompanied by changes in chromatin modification but the order and causality of events often remain unclear. Here we address this question using X-chromosome inactivation (XCI), which entails chromosome-wide gene silencing and heterochromatin formation. We initiate XCI in female, mouse embryonic stem cells by inducing Xist expression and monitor subsequent changes in transcription and chromatin modification by allele-specific TTseq and ChIPseq respectively. An unprecedented temporal resolution has enabled us to define early alterations in chromatin that are induced upon Xist RNA coating. Xist-induced repression begins with histone deacetylation, which involves the histone deacetylase HDAC3 and occurs before efficient loss of H3K4me3 and H3K4me1 modifications. Polycomb-associated repressive histone marks accumulate rapidly, starting with PRC1-associated H2AK119Ub and followed by PRC2-associated H3K27me3. However, polycomb accumulates initially at large premarked domains, some of which correspond to Xist entry sites, and then spreads into genes. We also show that spreading can only ensue when transcriptional silencing has occurred. These results establish a detailed epigenomic time course for XCI and reveal a hierarchy of events with chromatin playing an important role in transcriptional silencing of the X chromosome.

overall_design: RNAseq on WT and HDAC3 KO cell lines from TX1072 cell line. For WT and HDAC3KO samples RNAseq in 2 replicates (Rep1, Rep2) at 2 different times of DOX induction (0h, 24h).

first: Jan

last: Żylicz

first: Kristina

last: Žumer

first: Eusra

last: Mohammad

first: Simão

last: Teixeira da Rocha

first: Björn

last: Schwalb

first: Laurène

last: Syx

first: Patrick

last: Cramer

first: Edith

last: Heard


title: The ZZ domain of p300 mediates specificity of the adjacent HAT domain for histone H3

city: Irvine

first: Jiejun

last: Shi

state: CA

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

summary: Human p300 is a transcriptional co-activator and a major acetyltransferase that acetylates histones and other proteins facilitating gene transcription. The activity of p300 relies on the fine-tuned interactome that involves a dozen p300 domains and hundreds of binding partners and links p300 to a wide range of vital signaling events. Here, we report on a novel function of the ZZ-type zinc finger (ZZ) of p300 as a reader of histone H3. We show that the ZZ domain and acetyllysine recognizing bromodomain (BD) of p300 play critical roles in modulating p300 enzymatic activity and its association with chromatin. Acetyllysine binding of BD is essential for acetylation of histones H3 and H4, whereas interaction of the ZZ domain with H3 promotes selective acetylation of histone H3K27 and H3K18.

overall_design: ChIP-seq of Flag-p300, H3K27ac, H3K18ac were applied in human H1299 cells stably expressing WT or mutant (N1671A/D1690A) p300-BRPHZT fragment and control vector (V).

first: Yongming

last: Xue

first: Xiaobing


department: Cell, Developmental and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

summary: We used RIP-CHIP to determine the RNAs bound specifically to RNA binding protein Mei2 in early meiosis in fission yeast.

overall_design: We added a TAP tag to the C-terminal ends of two meiotic RNA binding proteins, Mei2 and Msa1. We used an untagged fission yeast strain as a negative control. These strains were nitrogen starved and allowed to progress into meiosis, after which they were harvested, lyzed and RNA immunoprecipitaion was performed. The RNAs purified after RIP were sequenced


title: Expression data from miR340 overexpressing human A549 cells

city: Wuhan

first: Zhao

middle: Lian

last: Zhong

address: Shizishan Street

institute: Huazhong Agriculture University

summary: To characterize the differentially expressed genes of miR340, we compared the gene expression profiles of miR-340 overexpressing human A549 cells with that of  empty vector transfected A549 cells

overall_design: The precursor form of miR-340 was overexpressed in A549 cells using pcDNA3.1 plasmid, and empty vector transfection was used as control. The miR340 or empty vector transfected cells were incubated at 37°C for 24 hr. Total RNA was extracted for RNA sequencing.

last: Lianzhong

first: Jin

last: Meilin


title: RNA-sequencing of cTECs, mTECs, and thymocyte maturation subsets SM, M1 and M2 from the CD4 and CD8 lineages from WT and Psmb11-deficient mice [DSP216]

city: Montréal

first: Claude

last: Perreault

state: Quebec

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

summary:
Purpose: Cortical thymic epithelial cells (cTECs) contain a unique type of proteasomes, thymoproteasomes. Indirect evidence suggests that the key role of PSMB11, a catalytic subunit of thymoproteasomes specific to cTECs, is to generate a unique repertoire of MHC I peptides. Notably, PSMB11-deficient mice display defective development of CD8 thymocytes. The objective of this study was to characterize the impact of PSMB11 on cTECs and thymocyte development. Since different types of proteasomes have non-redundant effects on gene expression, we hypothesized that thymoproteasomes should have a distinct impact on the transcriptome and thereby the function of cTECs.
Results: We report that PSMB11 in cortical thymic epithelial cells has dramatic effects on cTECs on both CD4 and CD8 thymocyte populations. PSMB11 modulates the expression of 850 genes in cTECs, 582 in CD4 thymocytes and 284 in CD8 thymocytes. PSMB11-regulated cTEC genes are involved mainly in cell-cell adhesion, extracellular matric organization and thymocyte chemotaxis. PSMB11-deficient cTECs acquire features of mTECs and perturb thymocyte development. Deletion of PSMB11 causes a major cell stress in both CD4 and CD8 thymocyte populations. Of note, PSMB11-deficiency had no impact on medullary thymic epithelial cells (mTECs), which originate from progenitors that express PSMB11 early in ontogeny.
Conclusion: We conclude that PSMB11 has pervasive effects on both CD4 and CD8 thymocytes via regulation of gene expression in cTECs.

overall_design: We performed RNA-sequencing in triplicate on cTECs, mTECs, and SM, M1 and M2 thymocytes from the CD4 and CD8 lineages, in order to identify differential gene expression between WT and Psmb11-deficient mice.

first: Sylvie

last: Brochu

first: Anca

last: Apavaloaei


title: RNA-sequencing of cTECs, mTECs, and thymocyte maturation subsets SM, M1 and M2 from the CD4 and CD8 lineages from WT and Psmb11-deficient mice [DSP405]


title: The polyploid state plays a tumor suppressive role in the liver

city: Dallas

first: Hao

last: Zhu

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Most cells in the liver are polyploid, but the functional role of polyploidy is unknown. We developed orthogonal mouse models to transiently and potently alter liver ploidy. Premature weaning, as well as knockdown of E2f8 or Anln, allowed us to toggle between diploid and polyploid states. While there was no impact of ploidy alterations on liver function, metabolism, or regeneration, more polyploid mice suppressed and more diploid mice accelerated tumorigenesis in mutagen and high-fat induced models. Mechanistically, the diploid state was more susceptible to Cas9-mediated tumor suppressor loss but was similarly susceptible to MYC oncogene activation, indicating that ploidy differentially protected the liver from distinct genomic aberrations.

overall_design: Liver tumor tissues were collected from DEN treated C3h mice, whose liver ploidy were altered by in vivo siRNAs, as well as DEN treated E2f8 WT/Het and KO mice.  The tumors were then fixed and the genomic DNA were isolated. The targeted cancer genes in these tumors were sequenced and the mutations were analyzed. Normal liver tissues from three mice were used as normal control.

first: Shuyuan

last: Zhang

first: Xin

last: Luo

first: Zhu

last: Hao


title: iRhom2 Promotes Lupus Nephritis through ADAM17-Dependent TNF-α and EGFR Signaling

city: New york

first: Yurii

last: Chinenov

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

summary: Lupus nephritis (LN) often results in progressive renal dysfunction. The inactive Rhomboid 2 (iRhom2) is a newly identified key regulator of A disintegrin and metalloprotease 17 (ADAM17), whose substrates, such as TNF-α and heparin-binding EGF (HB-EGF), have been implicated in the pathogenesis of chronic kidney disease. Here we demonstrate that deficiency of iRhom2 protects the lupus-prone Fcgr2b-/- mice from developing severe kidney damage without altering anti-double stranded (ds) DNA Ab production, by simultaneously blocking the HB-EGF/EGFR and the TNF-α signaling in the kidney tissues. Unbiased transcriptome profiling of kidneys and kidney macrophages revealed that TNF-α and HB-EGF/EGFR signaling pathways are highly upregulated in Fcgr2b-/- mice; alterations that were diminished in the absence of iRhom2. Pharmacological blockade of either TNF-α or EGFR signaling protected Fcgr2b-/- mice from severe renal damage. Finally, kidneys from LN patients showed increased iRhom2 and HB-EGF expression, with interstitial HB-EGF expression significantly associated with chronicity indices. Our data suggest that activation of iRhom2/ADAM17-dependent TNF-α and EGFR signaling plays a crucial role in mediating irreversible kidney damage in LN, thereby uncovering a novel target for selective and simultaneous dual inhibition of two major pathological pathways in the effector arm of the disease.

overall_design: [1] Analysis of total kidney transcriptomes in Fcgr2b-/- mice, Rhbdf2-/- mice; Rhbdf2 -/- Fcgr2b-/- mice and the wildtype control. [2] Analysis of CD45+F4/80hiCD11b+Ly6G-Ly6C- kidney macrophages transcriptomes in Fcgr2b-/- mice, Rhbdf2-/- mice; Rhbdf2 -/- Fcgr2b-/- mice and the wildtype control.

first: Xiaoping

last: Qing

first: Patricia

last: Redecha

first: Carl

last: Blobel

first: Jane

last: Salmon


title: RNA-sequencing of cTECs, mTECs, and thymocyte maturation subsets SM, M1 and M2 from the CD4 and CD8 lineages from WT and Psmb11-deficient mice [DSP393]

summary:
Purpose: Cortical thymic epithelial cells (cTECs) contain a unique type of proteasomes, thymoproteasomes. Indirect evidence suggests that the key role of PSMB11, a catalytic subunit of thymoproteasomes specific to cTECs, is to generate a unique repertoire of MHC I peptides. Notably, PSMB11-deficient mice display defective development of CD8 thymocytes. The objective of this study was to characterize the impact of PSMB11 on cTECs and thymocyte development. Since different types of proteasomes have non-redundant effects on gene expression, we hypothesized that thymoproteasomes should have a distinct impact on the transcriptome and thereby the function of cTECs.
Results: We report that PSMB11 has dramatic effects on cTECs and on both CD4 and CD8 thymocyte populations. PSMB11 modulates the expression of 850 genes in cTECs, 582 in CD4 thymocytes and 284 in CD8 thymocytes. PSMB11-regulated cTEC genes are involved mainly in cell-cell adhesion, extracellular matric organization and thymocyte chemotaxis. PSMB11-deficient cTECs acquire features of mTECs and perturb thymocyte development. Moreover, we found that deletion of PSMB11 causes a major cell stress in both CD4 and CD8 thymocyte populations. Of note, PSMB11-deficiency had no impact on medullary thymic epithelial cells (mTECs), which originate from progenitors that express PSMB11 early in ontogeny.
Conclusion: We conclude that PSMB11 has pervasive effects on both CD4 and CD8 thymocytes via regulation of gene expression in cTECs.


title: Endocardial Notch Signaling Promotes Cardiomyocyte Proliferation in the Regenerating Zebrafish Heart through Wnt Pathway Antagonism

city: Charlestown

first: Long

last: Zhao

state: MA

address: 149 13th Street

department: Cardiovascular Research Center

institute: Massachusetts General Hospital

summary: The goal of this study is to understand the molecular mechanisms underlying this Notch-induced muscle cell proliferation defect, we sequenced the transcriptome of control ventricles and Notch-suppressed ventricle at 5 days post-injury, when cardiomyocyte proliferation is normally robust.

overall_design: In order to identify downstream targets of Notch signaling of cardimyotyes proliferation during zebrafish heart regeneration, we compared transcriptome profiles between wildtype hearts and DN-MAML hearts by RNA sequencing strategy. The heart samples were collected, RNA extracted, and cDNA generated for library construction. The samples were collected in triplicate and sequenced at the PCPGM on an Illumina HiSeq 2000.

first: Raz

last: Ben-Yair

first: Caroline

last: Burns

first: C

middle: G


title: miRNA seq of feto-placental arterial endothelial cells (pfEC) after normal pregnancy vs pregnancy complicated by gestational diabetes (GDM)

city: Graz

first: Ursula

last: Hiden

address: Auenbruggerplatz 14

department: Obstetrics and Gynecology

country: Austria

institute: Medical University of Graz

summary: We report that the effect of GDM on gene expression differs between feto-placental endothelial cells of male vs female progeny, i.e. after pregnancy with a male or female offspring.

overall_design: Analysis of all detected miRNAs

first: Silvija

last: Cvitic

first: Jasmin

last: Strutz

first: Hubert

last: Hackl

first: Karl

last: Kashofer


title: mTORC2/Akt Activation in Adipocytes is Required for Mycobacterium tuberculosis Derived Inflammation in Adipose Tissue

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

summary: The association between type 2 DM (T2DM) and susceptibility to tuberculosis (TB) is well recognized. Patients with DM have 2-3 fold increased susceptibility to TB, treatment is longer and the outcome is worse than in non-diabetic TB patients. Here, we report that aerosol infection with M. tuberculosis is followed by leukocyte infiltration and proliferation, and expression of inflammatory markers in adipose tissue of lean mice leading to disrupted lipid metabolism and the induction of adipocyte hypertrophy. RNA-sequencing (RNAseq) in whole pgWAT adipose tissue at 8 wk after aerosol challenge revealed an upregulation of genes that were associated with antigen presentation, Th1 and type-1 interferon response, indicated the induction of T cell activation. This was found to be due to activated mTORC2/Akt signaling. By depleting Rictor (mTORC2 subunit) in adipocytes we noticed the restoration of inflammation and cell hypertrophy. Our study suggests that TB-induced inflammation in the adipose tissue is associated with improved glucose tolerance and is mediated by mTORC2/Akt pathway.

overall_design: primary murine adipose tissue from 5 uninfected and 6 Tb infected mice 8 weeks post infection

first: Amit

last: Singhal


title: Transcriptomic analysis of Multiple Myeloma bone marrow microenvironment

city: Toulouse

first: ludovic

last: Martinet

address: 2 av Hubert Curien

department: CRCT

institute: INSERM U1037

summary: We report the RNA sequencing of the non-tumoral CD138- fractions of 74 MM patient BM aspirates taken at the time of diagnosis.

overall_design: The sequencing of total RNA  from the non-tumoral CD138- fractions of 74 MM patient BM aspirates was performed using TruSeq Stranded mRNA Sample Preparation kit on a NextSeq 500 Illumina sequencing platform (Illumina) by 5 successive runs using NextSeq 500 High Output kit v2 (Illumina) generating in average 20 million pairs of reads per sample.

first: Hervé

last: Avet-Loiseau

first: Ludovic


title: Identification of genes associated with resistance to acute hepatopancreatic necrosis disease (AHPND) in Litopenaeus vannamei

city: Minato-ku

first: Sasiwipa

last: Tinwongger

state: Tokyo

address: 4-5-7 Konan

department: Applied marine bioscience

institute: Tokyo university of marine science and technology

summary: Acute hepatopancreatic necrosis disease (AHPND) is a shrimp farming disease, caused by a pathogenic Vibrio parahaemolyticus carrying a plasmid encoding Vp_PirAB-like toxin (VpAHPND). Whiteleg shrimp, Litopenaeus vannamei were fed food pellets containing formalin-killed VpAHPND (FKC-VpAHPND) to select for toxin resistance. To identify genes associated with Vp_PirAB-like toxin resistance, total RNA was sequenced to identify differentially expressed genes (DEGs) in the stomach and hepatopancreas among surviving shrimp (sur-FKC), AHPND-infected shrimp (Vp-inf) and normal shrimp (control). From a total of 79,591 genes, 194 and 224 DEGs were identified in the stomach and hepatopancreas transcriptomes, respectfully. The expressions of DEGs were validated by qPCR of ten genes. Only one gene, a gene homologous to L vannamei anti-lipopolysaccharide factor AV-R isoform (LvALF AV-R), was expressed significantly more strongly in sur-FKC than in the other groups. The association of LvALF AV-R expression and toxin resistance was affirmed from the surviving shrimp in a second-trial of FKC-VpAHPND feeding. These results suggest that LvALF AV-R may be involved in shrimp defense mechanisms against Vp_PirAB-like toxin virulence.

overall_design: Total RNA of stomach and hepatopancreas from 3 groups of control (N =3), Vp-inf (N=3), and sur-FKC (N=4) were prepared library with Truseq Stranded mRNA Library Prep Kit. RNA-seq was genrated by Illumina MiSeq


title: Derivation of hypoblast stem cells from rat embryonic stem cells.[RNA-seq]

city: Minneapolis

first: Dong Seong

last: Cho

state: MN

address: 421 Washington Ave S.E.

department: Chemical Engineering and Materials Science

institute: University of Minnesota

summary: We report the mRNA profiles of single cells with high-throughput sequencing (RNA-seq) of hypoblast stem cells derived from rat embryonic stem cells. The single-cell data was combined with the previously published dataset: transcriptomes of mouse embryo cells (inner cell mass or trophectoderm). The clustering revealed that rat embryonic stem cell-derived hypoblast stem cells were similar to the mouse inner cell mass cells.

overall_design: mRNA profiles of 34 single cells and one population control (bulk population) of hypoblast stem cells with RNA-seq.

first: Dong

first: Wei-Shou

last: Hu


title: Mutations in the Drosophila splicing regulator Prp31   as a model for Retinitis pigmentosa 11

city: Dresden

first: Holger

last: Brandl

state: Choose One...

address: Pfotenhauerstrasse 108

department: Bioinformatics Service

institute: Max Planck Institute of Molecular Cell Biology and Genetics

summary: A Drosophila mutant for the splicing factor Prp31 was generated and characterized as a model for Retinitis pigmentosa 11. The transcriptome of the mutant was compared to the genetic control white.

overall_design: Gene expression profiles of adult Drosophila melanogaster heads (2 days after eclosion, males and females) were generated by RNA-seq and analyzed.

first: Malte

last: Lehmann

first: Elisabeth

last: Knust


title: Network modeling reveals genetic interactions that influence C. elegans defense against infection

city: Cambridge

first: Erel

last: Levine

address: 52 Oxford St

institute: Harvard University

summary: Time respoved RNA-seq during Caenorhabditis elegans infection by Pseudomonas aeruginosa PA14.

overall_design: Worms were infected following a standard slow-killing assay. Animals were collected at multiple time points, and total RNA was extracted using a Trizol-based method. Sequencing followed a polyA enrichment.

first: Javier

last: Irazoqui


title: MicroRNA15a/16-1 represses the development of colorectal cancer by restraining the recruitment of immunosuppressive B lymphocytes

city: Shanghai

first: Ronhua

last: Liu

address: No.138, Yi Xue Yuan Rd.

institute: Department of Immunology, Fudan University

summary: B lymphocytes are emerging as abundant cellular components in various tumors; however, the mechanisms underlying their tumor-infiltration and their subsequent action remain to be extensively elucidated. In the present study, using a murine model of primary colorectal cancer (CRC), we found that deficiency of the small non-coding RNA cluster, microRNA15a/16-1 (miR-15a/16-1), promoted the accumulation of immunosuppressive B cells in neoplastic tissues, resulting in the repression of the proliferation and function of CD8+ T cells, and in the promotion of CRC.

overall_design: Colorectal miRNA profiles of healthy mice and CRC mice were generated by sequencing.

first: Ronghua

first: Yiwei

last: Chu


title: Characterization of a novel OTX2-driven self-renewal program in Group 3 and Group 4 medulloblastoma [ChIP-seq]

city: Winnipeg

first: Tamra

last: Werbowetski-Ogilvie

state: Manitoba

address: 611-745 Bannatyne Avenue

department: Biochemistry & Medical Genetics

institute: University of Manitoba

summary: Medulloblastoma (MB) is the most common malignant primary pediatric brain cancer. Among the most aggressive subtypes, Group 3 and Group 4 originate from stem/progenitor cells, frequently metastasize, and often display the worst prognosis, yet, as the names imply, we know the least about the molecular mechanisms driving their progression. Here, we show that the transcription factor orthodenticle homeobox 2 (OTX2) promotes self-renewal while inhibiting differentiation in vitro and increases tumor-initiating capacity from MB stem cell populations in vivo. Characterization of the OTX2 regulatory network revealed a novel relationship between OTX2 and genes associated with multiple axon guidance signaling pathways in Group 3 and Group 4 MB stem/progenitor cells. In particular, OTX2 levels were negatively correlated with semaphorin (SEMA) signaling, as expression of 9 SEMA pathway genes is upregulated following OTX2 knockdown with some being potential direct OTX2 targets. Importantly, this negative correlation between OTX2 and SEMA pathway genes was also observed in patient samples, with lower expression of SEMA4D associated with poor outcome in Group 3 and 4 tumors. Functional studies using established and newly derived MB cell lines demonstrated that increased levels of SEMA pathway genes are associated with decreased self-renewal and growth, and that RHO signaling, known to mediate the effects of SEMA genes, is contributing to the OTX2 KD phenotype. Our study provides critical mechanistic insight into the networks controlled by OTX2 in self-renewing MB cells and reveals novel roles for axon guidance genes and their downstream effectors as putative tumor suppressors and therapeutic targets in Group 3 and Group 4 MB.

overall_design: OTX2+ control tumorspheres

first: Margaret

last: Stromecki


title: RNA sequencing (RNA-SEQ) of WT and LFS patient specific iPSC derived pre-osteoblasts

city: New York

first: Seungyeul

last: Yoo

state: NY

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

summary:
Purpose: To understand molecular and cellular effects of sFRP2 overexpression in LFS patients
Methods: We performed RNA sequencing of 32 samples from WT, sFRP2OE, LFS, and sFRP2 knockdown MSCs or preosteoblasts in four differentiation time points and performed RNAsequencing.
Conclusion: molecular and cellular effects of sFRP2 overexpression in LFS patients

overall_design: cDNA library preparation and sequencing were performed at Novogen (http://www.novogen.com/home). Briefly, RNA quality was determined with an Agilent Bioanalyzer (RNA integrity number [RIN] > 7.0 for all samples). mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, and double stranded cDNA synthesized using random hexamers, M-MuLV Reverse Transcriptase (RNase H), and DNA Polymerase I. NEBNext Adaptor with hairpin loop structure were ligated to the cDNA in preparation for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Library of 150-200 bp fragments at an effective concentration of > 2nM were loaded onto an Illumina HiSeq 4000 for sequencing

first: Huen

middle: S

last: Kim

first: Jun

last: Zhu


title: Immune function of the serosa in a hemimetabolous insect egg

city: Leiden

first: Chris

last: Jacobs

state: Zuid-Holland

address: Sylviusweg 72

department: Institute of Biology

country: Netherlands

institute: Leiden University

summary:
The unparalleled success of the insects comprising more than a million species has long stood out to evolutionary biologists. A much overlooked evolutionary innovation of the insects is the serosa, an extraembryonic epithelium that covers yolk and embryo in their eggs. We have shown that this epithelium provides innate immune protection to eggs of the beetle Tribolium castaneum. It remained elusive, however, if this innate immune competence evolved in the Tribolium lineage, or is ancestral to all insects.
Here, we expand our studies to the bug Oncopeltus fasciatus that belongs to the basal main group of insects, the Hemimetabola. RNA sequencing reveals an extensive transcriptional response upon infection of the egg with Gram-positive and Gram-negative bacteria. We demonstrate the antimicrobial activity of upregulated peptides using in vitro bacterial growth inhibition assays, and describe two novel families of AMPs called Serosins and Ovicins. By qPCR, we determine that eggs become immune responsive when the serosa develops. Finally, in situ hybridizations show that transcripts of upregulated peptides are located in the serosal cells and not in the underlying embryo. We conclude that the serosa protects the O. fasciatus embryo against pathogens. This first evidence from hemimetabolous insect eggs suggests that immune competence is an ancestral property of the serosa. The evolutionary origin of the serosa with its immune function might have been one of the factors that facilitated the spectacular success of the insects.

overall_design: In total 9 samples are analysed retrieved from 48-64h old Oncopeltus fasciatus eggs (100 eggs per sample, collected at 25 degrees Celsius). We used a control (Naive) in which eggs were left untreated, a sterile injury (Sterile) in which eggs were pricked with a sterile tungsten needle and a septic injury (Septic) in which eggs were infected with a mixture of E.coli and M.luteus bacteria using a tungsten needle dipped in a bacterial suspension. For all 3 treatments, 3 replicates were obtained, leading to a total of 9 samples.

first: C

first: R

last: van der Hulst

first: Y

last: Chen

first: S

last: Roth

first: M

last: van der Zee


title: RNA-seq of subcellular fractions from nESC and EpiLC

first: Bo

last: Wen

address: 130 DongAn Road

department: Institutes of Biomedical Sciences

institute: Fudan University

summary: We analysed lncRNA subcellular location by performing RNAseq with fractionated nESC and epiblast-like cells (EpiLCs).

overall_design: RNA-seq of 3 subcellular fractions (chromatin, nucleoplasmic and cytoplasmic) from nESC and EpiLC.

first: Pin

last: Lv

first: Minzhe


title: Transfection experiment with vector containing TP73-AS1 sponge region and miR-941

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

summary: miRNA sponge, a special class of miRNA target,  has been emerging as a pivotal player in miRNA mediated regulatory network. Currently, the identified miRNA sponge genes mostly act on sequestering conserved miRNAs (e.g. miR-7, miR-145), however, the existence, potential function and evolutionary process of miRNA sponge genes for species-specific miRNA, especially for human specific miRNA, are largely unknown. In this study, we conducted a systematic analysis including sponge gene identification and subsequent function and evolutionary analyses for an authentic human-specific miRNA, miR-941.

overall_design: Total RNA after transfecting with vector containing TP73-AS1 sponge region and miR-941 and empty vector were generated by deep sequencing using Illumina HiSeq 2000

first: Xi

last: Jiang

first: Philipp

last: Khaitovich


title: Human prefrontal cortex Ribominus RNA sequencing

overall_design: Total RNA after depleting Ribosomal RNA of four human prefrontal cortex samples were generated by deep sequencing using Illumina HiSeq 2000