title: The midguts transcriptome of Aedes aegypti (Liverpool strain) females knock down AaMesh and feed AaMesh antibody versus those knock down GFP and feed pre-immune.

city: Beijing

first: Gong

last: Cheng

address: 4305 Biotechnology Building, Tsinghua University

institute: Tsinghua University

summary: We reported the RNA-seq based analyses of the transcriptional changes in the Aedes aegypti midguts knock down 3, 6days, feed antibody 18h transcriptome.

overall_design:
Comparison of the midguts transcriptome of Aedes aegypti females at two knockdown time points and one feed condition;

GFP dsRNA-3 or -6days: 3 or 6 days after 7day-old mosquitos were microinjected GFP dsRNA
AaMesh dsRNA-3 or -6days: 3 or 6 days after 7day-old mosquitos were microinjected AaMesh dsRNA
Pre-immune-18h: 18hrs after 7day-old wild type mosquitos were fed with Pre-immune
AaMesh antibody-18h: 18hrs after 7day-old wild type mosquitos were fed with AaMesh antibody

first: Xiaoping

last: Xiao

first: Rudian

last: Zhang


title: A Comprehensive, CRISPR-based Approach to Functional Analysis of Essential Genes in Bacteria

status: Public on Mar 09 2016

city: San Francisco

first: Jason

middle: Matthew

last: Peters

state: CA

address: 600 16th Street

department: Microbiology and Immunology

country: USA

institute: University of California, San Francisco

type: Expression profiling by high throughput sequencing

summary: Essential gene products underpin the core reactions required for cell viability, but are poorly studied in vivo due to a shortage of appropriate technologies. Using CRISPR interference, we created knockdowns of every essential gene in Bacillus subtilis and probed their phenotypes. Our high-confidence essential gene network, established using chemical genomics, showed extensive interconnections among distantly related processes and identified the modes of action for uncharacterized antibiotics. Importantly, mild knockdown of essential gene functions significantly reduced stationary-phase survival without affecting maximal growth rate, suggesting that essential protein levels are set to maximize viability of cells during stress. Finally, high-throughput microscopy indicated that cell morphology is relatively insensitive to mild knockdown but profoundly affected by depletion of gene function, revealing intimate connections between cell growth and shape. Our results provide a framework for systematic investigation of essential gene functions in vivo that is broadly applicable to diverse microorganisms and amenable to comparative analysis.

overall_design: 2 samples of B. subtilis NET-seq and 7 samples of B. subtilis mRNA-seq.

first: J

middle: M

first: M

middle: H

last: Larson

middle: S

last: Weissman

first: C

middle: A

last: Gross


title: The Promyelocytic Leukemia Zinc Finger Transcription Factor (PLZF) is Critical for Human Endometrial Stromal Cell Decidualization

city: Houston

first: Ramakrishna

last: kommagani

state: TX - Texas

address: M732, One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Whole genome binding profile of PLZF in human endometrial stromal cells (hESCs)

overall_design: ChIP-seq in decidualizing human endometrial stromal cells

first: R

last: Kommagani

middle: P

last: Lydon


title: HOX gene complement and expression in the planarian Schmidtea mediterranea

status: Public on Mar 08 2016

city: Portland

first: Bret

middle: J

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

summary: Background:  Freshwater planarians are well known for their regenerative abilities.  Less well known is how planarians maintain spatial patterning in long-lived adult animals or how they re-pattern tissues during regeneration.  HOX genes are good candidates to regulate planarian spatial patterning, yet the full complement or genomic clustering of planarian HOX genes has not yet been described, primarily because only a few have been detectable by in situ hybridization, and none have given morphological phenotypes when knocked down by RNAi.  Results:  Because the planarian Schmidtea mediterranea (S. med) is unsegmented, appendage-less, and morphologically simple, it has been proposed that it may have a simplified HOX gene complement.  Here we argue against this hypothesis and show that S. med has a total of 13 HOX genes, which represent homologs to all major axial categories, and can be detected by whole-mount in situ hybridization using a highly-sensitive method.  In addition, we show that planarian HOX genes do not cluster in the genome, yet 5/13 have retained aspects of axially-restricted expression.  Finally, we confirm HOX gene axial expression by RNA-deep-sequencing 6 anterior-to-posterior “zones” of the animal, which we provide as a dataset to the community to discover other axially-restricted transcripts.  Conclusions:  Freshwater planarians have an unappreciated HOX gene complexity, with all major axial categories represented.  However, we conclude based on adult expression patterns that planarians have a derived body plan and their asexual lifestyle may have allowed for large changes in HOX expression from the last common ancestor between arthropods, flatworms, and vertebrates.  Using our in situ method and axial zone RNAseq data, it should be possible to further understand the pathways that pattern the anterior-posterior axis of adult planarians.

overall_design: 10 animals were immobilized on peltier coolers and carefully amputated into 6 Anterior-Posterior zones, as illustrated in Figure 2 of the manuscript.  RNA was extracted from each zone, and deep sequenced to a depth >52 million reads.

first: Ko

middle: W

last: Currie

first: Shu

last: Zhu

first: David

middle: D

last: Brown

first: Veronique

last: Voisin

first: Chang

last: Xu

first: Gary

last: Bader


title: Epigenetic Analysis of Eµ-Myc B-cell lymphoma using both H3K27me3 CHiP-Seq and Bisulfite-Seq (reduced representation).

city: Los Angeles

first: Larry

last: Lam

address: 610 Charles Young Drive East

department: Molecular, Cell, and Developmental Biology

institute: University of California, Los Angeles

type: Methylation profiling by high throughput sequencing

summary: We used RRBS and H3K27me3 to understand epigenetic changes in resistant cell lines to DNA crosslinking agent, mafosfamide, (Parental, R100, R500, R1000, R2000, R4000) via dose escalation.

overall_design: Resistant strains were generated from a parental Eµ-Myc B-cell lymphoma line via dose escalation of mafosfamide over a 34-day peroid.

first: Colin

last: Flinders

first: Roberto

last: Ferrari

first: Liudmilla

last: Rubbi


title: Transcriptomic differences between euryhaline and stenohaline malaria vector sibling species in response to salinity stress

city: Notre Dame

first: Hilary

middle: April

last: Uyhelji

state: IN

address: 317 Galvin Life Science Center

department: Biological Sciences

institute: University of Notre Dame

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

sample_organism:
Anopheles merus
Anopheles coluzzii

platform_organism:
Anopheles merus
Anopheles coluzzii

overall_design: Refer to individual Series


title: Comparison of gene expression between female Schistosoma mansoni heads and tails

city: Dallas

first: James

last: Collins

state: TX

address: 6001 Forest Park

department: Pharmacology

institute: UT Southwestern

summary: We report differences in gene expression between the anterior and posterior of female Schistosoma mansoni parasites

overall_design: Three Biological Replicates


title: Sex Bias in CNS Autoimmune Disease Mediated by Androgen Control of Autoimmune Regulator

city: Chapel Hill

first: Joshua

last: Starmer

state: NORTH CAROLINA

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: Male gender is protective against multiple sclerosis and other T cell-mediated autoimmune diseases. This protection may be due, in part, to higher androgen levels in males. Androgen binds to the androgen receptor (AR) to regulate gene expression, but how androgen protects against autoimmunity is not well-understood. Autoimmune Regulator (Aire) prevents autoimmunity by promoting self-antigen expression in medullary thymic epithelial cells, such that developing T cells that recognize these self-antigens within the thymus undergo clonal deletion. Here, we show that androgen upregulates Aire-mediated thymic tolerance to protect against autoimmunity. Androgen recruits AR to Aire promoter regions, with consequent enhancement of Aire transcription. In mice and humans, thymic Aire expression is higher in males compared to females. Androgen administration and male gender protect against autoimmunity in a multiple sclerosis mouse model in an Aire-dependent manner. Thus, androgen control of an intrathymic Aire-mediated tolerance mechanism contributes to gender differences in autoimmunity.

overall_design: RNA-seq comparison of male vs. female expression in mTEC cells. Pools of 10 mice each were used for each replicate (two for male and two for female)

first: Meng-lei

first: Pearl

last: Bakhru

first: Bridget

last: Conley

first: Jennifer

last: Nelson

first: Meghan

last: Free

first: Aaron

last: Martin

first: Elizabeth

last: Wilson

first: Maureen

last: Su


title: The role of PIWIL4 in breast cancer

city: New Haven

last: Liu

state: CT

address: 10 Amistad st

institute: Yale University

type: Non-coding RNA profiling by high throughput sequencing

summary: PIWI proteins bind to PIWI-interacting RNAs (piRNAs) and play key roles in the biogenesis and functions of piRNAs. It has been reported that PIWI proteins are essential for stem cell self-renewal and germline development in diverse organisms, and are ectopically expressed in multiple forms of cancer. However, the role of PIWI in cancer remains elusive. Here we report that one of the four PIWI proteins in humans, PIWIL4, is highly expressed in both breast cancer tissues and the cytoplasm of MDA-MB-231 cell line derived from breast cancer. Reducing PIWIL4 expression drastically impairs migration ability of MDA-MB-231 cells, significantly increases their apotosis, and mildly affects their proliferation. Our transcriptome and proteome analyses reveal that these functions are at least partially achieved via the PIWIL4 regulation of TGF-beta and FGF signaling pathways and major histocompatibility complex (MHC) class II proteins. These findings suggest that PIWIL4 may serve as a potential therapeutic target for breast cancer.

overall_design: Examination of small RNAs in two conditions

first: Haifan

last: Lin


title: Transcriptomic differences between euryhaline and stenohaline malaria vector sibling species in response to salinity stress [set2]

summary: We use RNA-Seq to explore the reaction norm of gene expression of larval Anopheles coluzzii and An. merus to a gradient of salinity.

overall_design: After rearing in freshwater, separate pools of 18 h post-hatch larval instars of An. merus and An. coluzzii were briefly (6 h) exposed to one of six water salinities: 0%, 10%, 20%, 30%, 40%, or 50% the salinity of seawater. The last sample (G-50-RC) was split across 5 lanes for sequencing, resulting in total 10 fastq files associated with subparts G-50-RCa, G-50-RCb, G-50-RCc, G-50-RCd, G-50-RCe.

first: Changde

last: Cheng

first: Nora

last: Besansky


title: Histone H3 globular domain acetylation identifies new class of enhancers

status: Public on Mar 12 2016

city: London

first: Pradeepa

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

country: United Kingdom

institute: Queen Mary University of London

summary: We report the acetylation of lysine residues in the globular domain of H3 (H3K64ac and H3K122ac) marks active gene promoters and also a subset of active enhancers in mouse embryonic stem cells (mESCs), human erythroleukemic cell line (K562). Moreover, we find a novel class of active functional enhancers in ESCs that are marked by H3K122ac but which lack H3K27ac. This work suggests that a more complex analysis of histone acetylation is required to identify enhancers than was previously considered.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of histone modifications in mouse ESCs (2 biological replicates) and K562 cells

first: Graeme

last: Grimes

first: Wendy

last: Bickmore


title: Small and large RNA sequencing of mouse livers receiving small hairpin RNAs

city: Seattle

first: Paul

last: Valdmanis

state: WA

address: 1705 NE Pacific St, HSB J-309

department: Medicine

institute: University of Washington

summary: Adeno-associated viral (AAV) small hairpin (shRNA) expression vectors are a promising therapeutic but can induce severe liver toxicity when delivered at high albeit undefined doses.  Using various AAV-shRNA vectors under the high-expressing U6 and low-expressing H1 promoters, we found that dose-limiting toxicity was strongly correlated with an shRNA concentration of  >12% of total microRNA levels.  Toxicity was associated with a specific reduction in the first synthesized 22nt isoform of miR-122-5p, resulting in the specific de-repression of miR-122 target mRNAs.  A causative link between miR-122 reduction and toxicity was established when an AAV-sh-miR-122 vector producing >20% of the total liver miRNAs prevented liver toxicity.  Consistent with these results, miR-122 knockout mice, which in part adapt to an absence of miR-122 reduction, also show no toxicity with high dose AAV-shRNA delivery.

overall_design: RNA sequencing of 12 liver samples, 2 receiving H1-shRNAs, 7 with U6-shRNAs and 3 controls; small RNA sequencing of 95 samples including 18 with CMV-driven miR-122 expression in HEK293 cells, 13 in miR-122 knockout mice, 9 samples in mice heterozygous for miR-122, 5 samples with Cre-mediate excision of miR-122, 19 samples immunoprecipitated with Ago2 and 31 additional liver samples (3 control, 11 receiving H1-shRNAs and 17 receiving U6-shRNAs).  Small RNA libraries were barcoded (first 4 nucleotides) at the 5' end and ligated to linker-1 (5'-CTGTAGGCACCATCAAT) at the 3' end.

middle: N

first: Mark

last: Kay


title: The effect of IL-17A on osteoblastogenesis of PαS cells

city: Tokyo

first: Takehito

last: Ono

address: Yushima, 1-5-45

department: Department of Cell Signaling

country: Japan

institute: Tokyo Medical and Dental University

summary: The goal of this study was to elucidate the effects of inflammation on bone metabolism. As we found IL-17A is induced immediately after bone injury and Il17a−/− mice showed delayed healing, we analyzed the effects of IL-17A on mesenchymal cells in the repair tissue. Most of the IL-17RA+ cells were PαS cells. We collected these cells and analyzed their response to IL-17A by RNA sequencing. This analysis will provide a mechanistic insight into the mechanism of how IL-17A promote bone formation in the context of bone fracture healing.

overall_design: PαS cells were harvested from the injury tissue of wild-type mice and cultured with or without IL-17A or BMP-2. RNAs were harvested at day 7.

first: Kazuo

last: Okamoto

first: Tomoki

last: Nakashima

first: Takeshi

last: Nitta

first: Shohei

last: Hori

first: Yoichiro

last: Iwakura

first: Hiroshi

last: Takayanagi


title: Lincomycin effect on PIFq-regulated transcriptome

city: Cerdanyola del Vallès

first: Guiomar

last: Martín

state: Barcelona

address: Vall Moronta

country: Spain

institute: Centre for Research in Agricultural Genomics

summary: RNA-seq experiment of WT and pifq mutant seedlings grown for 3 days in darkness in presence or absence of Lincomycin.

overall_design: Transcriptome profiles of the wild-type (WT) and pif1pif3pif4pif5 (pifq) quadruple mutant seedlings grown for 3 days in the dark in presence or absence of Lincomycin. Biological triplicate samples were analyzed from libraries constructed using a 3'-capture, 5' to 3' directional method.

first: Elena

last: Monte

first: Peter

last: Quail


title: RNA Seq analysis of e12.5 mouse pancreatic buds from control and Pdxcre; Gata4fl/fl;Gata6fl/fl; Tom mice

city: Aurora

first: Lori

last: Sussel

state: CO

address: 1775 Aurora Ct.

institute: University of Colorado

summary: about 250 genes were significantly changed after Gata4 and Gata6 were specifically deleted in the pancreatic progenitor cells

overall_design: 6 pancreatic buds were pooled for the control, and 12 pancreatic buds were pooled for the Pdxcre; Gata4fl/fl; Gata6fl/fl. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 20 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. Significantly differentially expressed genes were calculated using DEseq

first: Shouhong

last: Xuan


title: Differentially expressed vascular development genes for iPSC-ECs from CDI

city: Madison

first: Hamisha

last: Ardalani

state: WI

address: 330 N. Orchard St.

institute: UW-Madison

summary: Here we report genes upregulated for iPSC-ECs cultured in PEG hydrogels relative to control cells on tissue culture polystyrene (TCP) surfaces included adhesion, matrix remodeling, and Notch signaling pathway genes relevant to in vivo vascular development.

overall_design: Comparison between differentially expressed genes in 2D versus 3D culture of iPSC-ECS

first: William

last: Murphy

first: Matthew

last: Zanotelli

first: Scott

last: Swanson


title: An Integrated Metabolic Atlas of Clear Cell Renal Cell Carcinoma

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: Changes in cellular metabolism contribute to the development and progression of tumors, and can render tumors vulnerable to interventions. However, studies of human cancer metabolism remain limited due to technical challenges of detecting and quantifying small molecules, the highly interconnected nature of metabolic pathways, and the lack of designated tools to analyze and integrate metabolomics with other –omics data. Our study generates the largest comprehensive metabolomics dataset on a single cancer type, and provides a significant advance in integration of metabolomics with sequencing data. Our results highlight the massive re-organization of cellular metabolism as tumors progress and acquire more aggressive features. The results of our work are made available through an interactive public data portal for cancer research community.

overall_design: 10 RNA samples from human ccRCC tumors analyzed from the high glutathione cluster

first: A

last: Hakimi

first: Ed

last: Reznik

first: James

last: Hsieh


title: DUX4 recruits p300/CBP through its C-terminus and induces global H3K27 acetylation changes

status: Public on Mar 10 2016

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

summary: Ectopic expression of the double homeodomain transcription factor DUX4 causes facioscapulohumeral muscular dystrophy (FSHD). Mechanisms of action of DUX4 are currently unknown. Using immortalized human myoblasts with a titratable DUX4 transgene, we identify by mass spectrometry an interaction between the DUX4 C-terminus and the histone acetyltransferases p300/CBP. Chromatin immunoprecipitation shows that DUX4 recruits p300 to its target gene, ZSCAN4, displaces histone H3 from the center of its binding site, and induces H3K27Ac in its vicinity, but C-terminal deleted DUX4 does not. We show that a DUX4 minigene, bearing only the homeodomains and C-terminus, is transcriptionally functional and cytotoxic, and that overexpression of a nuclear targeted C-terminus impairs the ability of WT DUX4 to interact with p300 and to regulate target genes. Genomic profiling of DUX4, histone H3, and H3 modifications reveals that DUX4 binds two classes of locus: DNase accessible H3K27Ac-rich chromatin and inaccessible H3K27Ac-depleted MaLR-enriched chromatin.  At this latter class, it acts as a pioneer factor, recruiting H3K27 acetyltransferase activity and opening the locus for transcription.  In concert with local increased H3K27Ac, the strong H3K27Ac peaks at distant sites are significantly depleted of H3K27Ac, thus DUX4 uses its C-terminus to induce a global reorganization of H3K27 acetylation.

overall_design: Two biological samples were analyzed with 4 antibodies for ChIP-Seq and in triplicate for RNA-Seq.

first: Michael

last: Kyba


title: Psh1-mediated Proteolysis Prevents the Budding Yeast Centromeric Histone Variant from Mislocalizing to Promoter Nucleosomes

first: Sue

last: Biggins

address: 1100 Fairview Ave N MS A2-168

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center


title: Psh1-mediated Proteolysis Prevents the Budding Yeast   Centromeric Histone Variant from Mislocalizing to Promoter Nucleosomes [RNA-seq]

summary: Precise localization of the histone H3 variant CENP-A(Cse4) to centromeres is essential for accurate chromosome segregation. In budding yeast, CENP-A(Cse4) is regulated by ubiquitin-mediated proteolysis to ensure its exclusive localization to the centromere. Overexpression of CENP-A(Cse4) is lethal when the CENP-A(Cse4) E3 ubiquitin ligase, Psh1, is deleted. CENP-A(Cse4) mislocalizes to promoters in this condition, so we investigated if there was an effect on gene expression of downstream genes using RNA-seq.

overall_design: RNA-seq from two or three biological replicates each, at t0 and t2 hours after adding galactose for each of 6 experimental genotypes.

first: Erica

last: Hildebrand


title: ROR-γ drives androgen-receptor expression and represents a therapeutic target in castration-resistant prostate cancer

city: Sacramento

first: Junjian

last: Wang

state: california

department: Biochemistry and molecular medicine

institute: UC Davis

summary: The androgen receptor (AR) is overexpressed and hyperactivated in human castration-resistant prostate cancer (CRPC). However, the determinants of AR overexpression in CRPC are poorly defined. Here we show that retinoic acid receptor–related orphan receptor γ (ROR-γ) is overexpressed and amplified in metastatic CRPC tumors, and that ROR-γ drives AR expression in the tumors. ROR-γ recruits nuclear receptor coactivator 1 and 3 (NCOA1 and NCOA3, also known as SRC-1 and SRC-3)  to an AR–ROR response element (RORE) to stimulate AR gene transcription. ROR-γ antagonists suppress the expression of both AR and its variant AR-V7 in prostate cancer (PCa) cell lines and tumors. ROR-γ antagonists also markedly diminish genome-wide AR binding, H3K27ac abundance and expression of the AR target gene network. Finally, ROR-γ antagonists suppressed tumor growth in multiple AR-expressing, but not AR-negative, xenograft PCa models, and they effectively sensitized CRPC tumors to enzalutamide, without overt toxicity in mice. Taken together, these results establish ROR-γ as a key player in CRPC by acting upstream of AR and as a potential therapeutic target for advanced PCa.

overall_design: A total of 6 samples were analyzed in this study.  The study included one cell line C4-2B. C4-2B cells were cultured in medium containing vehicle control and/or SR2211 and/or XY011 and/or Enzalutamide (ENZ). The untreated C4-2B cells served as controls for the study.

first: Hong-Wu

last: Chen


title: Transcriptomic differences between euryhaline and stenohaline malaria vector sibling species in response to salinity stress [set1]

first: Hilary

last: Uyhelji

summary: We use RNA-Seq to investigate gene expression differences in response to saltwater exposure by the larval stages of the obligate freshwater mosquito Anopheles coluzzii (formerly An. gambiae "M" form), and the euryhaline An. merus.

overall_design: After rearing in freshwater, both young and old larval instars of each species were briefly (6 h) exposed to either saltwater (SW) or freshwater (FW) conditions to test the impact of salinity on mRNA levels.

first: Changde

last: Cheng

first: Nora

last: Besansky


title: Genome wide analysis of binding of Polyhomeotic and polymerization defective Polyhomeotic in Drosophila S2 cells

city: Montréal

first: Nicole

last: Francis

state: Quebec

address: 110, avenue des Pins Ouest

department: Département de biochimie et medécine moléculaire

country: Canada

institute: Université de Montréal

summary: To understand the role of the conserved Sterile Alpha Motif of the Polycomb Group protein Polyhomeotic, the genome wide distribution of wild type and polymerization defective Polyhomeotic containing mutations in the SAM domain was determined by ChIP-SEQ.

overall_design: ChIP-seq Identification of polyhomeotic wild type (PH-WT) and mutant (PH-ML)  binding sites.


title: Psh1-mediated Proteolysis Prevents the Budding Yeast   Centromeric Histone Variant from Mislocalizing to Promoter Nucleosomes [ChIP-Seq]

summary: Precise localization of the histone H3 variant CENP-A(Cse4) to centromeres is essential for accurate chromosome segregation. In budding yeast, CENP-A(Cse4) is regulated by ubiquitin-mediated proteolysis to ensure its exclusive localization to the centromere. Overexpression of CENP-A(Cse4) is lethal when the CENP-A(Cse4) E3 ubiquitin ligase, Psh1, is deleted.  To identify the genomic sites of CENP-A(Cse4) mislocalization in this condition, we investigated the genome-wide mislocalization pattern of CENP-A(Cse4) by ChIP-seq.

overall_design: Flag-Cse4 ChIP DNA and Input MNased chromatin DNA were sequenced for one biological replicate from each of 4 experimental strains.


title: The macrophage IRF8-IRF1 regulome is required for protection against infections, and is associated with chronic inflammation (ChIP-Seq)

status: Public on Mar 07 2016

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

institute: McGill University

summary: IRF8 and IRF1 are transcriptional regulators that play critical roles in the development and function of myeloid cells, including activation of macrophages by pro-inflammatory signals such as interferon gamma. Loss of IRF8 or IRF1 function causes severe susceptibility to infections in mice and in humans. We used chromatin immunoprecipitation sequencing and RNA sequencing in wild type, and in IRF8 and IRF1 mutant primary macrophages to systematically catalog all the genes bound by (cistromes) and transcriptionally activated (regulomes) by IRF8, IRF1, PU.1 and STAT1 including modulation of epigenetic histone marks. Of seven binding combinations identified, two (cluster 1: IRF8/IRF1/STAT1/PU.1; cluster 5: IRF1/STAT1/PU.1) were found to have a major role in controlling macrophage transcriptional programs both at basal level and following IFNγ activation. They direct expression of a set of genes, the IRF8/IRF1 regulome, that play critical roles in host inflammatory and anti-microbial defenses in mouse models of neuroinflammation and of pulmonary tuberculosis, respectively. In addition, this IRF8/IRF1 regulome is enriched for genes mutated in human primary immuno-deficiencies, and with loci associated for several inflammatory diseases in humans.

overall_design: Chromatin immunoprecipitations followed by high throughput sequencing of IRF8, IRF1 and PU.1 transcription factors ChIP prior to and following 0.5h and 3h interferon gamma stimulation on wild type (B6) bone marrow derived macrophages (BMDM). Histone H3 lysine 4 mono-methylation was evaluated by ChIP-seq on untreated wild type BMDMs. H3 lysine 27 acetylation was assessed in wild type (B6) and in IRF8 or IRF1 mutant BMDM prior to and after 3h of interferon gamma stimulation.

first: Philippe

last: Gros


title: The macrophage IRF8-IRF1 regulome is required for protection against infections, and is associated with chronic inflammation (RNA-Seq)

overall_design: Sequencing of RNA extracted for untreated or 3h IFNg-treated bone marrow derived macrophages (BMDM) obtained from wild type (B6) and in IRF8 or IRF1 mutant mice.


title: Characterization of miP1a/b (microProteins) overexpression plants, including a constans mutant (co-SAIL)

city: Frederiksberg C

first: Daniel

last: Straub

address: Thorvaldsensvej 40

department: Plant and Environmental Sciences

country: Denmark

institute: University of Copenhagen

summary: MicroProteins are short, single domain proteins that act by sequestering larger, multidomain proteins into non-functional complexes. MicroProteins have been identified in plants and animals, where they are mostly involved in the regulation of developmental processes. Here we show that two Arabidopsis thaliana microProteins, miP1a and miP1b, physically interact with CONSTANS (CO) a potent regulator of flowering time. The miP1a/b-type microProteins evolved in dicotyledonous plants and have an additional carboxy-terminal PF(V/L)FL motif. This motif enables miP1a/b microProteins to interact with TOPLESS/TOPLESS-RELATED (TPL/TPR) proteins. Interaction of CO with miP1a/b/TPL causes late flowering due to a failure in the induction of FLOWERING LOCUS T (FT) expression under inductive long day conditions. Both miP1a and miP1b are expressed in vascular tissue, where CO and FT are active. Genetically, miP1a/b act upstream of CO thus our findings unravel a novel layer of flowering time regulation via microProtein-inhibition.

overall_design: RNA-Seq transcriptome analysis of four biological samples were analysed with two technical replicates. Columbia wildtype plants Col-0, constans mutant plants co-SAIL, and two transgenic lines overexpressing a microProtein (miP1a and miP1b) were sequenced.

first: Moritz

last: Graeff

first: Tenai

last: Eguen

first: Ulla

last: Dolde

first: Vandasue

last: Rodrigues

first: Ronny

last: Brandt

first: Stephan

last: Wenkel


title: Differential expression analysis of Gcn5 knockdown and triple knockdown of TBP and TBP-related factors (TKD) in Xenopus laevis embryos at early developmental stage 10.5

city: Nijmegen

first: Gert

middle: Jan C.

last: Veenstra

address: Geert Grooteplein 28

department: Molecular Developmental Biology

country: Netherlands

institute: Faculty of Science, Radboud Institute for Molecular Life Sciences

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

overall_design: Refer to individual Series


title: Differential expression analysis of Gcn5 knockdown embryos at early developmental stage 10.5 in Xenopus laevis

summary: We sequenced cDNA prepared from ribosomal RNA depleted total RNA of 10-10 embryos injected with Gcn5-antisense oligonucleotides and with water to create expression profiles of Gcn5 knockdown and control, respectively, in Xenopus laevis at early embryonic developmental stage 10.5. (according to Nieuwkoop and Faber), and we executed differential expression analysis of sequence count data (DEseq).

overall_design: Differential expression analysis using RNA sequencing

first: E

last: Gazdag

first: I

last: Kruijsbergen

first: G

middle: C


title: Genome wide mapping of NR4A binding reveals cooperativity with ETS factors to promote epigenetic activation of distal enhancers in acute myeloid leukemia cells

city: Houston

first: Orla

last: Conneely

address: One Baylor Plaza

institute: Baylor College of Medicine

first: Ryan

last: Duren

first: Seth

last: Boudreaux


title: High-throughput discovery of post-transcriptional cis-regulatory elements (miRNA-seq)

city: Ithaca

first: Andrew

last: Grimson

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

summary: Post-transcriptional gene regulation controls the amount of a protein produced from an individual mRNA transcript by altering mRNA decay and translation rates. Many putative post-transcriptional cis-regulatory elements have been identified from computational, molecular biology, and biochemical studies studies; however, identifying which sequence elements are sufficient to regulate expression remains challenging. We created a high-throughput, cell-based screen that tested the post-transcriptional regulatory potential for thousands of short sequence elements. Sequences with known effects have the expected performance in this screen, showing this methodology is robust. Hundreds of novel short sequences were identified as being able to alter gene expression, both by increasing and decreasing protein production from the fluorescence reporter, and we validated the effects for fifty of these sequences. Importantly, sequences discovered in this screen are conserved in human 3′UTRs, and furthermore, the sequences can regulate expression in the context of those endogenous 3′UTRs. Hundreds of previously unknown post-transcriptional cis-regulatory elements exist, many of which increase gene expression. These results suggest that each human 3′UTR has many small cis-regulatory elements that interact with RNA binding proteins, and these interactions control the fate of an mRNA transcript.

overall_design: miRNAs were sequenced from HEK293-FLP cells

first: Erin

last: Wissink


title: High-throughput discovery of post-transcriptional cis-regulatory elements (8-nt)

summary: Post-transcriptional gene regulation controls the amount of a protein produced from an individual mRNA transcript by altering mRNA decay and translation rates. Many putative post-transcriptional cis-regulatory elements have been identified from computational, molecular biology, and biochemical studies studies; however, identifying which sequence elements are sufficient to regulate expression remains challenging. We created a high-throughput, cell-based screen that tested the post-transcriptional regulatory potential for thousands of short sequence elements. Sequences with known effects have the expected performance in this screen, showing this methodology is robust. Hundreds of novel short sequences were identified as being able to alter gene expression, both by increasing and decreasing protein production from the fluorescence reporter, and we validated the effects for fifty of these sequences. Importantly, sequences discovered in this screen are conserved in human 3?UTRs, and furthermore, the sequences can regulate expression in the context of those endogenous 3?UTRs. Hundreds of previously unknown post-transcriptional cis-regulatory elements exist, many of which increase gene expression. These results suggest that each human 3?UTR has many small cis-regulatory elements that interact with RNA binding proteins, and these interactions control the fate of an mRNA transcript.

overall_design: Two screens were performed in which variable 8-nt sequences were assayed in the context of a human 3' UTR. 8mers that increase gene expression have increased GFP intensity, and vice versa, and these cells undergoing differential regulation were sorted and sequenced. dsRed was used as a control fluorophore


title: Differential expression analysis of triple knockdown of TBP and TBP-related factors (TKD) in Xenopus laevis embryos at early developmental stage 10.5

summary: We sequenced cDNA prepared from ribosomal RNA depleted total RNA of 10-10 embryos co-injected with TBP-,TBP2- and TLF-AS antisense oligonucleotides and with water to create expression profiles of triple knockdown of TBP/TBP-related factors (TKD) and control, respectively, in Xenopus laevis at early developmental stage 10.5. (according to Nieuwkoop and Faber). We executed differential expression analysis of sequence count data (DEseq).


title: Mechanisms of Fibrotic Aortic Valve Stenosis

city: Iowa City

first: Henry

last: Keen

state: IA

institute: University of Iowa

summary: To examine molecular mechanisms of aortic valve stenosis in mice with hypertension and hypercholesterolemia, RNA-Seq was used during the developmental phase of  stenosis to identify new gene targets.

overall_design: Four groups of mice were studied: controls (CON), hypertensive  (HT), hypercholesterolemic (HC), and HC/HT. Transgenic mice overexpressing human renin and human angiotensinogen served as the HT model and ApoE knockout mice served as the HC model.    A sample size of N=4 was used for each of the four groups.

first: Yi

last: Chu

middle: L

first: Curt

last: Sigmund

first: Robert

last: Weiss

first: Donald

last: Heistad


first: Junjian

last: Wang

overall_design: A total of 16 samples were analyzed in this study.  The study included one cell line C4-2B. C4-2B cells were cultured in medium containing vehicle control or SR2211 (5 µM) for 24 hours, cells then were collected for ChIP seq assay

first: Hong-Wu

last: Chen


title: An ancient symbiotic fungal gene network revealed by comparative transcriptomics [Grosea_symbiotic_tissues]

city: Castanet-Tolosan

first: Christophe

last: Roux

address: Chemin de Borde Rouge

country: France

institute: University of Toulouse/CNRS

summary:
Purpose: We here wanted to describe the gene regulation of Gigaspora rosea in association with phyllogenetically divergent plant hosts, and compare these results with gene regulation occuring in R. irregularis, the model arbuscular mycorrhizal fungus.
Methods: mRNA from Medicago truncatula (legume), Brachypodium distachyon (grass) in association with G. rosea, and extra radical mycelium of G.rosea were sequenced by Illumina. Reads were mapped on a in-house de novo transcript assembly with the software CLC workbench. Fungal gene expression in the different host plants was compared to extra radical hyphae as reference.
Results:  Sets of 1891 and 1566 G. rosea genes were highly overexpressed (fold change >5 ; FDR <0,05 and experimental value difference > 10) , in M. truncatula and B. distachyon respectively compared to ERM, among which 802 of them were up-regulated in both plants. Non common up-regulated genes are mainly found non statistically robust in one condition.
Conclusions: Our study represents the first transcriptomic analysis on several hosts for this fungal species. These results showed that the interaction between plants and AMF is highly conserved.

sample_organism:
Medicago truncatula
Brachypodium distachyon
Gigaspora rosea

overall_design: Extra radical and intra radical hyphae in association with 2 phylogenetically divergent plants were produced and gene expression in the different plants were compared to gene expression in extra radical hyphae.

first: Nianwu

last: Tang


title: SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells

city: San Francisco

first: Barbara

last: Panning

state: CALIFORNIA

address: 600, 16TH STREET, S374 - Genentech Hall,

department: Biochemistry and Molecular biology

institute: University of California, San Francisco


title: Epigenomic Landscapes of Retinal Rods and Cones

city: Baltimore

first: Alisa

last: Mo

state: MD

address: 725 N. Wolfe St. PCTB805

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: Both rod and cone photoreceptors are critical for mammalian vision yet they have important functional differences. In this study, we investigate patterns of DNA methylation and chromatin accessibility in mouse rods and cones. Unexpectedly, we find that a substantial fraction of hypo-methylated regions in the rod methylome are in inaccessible chromatin. These regions show marks of active regulatory regions earlier in neuronal development and could remain undermethylated in adult rods due to their highly compact chromatin. We further identify rod- and cone-enriched regions of accessible chromatin that correspond with cell type-specificity of nearby photoreceptor gene expression. We predict novel DNA signatures of rod and cone specificity and show that NR2E3 function is necessary for rods to gain their complete ensemble of epigenomic features. Taken together, our data capture the epigenomic landscapes of retinal rods and cones, including differences relevant to chromatin structure and photoreceptor biology.

overall_design: RNA-seq, MethylC-seq, ATAC-seq, and native histone ChIP-seq in the retina

first: Chongyuan

last: Luo

first: Fred

last: Davis

first: Eran

last: Mukamel

first: Sean

middle: R

last: Eddy

first: Joseph

last: Ecker

first: Jeremy

last: Nathans


title: Gigaspora rosea gene regulation in early steps of AMF-plant symbiosis

summary:
Purpose: we here adress the gene regulation of G.rosea in response to plant signals in the switch from asymbiotic to presymbiotic growth.
Methods:  -Strigolactone response: Spores of G.rosea were treated with GR24 (a synthetic strigolactone analog) and collected at 2 days after treatment. Control conditions: spores treated with solvent (M medium acetone 0.1%. Assay and control were performed in triplicates. -Root exsudate response: a cellophane membrane allowing molecule exchanges was deposited on in vitro Daucus carotta roots. Spores were spotted on this membrane and collected 10 days later. Control conditions: spores were spotted on cellophane membrane directly deposited on solid M medium. Assay and control were performed in triplicates. -Fungal gene expression were analyzed on mRNA were sequenced by Illumina HiSeq. sequencing Reads were firstly used in the de novo assembly of Gigaspora rosea Non Redundent Virtual Transcript and then mapped on the assembled transcriptome using CLC genomics workbench.
Results: while GR24 triggered the regulation of only few genes which includes 32 genes upregulated (fold chang >2; FDR<0,05, experiment difference>10) and 61 downregulated (fold change < -2; FDR<0,05,experiment difference>10) genes, root exudates regulated several times more genes. A total of 390 genes were up-regulated by root exudates and 442 genes were down-regulated. Moreover, a majority of the genes (23 of 32 upregulated and 25 of 61 downregulated genes) regulated by GR24 were also regulated by root exudates. This is in consistant with the fact that strigolactones secreted from plant root are already characterized as a group of plant signals during AM symbiosis. The result that a large part of genes were differentialy expressed in reponse to root exudates but not GR24 suggested the presence of other plant signals than strigolactones.
Conclusions: as a key player during the switch from asymbiotic to presymbiotic growth of G.rosea, plant root secreted signals - including but not limited to striglactones - significantly modified the expression of many G.rosea genes. The genes differentially expressed are mainly involved in oxidation-redution and metabolic processes that might contribute to prepare G.rosea for the following steps of symbiotic association with the host plant.

overall_design: mRNA profiles spores treated with strigolactone or root exudates were generated by deep sequencing, in triplicate, using Illumina.


title: Direct Conversion from Mouse Fibroblasts Informs the Identification of Hemogenic Precursor Cells In Vivo

first: Betty

last: Chang

address: 1425 Madison Ave

institute: Mount Sinai School of Medicine

summary: Definitive hematopoiesis emerges via an endothelial-to-hematopoietic transition in the aorta-gonad-mesonephros (AGM) region and placenta. We have recently demonstrated the induction of hematopoietic stem/progenitors (HSPCs) from mouse fibroblasts with a combination of transcription factors progressing through endothelial-like precursors. Here, guided by our in vitro programming experiments we analyzed mouse placentas for the presence of the precursor phenotype. We identified a small population of CD34+ Sca1+Prom1+ (34PS) cells in mid-gestation placentas that do not express the pan-hematopoietic marker CD45. After isolation and culture 34PS cells acquire CD45 and generate large hematopoietic as well as cobblestone colonies. Prom1+ cells localize to the placental vascular labyrinth where HSPCs emerge. 34PS cells express markers associated with the hemogenic endothelium (CD31, Tie2, VE-Cadherin, Sox17, Runx1, Scl) and also markers identified by direct induction (Itga6/CD49f). This population is heterogeneous for the early hematopoietic marker CD41 and expresses the programming transcription factors. Remarkably, global gene expression profiles of placental 34PS cells correlate with AGM-derived hemogenic endothelium and fibroblast-derived precursors. Finally, when co-cultured with stroma placental 34PS cells give rise to B/T lymphoid cells as well as mixed colonies containing erythroid, myeloid and megakaryocytic cell lineages. In summary, we show that direct in vitro conversion provided a cell surface phenotype for the isolation of hemogenic precursors in vivo. Our findings provide insights into the specification of definitive hemogenesis in the placenta, in depth characterization of hemogenic precursor populations and the first evidence that direct in vitro conversion approaches can be used as a valuable tool to address basic developmental questions in vivo.

overall_design:
mRNAseq profiling on populations isolated by selected marker fluorescence activated cell sorting
The 'E10_E12_HSPC_SingleCell_FPKM.txt.gz' contains the processed data for GSM1890353-GSM1890496.

first: Carlos-Filipe

last: Pereira

first: Kateri

last: Moore

first: Ihor

last: Lemischka


title: MicroRNA-mediated regulation of gene expression in the response of rice plants to fungal elicitors

status: Public on Mar 06 2016

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis


title: Whole transcriptome profiles of different brain regions from a Chlorocebus sabaeus model of Parkinson's disease with and without human parthenogenetic stem cell derived neural stem cell transplantation.

status: Public on Mar 05 2016

city: san diego

first: Marwa

last: Khater

address: 11990 cypress valley dr

institute: UCSD

summary: RNAseq was performed on caudate, putamen, and substantia nigra samples from animals treated with MPTP to induce a Parkinson's-like condition, and then transplanted with hpNSCs or control buffer. The goal of the study was to determine if there were any difference in gene expression caused by the transplanted cells.

overall_design: Animals were treated with MPTP to induce a Parkinson's-like condition, and received either hpNSC transplantation or injections of buffer. Biopsies of the caudate, putamen, and substantia nigra from each animal were analyzed by RNAseq.

first: Louise

last: Laurent


title: IL-17A induces inhibition of OB function

city: Madrid

first: Ozge

last: Uluckan

address: calle melchor fernandez almagro, 3

institute: CNIO

summary: We report that IL-17A has an inhibitory effect on osteoblastogenesis.

overall_design: Pre-osteoblasts were treated with vehicle or 50ng/ml IL-17A for 7 days.

first: Osvaldo

last: Grana

first: Erwin

last: Wagner


title: Physiology study of Escherichia coli harboring high intracellular ATP driven by artificial Pck expression

city: Bucheon

first: Hyojung

last: Lee

address: Rm 718 Dasol Bd., 43 Jibong-ro, Wonmi-gu

department: Biotechnology

country: South Korea

institute: The Catholic University of Korea

summary: We have previously reported that phosphoenolpyruvate carboxykinase(Pck) overexpression under glycolytic conditions enables Escherichia coli to harbor a high intracellular ATP pool resulting in enhanced recombinant protein synthesis and biohydrogen production. To understand possible reasons of the high ATP haboring cell, we carried out transcriptome and metabolic flux analysis.

overall_design: Comparison of main metabolic gene and regulator expression profiling using RNA-seq data of BL21(DE3) vs. BL21(DE3)_Pck_over under glucose LB

first: Pil

last: Kim

first: Hyo


title: Genome-wide maps of Meis1, Hoxa9 and Pbx binding sites in murine myeloid leukemia cells

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

institute: Japanese Foundation for Cancer Research

summary: We have searched genome-wide binding sites of homeodomain proteins important for leukemogenesis in Hoxa9- and Meis1- induced myeloid leukemia cells. Thousands of binding sites of these three family proteins have been identified and many of them are co-localized with those of each others. Hoxa9 and Pbx binding sites were compared between the presence and absence of Meis1 by its knockout in the same cells. In combination of the results with gene expression profiles of the same cells, important downstream target genes of Meis1 in leukemogenesis have been identified.

overall_design: Examination of binding sites of 3 transcription factors in a single cell with 2 different conditions

first: Takashi

last: Yokoyama


title: CRISPResso: sequencing analysis toolbox for CRISPR genome editing

status: Public on Mar 04 2016

city: boston

first: Luca

last: Pinello

state: MA

address: 450 brookline avenue

institute: Dana-Farber Cancer Institute

summary: CRISPResso is a software pipeline for the analysis of targeted CRISPR-Cas9 deep sequencing data. This algorithm allows for the quantification of both non-homologous end joining (NHEJ) and homologous directed repair (HDR) occurrences (https://github.com/lucapinello/CRISPResso)

overall_design: Cells nucleofected with either CRISPR/Cas9 alone or with CRISPR/Cas9 and a homologous donor template were subjected to targeted high-throughput sequencing of the beta-globin locus. Here, one sample with just CRISPR/Cas9 edited cells and 2 samples with CRISPR/Cas9 and donor edited cells were analyzed.

first: Megan

last: Hoban


title: Characterizing the heterogeneity of triple-negative breast cancers using RNA Sequencing

city: Indianapolis

first: Milan

last: Radovich

state: Indiana

address: 980 W. Walnut St, Room C312

institute: Indiana University School of Medicine

summary: Triple-negative breast cancers (TNBCs) are a heterogeneous set of tumors defined by an absence of actionable therapeutic targets (ER, PR, and HER-2). Microdissected normal ductal epithelium from healthy volunteers represents a novel comparator to reveal insights into TNBC heterogeneity and to inform drug development. Using RNA-sequencing data from our institution and The Cancer Genome Atlas (TCGA) we compared the transcriptomes of 94 TNBCs, 20 microdissected normal breast tissues from healthy volunteers from the Susan G. Komen for the Cure Tissue Bank, and 10 histologically normal tissues adjacent to tumor. Pathway analysis comparing TNBCs to optimized normal controls of microdissected normal epithelium versus classic controls composed of adjacent normal tissue revealed distinct molecular signatures. Differential gene expression of TNBC compared with normal comparators demonstrated important findings for TNBC-specific clinical trials testing targeted agents; lack of over-expression for negative studies and over-expression in studies with drug activity. Next, by comparing each individual TNBC to the set of microdissected normals, we demonstrate that TNBC heterogeneity is attributable to transcriptional chaos, is associated with non-silent DNA mutational load, and explains transcriptional heterogeneity in addition to known molecular subtypes. Finally, chaos analysis identified 146 core genes dysregulated in >90 % of TNBCs revealing an over-expressed central network. In conclusion, use of microdissected normal ductal epithelium from healthy volunteers enables an optimized approach for studying TNBC and uncovers biological heterogeneity mediated by transcriptional chaos.

overall_design: RNA sequencing data from 10 TNBC tumors is included in this submission.  No data from the 84 TCGA TNBCs or normal breast tissues are included in this submission.  Reference dbGaP accession phs000644.v1.p1 for data from normal tissues.


title: MicroRNA-mediated regulation of gene expression in the response of rice plants to fungal elicitors [miRNA-Seq]

summary: Elicitor-responsive miRNAs and their targets in rice

overall_design: Rice small RNA profiling in two tissues (leaf and root) and two time points (30 minutes and 2 hours) of elicitor treatment (Margaporthe oryzae). Three replicates of each condition.

last: Baldrich

first: Sonia

last: Campo

first: Ming-Tsung

last: Wu

first: Tze-Tze

last: Liu

first: Yue-Ie

last: Hsing

first: Blanca

last: San Segundo


title: Zika Virus Targets Human Cortical Neural Precursors and Attenuates Their Growth

city: Atlanta

first: Bing

last: Yao

state: GA

address: 615 Michael St. Rm 323

institute: Emory University

summary: The suspected link between infection by Zika virus (ZIKV), a re-emerging flavivirus, and microcephaly, is an urgent global health concern. The direct target cells of ZIKV in developing human fetuses are not clear. Here we show that ZIKV serially passaged in monkey and mosquito cell lines infects human induced pluripotent stem cells (hiPSCs)-derived cortical neural progenitor cells (hNPCs) with much higher efficiency compared to hiPSCs and hNPC-derived immature cortical neurons. Infected hNPCs produces infectious ZIKV particles. Importantly, ZIKV infection increases cell death and dysregulates cell cycle progression, resulted in attenuated hNPC growth. RNA-sequencing analysis of infected hNPCs further reveals transcriptional dysregulation, notably genes in cell cycle pathways. Our results identify human cortical neural precursors as a major and direct target of ZIKV infection and establish a tractable experimental model system to investigate the impact and mechanism of ZIKV on human brain development and a platform to screen therapeutic compounds.

overall_design: The suspected link between Zika virus infection and microcephaly is an urgent global health concern. Tang et al. report that Zika virus directly infects human cortical precursor cells with high efficiency, resulting in stunted growth and transcriptional dysregulation.


title: SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells[ChIP-seq]

first: Barbara

last: Panning

summary: The transcription factor SOX2 is central in establishing and maintaining pluripotency. The processes that modulate SOX2 activity to promote pluripotency are not well understood. Here, we show SOX2 is O-GlcNAc modified in its transactivation domain during reprogramming and in mouse embryonic stem cells (mESCs). Upon induction of differentiation SOX2 O-GlcNAcylation at serine 248 is decreased. Replacing wild type with an O-GlcNAc-deficient SOX2 (S248A) increases reprogramming efficiency. ESCs with O-GlcNAc-deficient SOX2 exhibit alterations in gene expression. This change correlates with altered protein-protein interactions and genomic occupancy of the O-GlcNAc-deficient SOX2 compared to wild type. In addition, SOX2 O-GlcNAcylation impairs the SOX2-PARP1 interaction, which has been shown to regulate ESC self-renewal. These findings show that SOX2 activity is modulated by O-GlcNAc modification, and provide a novel regulatory mechanism for this crucial pluripotency transcription factor.

overall_design: We performed FLAG chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) to compare SOX2 genomic distribution in fSOX2-Tg and fS248A-Tg mouse embryonic stem cells. We had two biological replicates for ChIP DNA and one input DNA per cell line. We had two sets of chromatin due to differences in fragment size distribution generated after sonication of the chromatin (long and short) and we decided to use both for library preparation. Long chromatin library was generated from chromatin that still had high molecular weight fragments (1-2Kb-500bp) even after sonication. Short chromatin library was generated using sheared chromatin that had majority of fragments under small molecular weight range (500-200 bp). We sequenced two biological replicates (long and short) and two technical replicates per sonication condition (two longs and two shorts) and one input per cell line. We multiplexed five samples. Sequences were generated using HiSeq 2000.

first: Sailaja

last: Peddada


title: Widespread differential expression of coding region and UTR sequences in neurons and other tissues

city: New York

first: Mary

middle: Alanna

last: Hynes

address: 1230 York Ave

institute: Rockefeller University

summary: Mature messenger RNAs (mRNAs) consist of coding sequence (CDS) and 5’ and 3’ untranslated regions, typically expected to show similar abundance within a given neuron. Examining mRNA from defined neurons we unexpectedly show extremely common unbalanced expression of cognate 3’ UTR and CDS sequences, observing many genes with high UTR relative to CDS, and others with high CDS to UTR. By in situ hybridization 19 of 19 genes examined show a broad range of UTR to CDS expression ratios in different neurons and other tissues. These ratios may be spatially graded or change with developmental age, but are consistent across animals. Further, for two genes examined, a UTR to CDS ratio above a particular threshold in any given neuron correlated with reduced or undetectable protein expression.  Our findings raise questions about the role of isolated UTR sequences in regulation of protein expression, and highlight the importance of separately examining UTR and CDS sequences in gene expression analyses.

overall_design: dopamine or serotonin neuronal mRNA was purified selectively by using dopamine transporter (DAT) and SLC6A4 (serotonin transporter)  BacTrap mice.  RNA sequencing was carried out using  Illumina HiSeq 2500.

first: Arif

last: Kocabas

first: Terence

last: Duarte

first: Saranya

last: Kumar


title: Transcriptional profiling of antigen-specific CD8 T cells from wildtype and mutant mice.

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

summary: To understand CD8 effector T cell differentiation in more detial we have used transcriptional profiling of antigen-specific CD8 T cells deficient in Blimp1, IL-2ra, or both, or Tbet. We reveal a common program of effector differentiation regulated by cytokine signaling and the combined activities of Blimp1 and T-bet, indicating remarkable redundancy and specificity in the control of genes involved in the differentiation of effector T cells.

overall_design: Bone marrow chimeric mice were generated containing congenically marked wildtype and mutant heamatopoietic cells. The mice were infected with primed with PR8 influenza virus. Six weeks later they were infected with the heterologous HKx31 influenza virus. Antigen-specific (NP366) positive CD8 T cells were sorted. RNA was exracted and RNA sequening performed.

first: Annie

last: Xin

first: Axel

last: Kallies

first: Warren

last: Leonard

first: Yang

last: Liao

first: Gordon

last: Smyth


title: Knockdown of SR protein family in P19 cells and RNA-seq of cytoplasmic and whole cell polyA+ RNA

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

department: Institute for Cell Biology and Neuroscience

country: Germany

institute: Goethe University Frankfurt

summary: Our data suggest that all SR proteins contribute to mRNA export via NXF1. To identify endogenous export targets we depleted all seven SR proteins individually from P19 WT cells prepared cytoplasmic fractions. We sequenced the cytoplasmic fraction and as a control whole celll RNA from the identical sample.

overall_design: Knockdown of seven SR Proteins plus control, total RNA and cytoplasmic RNA, polyA+ enriched, 2 biological replicates per condition, 2 technical replicates per condition

first: Karla

last: Neugebauer


title: Transcriptomic analysis of human iPS cells derived from fragile X syndrome patients during neural differentiation

city: Memphis

first: Xiaolong

last: Chen

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hospital

summary: Fragile X syndrome (FXS) is one of the most prevalent inherited intellectual disabilities. The patients carry the expansion of over 200 CGG repeats located at the 5′ untranslated region of fragile X mental retardation 1 (FMR1). As a result, the FMR1 promoter becomes hypermethylated leading to decreased or absent expression of its encoded RNA-binding protein fragile X mental retardation protein (FMRP). We previously generated human induced pluripotent stem (iPS) cells from fibroblasts of a FXS patient (FXS-iPSC) with expanded CGG-repeats at the FMR1 promoter. In the present work, we explored the transcriptional misregulation during the embryonic neurogenesis by in-vitro differentiation of FXS-iPSC into neurons through the intermediate stages. At each differentiation stage, we collected RNA and performed RNA-seq. After an integrated analysis, we found up-regulation of many genes encoding TFs for neuronal differentiation (WNT1, BMP4, POU3F4, TFAP2C, and PAX3), down-regulation of potassium channels (KCNA1, KCNC3, KCNG2, KCNIP4, KCNJ3, KCNK9, and KCNT1) and altered temporal regulation of SHANK1 and NNAT in FXS-iPSC derived neurons, indicating impaired neuronal differentiation and function in FXS patients. Furthermore, we found the cholesterol synthesis genes (e.g., SQLE, LSS, and FASN) are up-regulated during the in-vitro neuronal differentiation of FXS-iPSC, which may contribute to the obesity phenotype of FXS patients. In conclusion, we demonstrated that the FMRP deficiency in FXS patients has significant impact on the gene expression patterns during development, and also discovered many potential candidate genes for the cure of FXS symptoms such as neuronal abnormalities and obesity.

overall_design: Eight samples at four different time including iPSC, iPSC aggregates, neuroepithelia aggregates, neuron.

first: Ping

last: Lu


title: ChIP-seq and RNA-Seq analyses of epithelial and mesenchymal cells - HMLE, N8, N8-CTx

city: Cambridge

first: Diwakar

last: Pattabiraman

address: 9 Cambridge Center

institute: Whitehead Institute

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

overall_design: Refer to individual Series


title: MicroRNA-mediated regulation of gene expression in the response of rice plants to fungal elicitors [degradome]

first: Patricia

last: Baldrich Gonzalez

last: Baldrich

first: Sonia

last: Campo

first: Ming-Tsung

last: Wu

first: Tze-Tze

last: Liu

first: Yue-Ie

last: Hsing

first: Blanca

last: San Segundo


title: Investigation of small RNA and RNA-seq transcripts from soybean (Glycine max) DCL1 mutants

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: In plants, DICER-LIKE1 is a critical enzyme in the biogenesis pathway of plant miRNAs. Zinc-finger nucleases were used to generate single and double-mutants of soybean DCL1 homologs. We created several small RNA libraries to investigate the effect on miRNA abundance in these various mutants. RNAseq transcript data was also generated in order to investigate targets of those impacted miRNAs.

overall_design: Genome-wide small RNA profiling was done by Illumina TruSeq sample preparation followed by high-throughput sequencing with Illumina HiSeq 2000 platform.

first: Shaun

last: Curtin

first: Reza

last: Hammond


title: RNA-Seq comparisons of gene expression profiles of epithelial and mesenchymal cells - HMLE, N8, N8-CTx

summary: We find that treating mesenchymal NAMEC8 cells with cholera toxin (CTx) to elevate intracellular cAMP levels and activate PKA induces a mesenchymal-to-epithelial transition whereby the cells assume an epithelial state (N8-CTx). NAMEC8 cells undergo epigenetic reprogramming triggered by active PHF2, a histone demethylase, which demethylates H3K9me2 and H3K9me3 regions of epithelial genes silencing in the mesenchymal state

overall_design: Performing RNASeq with HMLE (immortalized human mammary epithelial cells), their mesenchymal CD44hi counterparts, NAMEC8 and the CTx-reverted versions of NAMEC8 a.k.a N8-CTx

first: Jordan

last: Krall

first: Robert

last: Weinberg


title: High-throughput discovery of post-transcriptional cis-regulatory elements

city: Ithaca

first: Andrew

last: Grimson

address: 445 Biotechnology Building

institute: Cornell University


title: RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes in Human Normal and Cancerous Tissues

city: Shanghai

first: Chunyang

last: Bao

state: Shanghai

address: Shanghai Medical College, Fudan University 1207 Rm., 2# Bldg., 270 Dong An Rd.

department: Fudan University Shanghai Cancer Center

country: China

institute: Fudan University

summary: Circular RNAs (circRNAs) represent a novel class of widespread and diverse endogenous RNAs that may regulate gene expression in eukaryotes. However, the regulation and function of human circRNAs remain largely unknown. Here we generate ribosomal-depleted RNA sequencing data from six normal tissues and seven cancers, and detect at least 27,000 circRNA candidates.

overall_design: RNA profiles of six normal tissues and seven cancers were generated by deep sequencing, using Illumina HiSeq 2000.

first: Qiupeng

last: Zheng

first: Xianghuo

last: He

first: Shenglin

last: Huang


title: ChIP-seq comparisons of H3K9me2, H3K9me3 and PHF2 occupancy profiles of epithelial and mesenchymal cells - N8, N8-CTx

first: Diwakar

last: Pattabiraman

overall_design: Performing ChIP-Seq on NAMEC8 and the CTx-reverted version of NAMEC8 a.k.a N8-CTx


title: Saffron Transcriptome and Gene Expression

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

summary: In this study, we aim to present a global transcriptome analysis of medicinal/spice plant, Crocus sativus. We generated about 206 million high-quality reads from five tissues (corm, leaf, Tepal, stamen and stigma) using Illumina platform. We performed an optimized de novo assembly of the reads and estimated transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses among tissue samples.

overall_design: We collected different tissue samples from the mature plants. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequence data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were used for de novo assembly optimization. The reads were further mapped to the saffron transcripts via CLC Genomics Workbench and differential gene expression analysis was performed using DESeq software.

first: Rajesh

last: Ghangal

first: Mohit

last: Verma


title: OSKM induce extraembryonic endoderm stem (iXEN) cells in parallel to iPS cells

status: Public on Mar 03 2016

city: East Lansing

first: Michael

last: Halbisen

state: MI

address: 603 Wilson Rd RM 419

department: Biochemistry and Molecular Biology

institute: Michigan State University

summary:
While the reprogramming factors OCT4, SOX2, KLF4, and MYC (OSKM) can
reactivate the pluripotency network in terminally differentiated cells, they also regulate expression of non-pluripotency genes in other contexts, such as the mouse primitive endoderm. The primitive endoderm is an extraembryonic lineage established alongside the pluripotent epiblast in the blastocyst, and is the progenitor pool for extraembryonic endoderm stem (XEN) cells. Several studies have shown that endodermal genes are upregulated in fibroblasts undergoing reprogramming, although whether endodermal genes promote or inhibit acquisition of pluripotency is unclear. We show that, in fibroblasts undergoing conventional reprogramming, OSKM-induced expression of endodermal genes leads to formation of induced XEN (iXEN) cells, which possess key properties of blastocyst-derived XEN cells, including morphology, transcription profile, self-renewal, and multipotency. Our data show that iXEN cells arise in parallel to iPS cells, indicating that OSKM are sufficient to drive cells to two distinct fates during reprogramming.

overall_design: Sequence-based mRNA transcriptional profiling of three different cell lines (MEF, XEN, iXEN) with multiple biological replicates, under two different growth medium conditions (ESC medium, XEN medium) for XEN and iXEN cells.

first: Anthony

last: Parenti

first: Kai

last: Wang

first: Keith

last: Latham

first: Amy

last: Ralston


title: Roles of Yap1 in mouse embryonic stem cells

city: Austin

first: Jonghwan

last: Kim

state: TX

address: 2506 Speedway NMS 4.246

department: Department of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology

institute: University of Texas at Austin

summary: We report that Yap1 is dispensable for the maintenance of ES cells while Yap1 is required for the differentiation of ES cells using global gene expression profile

overall_design: RNA-seq analysis upon KD of Yap1 in ES and differentiated ES cells and overexpression of Yap1


title: Transcriptome analysis of cryptococcal IPK mutants

city: Westmead

first: Julianne

middle: T

last: Djordjevic

state: NSW

address: 176 Hawkesbury Road

department: Centre for Infectious Diseases and Microbiology

institute: Westmead Institute for Medical Research

summary: In eukaryotes, inositol polyphosphates perform essential metabolic and signaling functions. Using human fungal pathogen Cryptococcus neoformans as a model, we created mutants in three inositol polyphosphates kinases: Arg1, Ipk1 and Kcs1.  Each of the mutants produces a unique repertoire of inositol polyphosphates, different from the wild type strain. Comparative phenotypic and transcriptome analyses of wild type and mutant strains indicates that inositol polyphosphate PP-IP5 (IP7) is the key regulator of gene expression, fitness and virulence in C. neoformans.

overall_design: Comparison of WT and mutants (Darg1, Dkcs1 and Dipk1) grown in broth culture in the absence of stress.

first: Sophie

last: Lev

first: Desmarini

last: Desmarini


title: The macrophage IRF8-IRF1 regulome is required for protection against infections, and is associated with chronic inflammation

city: MONTREAL

first: David

last: Langlais

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

institute: McGill University


title: RUNX super-enhancer control through the Notch pathway by Epstein-Barr virus transcription factors regulates B cell growth

city: London

first: Richard

last: Jenner

address: 72 Huntley Street

department: Cancer Biology

institute: UCL Cancer Institute

summary: In B cells infected by the cancer-associated Epstein-Barr virus (EBV), RUNX3 and RUNX1 transcription is manipulated to control cell growth. The EBV-encoded EBNA2 transcription factor (TF) activates RUNX3 transcription leading to RUNX3-mediated repression of the RUNX1 promoter and the relief of RUNX1-directed growth repression. We show that EBNA2 activates RUNX3 through a specific element within a -97 kb super-enhancer in a manner dependent on the expression of the Notch DNA-binding partner RBP-J. We also reveal that the EBV TFs EBNA3B and EBNA3C contribute to RUNX3 activation in EBV-infected cells by targeting the same element. Uncovering a counter-regulatory feed-forward step, we demonstrate EBNA2 activation of a RUNX1 super-enhancer (-139 to -250 kb) that results in low-level RUNX1 expression in cells refractory to RUNX1-mediated growth inhibition. EBNA2 activation of the RUNX1 super-enhancer is also dependent on RBP-J. Consistent with the context-dependent roles of EBNA3B and EBNA3C as activators or repressors, we find that these proteins negatively regulate the RUNX1 super-enhancer, curbing EBNA2 activation. Taken together our results reveal cell-type specific exploitation of RUNX gene super-enhancers by multiple EBV TFs via the Notch pathway to fine tune RUNX3 and RUNX1 expression and manipulate B-cell growth.

overall_design: Examination of EBNA2 protein binding using a monoclonal antibody (PE2) in single ChIP-seq experiments carried out in the human GM12878 EBV transformed lymphoblastoid cell line.

first: Andrea

last: Gunnell

first: Helen

middle: M

last: Webb

first: C

last: Wood

last: McClellan

first: Billy

last: Wichaidit

first: Bettina

last: Kempkes

middle: G

first: Cameron

last: Osborne

first: Paul

last: Farrell

first: Michelle

last: West


title: Digital gene expression tag profiling of pig subcutaneous adipose tissue from postnatal 0 day to 7 years

city: Rongchang

first: Jie

last: Zhang

state: Chongqing

address: Xueyuan road #160

department: College of Animal Science

institute: Southwest University

summary: Adipose tissues have important roles in the pathogenesis of obesity and its comorbidities by secreting cytokines involved in the regulation of metabolism. In mammals, part of the extends life span across species from yeast to primates is thought to be mediated by decreases in adipose mass. Indeed, depletion or expansion of adipose tissue using genetic or surgical approaches has been shown to impact the risk of many metabolic diseases and affect mean and maximum lifespan in rodents. An age-related function changes in adipose tissue is well documented in several species and may predispose to obesity and metabolic alterations also associated with advancing age, such as insulin resistance or hyperlipidemia. As a result, comparing gene expression profiles of adipose tissue from different ages may elucidate the molecular mechanisms underlying adipose tissue changes. Here, we used Digital Gene Expression tag profiling (DGE) to determine the gene expression profiles of postnatal 0 day, 30 days, 180 days and 7 years subcutaneous adipose tissues from pigs.

overall_design: A large-scale analysis of gene expression of postnatal 0 day, 30 days, 180 days and 7 years subcutaneous adipose tissues from pigs using digital gene expression tag profiling approach.

first: J

first: M

middle: Z

last: Li

first: X


title: H2ABbd ChIP-seq and MeDIP sequence result

city: Ann Arbor

first: Yibin

last: Chen

address: 1115 w medical drive

institute: university of Michigan

summary: H2ABbd is a unique histone H2A variant that shares only 40 ~ 50 % sequence identity with canonical H2A. It has only been identified in mammals and has quickly evolved with remarkable sequence diversity among different species. H2ABbd is ubiquitously expressed in most cells and tissues. It is mainly deposited in gene body region.The localization of H2ABbd is associated with methylated CpG islands in mouse ES cells.H2ABbd facilitates transcription elongation to go through methylated CpG islands in the gene bodies. One typical example is that H2ABbd regulates transcription elongation at imprinted loci.

overall_design: We found H2ABbd enriched in some methylated loci. Using ChIP-seq and MeDIP-seq, we test the correlation of H2ABbd and DNA methylation.

first: Xiaochun

last: Yu


title: RNA-Seq profiling of Ewing's sarcoma and MSC cell lines

city: Oxford

first: Helio

last: Pais

address: Jonh Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: Comparison of expression profile of Ewing's sarcoma with cell of origin, mesenchymal stem cells with the goal of identifying novel therapeutic targets.

overall_design: 3 Ewing's cell lines compared to 2 MSC cell lines

first: Terence

last: Rabbitts

first: Jennifer

last: Town


title: NGS-mRNA in colonic mucosal tissues in wild type control and Sgo1-/+

city: Oklahoma City

first: Hiroshi

middle: Y

last: Yamada

state: Oklahoma

department: Medicine

institute: OUHSC

summary: We compare mRNA expression profiles between wild type control and Sgo1-/+ chromosome instability model mice

overall_design: Characterize influence of chromosome instability on colon


title: Transcriptional profiling of Klebsiella pneumoniae defines signatures for planktonic, sessile and biofilm-dispersed cells

city: Clermont-Ferrand

first: Damien

last: BALESTRINO

address: 28 Place Henri Dunant

institute: Université Clermont Auvergne

summary:
Purpose: The goal of this study was to use RNA-seq to define the Klebsiella pneumoniae transcriptome recorded under 5 different experimental conditions, and to identify signature genes of each condition by comparing global transcriptional profiles.
Methods: mRNA profiles were generated for Klebsiella pneumoniae CH1034 clinical isolate, in triplicate, by deep sequencing. Total RNAs were harvested from bacteria cultured at 37°C in M63B1 minimal media under different conditions: (i) planktonic aerobic condition at OD 620nm=0.250 (exponential growth-phase), (ii) overnight planktonic aerobic condition (stationnary growth-phase), (iii) biofilm in a flow-cell chamber after 7 hours of incubation (7-hours old biofilm), (iv) biofilm in a flow-cell chamber after 13 hours of incubation (13-hours old biofilm), (v) bacteria self-dispersed from biofilm recovered in the flow-cell effluent (biofilm-dispersed bacteria). Ribosomal RNAs were removed using the Bacteria Ribo-Zero Magnetic kit (Epicentre Biotechnologies). Libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Illumina), and 50bp single-reads were obtained by HiSeq 2000 (Illumina).The sequence reads that passed FastQC quality filters were mapped to the CH1034 genome using Burrows–Wheeler Aligner (BWA) (0.7.12-r1039 version). The transcript levels were determined using HTSeq-count (0.6.1p1 version) with union mode followed by DESeq (1.16.0 version) analysis. qRT–PCR validation was performed using SYBR Green assays.
Results: We found that each condition has a specific transcriptional profile, and we identify 4 robust signature genes for each.
Conclusion: Our study represents the first detailed analysis of K. pneumoniae transcriptomes under different experimental conditions generated by RNA-seq technology. The data reported here should permit the dissection of complex biologic functions involved in the transition between the sessile and planktonic modes of growth.

overall_design: Determination of the transcriptional profiling of Klebsiella pneumoniae under 5 different experimental conditions. mRNA profiles were generated for bacteria under exponential planktonic growth-phase, stationary planktonic growth-phase, 7 hours-old biofilm, 13 hours-old biofilm and biofilm-dispersed modes, each in three biological replicates, by deep sequencing using Illumina HiSeq

first: Cyril

last: Guilhen

first: Nicolas

last: Charbonnel

first: Nathalie

last: Gueguen

first: Agnès

last: Iltis

first: Christiane

last: Forestier

last: Balestrino


title: Micro RNA 172 (miR172) signals epidermal infection and is expressed in cells primed for bacterial invasion in Lotus japonicus roots and nodules

city: Aarhus

first: Jens

last: Stougaard

address: Gustav Wieds Vej 10

department: Department of Molecular Biology and Genetics

institute: Centre for Carbohydrate Recognition and Signalling, Aarhus University

summary:
Legumes interact with rhizobial bacteria to form nitrogen-fixing root nodules. Host signalling following mutual recognition ensures a specific response, but is only partially understood. Focusing on the stage of epidermal infection with Mesorhizobium loti, we analysed endogenous small RNAs (sRNAs) of the model legume Lotus japonicus to investigate their involvement in host response regulation. We used Illumina sequencing to annotate the L. japonicus sRNA-ome and isolate infection-responsive sRNAs, followed by candidate-based functional characterization.

Sequences from four libraries revealed 219 novel L. japonicus micro RNAs (miRNAs) from 114 newly assigned families, and 76 infection-responsive sRNAs. Unlike infection-associated coding genes such as NODULE INCEPTION (NIN), a micro RNA 172 (miR172) isoform showed strong accumulation in dependency of both Nodulation (Nod) factor and compatible rhizobia. The genetics of miR172 induction support the existence of distinct epidermal and cortical signalling events. MIR172a promoter activity followed a previously unseen pattern preceding infection thread progression in epidermal and cortical cells. Nodule-associated miR172a expression was infection-independent, representing the second of two genetically separable activity waves.

The combined data provide a valuable resource for further study, and identify miR172 as an sRNA marking successful epidermal infection. We show that miR172 acts upstream of several APETALA2-type (AP2) transcription factors, and suggest that it has a role in fine-tuning AP2 levels during bacterial symbiosis.

overall_design: Small RNA responses during early bacterial symbiosis development (3 dpi) in Lotus japonicus wild type plants were analyzed using Illumina deep sequencing. A total of 4 small RNA libraries were sequenced, including mock treated and inoculated root samples of two biological replicates each.

first: Dennis

middle: B

last: Holt

first: Vikas

last: Gupta

first: Dörte

last: Meyer

first: Nikolaj

last: Abel

first: Stig

middle: U

last: Andersen

first: Katharina

last: Markmann


title: miRNA-1343 attenuates pathways of fibrosis by targeting the TGF-beta receptors [RNA-seq]

city: Cleveland

first: Ann

last: Harris

state: OH

address: 10900 Euclid Ave

department: Genetics and Genome Sciences

institute: Case Western Reserve University

summary: miRNA-1343 is an uncharacterized miRNA predicted to target a number of genes involved in epithelial cell function including TGF-beta signaling, cell adhesion, and cell proliferation. We transiently overexpressed miRNA-1343 or a non-targeting control miRNA in A549 and 16HBE14o- human airway cell lines. As predicted, RNA-seq following miRNA-1343 overexpression showed significant downregulation of genes involved in these pathways. Furthermore, genes involved in cholesterol and lipid biosynthesis were found to be significantly upregulated by miRNA-1343 overexpression.

overall_design: mRNA profiles from A549 and 16HBE14o- cells transiently transfected with miRNA-1343 or a negative control (NC) miRNA, in quintuplicate.

first: Lindsay

last: Stolzenburg

first: Sarah

last: Wachtel

first: Hong

last: Dang


title: The methyl binding domain 3 (MBD3) family proteins promote Tet2 enzymatic activity for mediating 5mC conversion [HTS]

first: Wei

last: Li

address: DongAn Road 130

institute: FuDan University

summary: Ten-eleven translocation (TET) proteins are key players involved in the dynamic regulation of cytosine methylation and demethylation. Inactivating mutations of TET2 are frequently found in human malignancies, highlighting the essential role of TET2 in cellular transformation. However, the factors that control TET enzymatic activity remain largely unknown. Here we found that MBD3 and its analogue MBD3L2 can specifically modulate the enzymatic activity of Tet2 protein, but not Tet1 and Tet3 proteins, in converting 5mC into 5hmC. Moreover, MBD3L2 is more effective than MDB3 in promoting Tet2 enzymatic activity via strengthening the binding affinity between Tet2 and the methylated DNA target. Further analysis revealed pronounced decreases in 5mC levels at MBD3L2 and Tet2 co-occupied genomic regions, most of which are promoter elements associated with either cancer-related genes or genes involved in the regulation of cellular metabolic processes. Our data add new insights into the regulation of Tet2 activity by MBD3 and MBD3L2 in modulating its target gene activities in cancer development and have important applications in understanding how dysregulation of TET2 may contribute to human malignancy.

overall_design: ChIP-Seq experiments were performed for HA-Tet2 and HA-MBD3L2 in HEK293T cells overexpressing these two proteins. Comparative hMeDIP-Seq experiments were  conducted to compare the genome-wide distribution of 5hmC in HEK293T cells after transfection of Tet2 and MBD3L2 simultaneously or individually. RRBS experiments were used to detect the global methylation level change after transfection of Tet2 and MBD3L2.

first: Lina

last: Peng

first: Ruitu

last: Lv


title: The methyl binding domain 3 (MBD3) family proteins promote Tet2 enzymatic activity for mediating 5mC conversion

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

overall_design: Refer to individual Series


title: Role of Fun30 remodelers in retrotransposon regulation

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

institute: Universitätsklinikum Hamburg-Eppendorf

type: Expression profiling by genome tiling array

type: Genome binding/occupancy profiling by genome tiling array


title: Peroxisome Proliferator-activated Receptor gamma- Deficiency in Endothelial Cells Impairs Angiogenic Capacity by Loss-of E2F1 Mediated Wnt Effector Genes

city: Helsinki

first: Oyediran

middle: Olulana

last: Akinrinade

address: Biomedicum Helsinki 2U, E107b

department: Institute of Clinical Medicine

country: Finland

institute: University of Helsinki, Finland

summary:
Some of the functions and mechanisms of PPARγ-mediated regulation of vascular homeostasis have been revealed, the potential role of PPARγ in angiogenesis is obscure.
In human ECs, PPARγ-deficiency was studied using siRNA strategy and RNA sequencing was utilized to reveal angiogenesis-associated targets for PPARg.

overall_design: Our aim is to reveal the possible role of PPARy in angiogenesis.

first: Sanna

last: Vattulainen

first: Marlene

last: Rabinovitch

first: Tero-Pekka

last: Alastalo


title: The genomic landscape of pediatric T-cell acute lymphoblastic leukemia reveals novel X-linked somatic mutations associated with apoptosis resistance.

status: Public on Mar 02 2016

city: Montreal

first: Daniel

last: Sinnett

state: Quebec

address: 3175 Cote-Sainte-Catherine

institute: CHU Sainte-Justine


title: Role of Fun30 remodelers in retrotransposon regulation [MNase-Seq]

summary: Retrotransposable elements are genomic parasites that are both key drivers of evolution and the ancestors of retroviruses. Although host cells have developed numerous mechanisms to keep these elements in check, there is also evidence from yeast to mammals that stressed cells sometimes activate transposition.   Here we show that the fission yeast tf2 retrotransposons are regulated by alternative transcription start site (TSS) usage. Which TSS is used is determined by nucleosome positioning, which is in turn controlled by the Fun30 chromatin remodelers Fft2 and Fft3. By maintaining a high level of nucleosome occupancy at retrotransposon-flanking Long Terminal Repeat (LTR) elements, Fft2 and Fft3 promote the use of a downstream TSS and the production of RNA incapable of reverse transcription and retrotransposition. More generally, we show that Fft2 and Fft3 are involved in repressing the transcriptional response to stress, of which retrotransposon activation is a part. Finally, we show that in stressed cells retrotransposon TSS usage switches, allowing the production of full-length retrotransposon RNA. We propose that allowing retrotransposon transcription from a nonproductive TSS allows for the rapid activation of these elements in times of stress, while preventing their uncontrolled proliferation in the genome.

overall_design: For MNase samples, duplicate mutant mononucleosome fractions were compared with duplicate WT mononucleosomes

first: Jenna

last: Persson

first: Agata

last: Smialowska

first: Karl

last: Ekwall


title: The genomic landscape of pediatric T-cell acute lymphoblastic leukemia reveals novel X-linked somatic mutations associated with apoptosis resistance. [Exome-Seq]

summary:
Background. T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy with a dismal prognosis. It represents 15% of pediatric ALL and has a threefold higher incidence among males. T-cell transformation is a multi-step process involving cooperating events leading to altered T-cell signaling, proliferation, differentiation and survival. Many recurrent alterations have been identified and help define molecular subgroups of T-ALL, however the full range of events involved in driving transformation remain to be defined.
Results. Using an integrative approach combining genomic and transcriptomic data, we performed comprehensive molecular characterization of 30 pediatric T-ALLs. We identified common T-ALL targets and confirmed the overall poor outcome of early immature cases. We also showed that deletion of the CDKN2A locus is associated with lower risk of relapse. In addition, we identified novel T-ALL drivers including a member of the spliceosome machinery U2AF1 as well as novel X-linked tumor suppressors MED12 and USP9X, that had never been associated to T-ALL before. Interestingly, almost 60% of these events were found in early immature cases which represented only 35% of the cohort. Functional validations further demonstrated the putative role of these novel T-ALL genes in driving transformation by demonstrating the aberrant splicing provoked by U2AF1 p.R35L and the protective effect against apoptosis of MED12 and USP9X repression.
Conclusions. This study highlights the underlying genomic complexity of pediatric T-ALL, and the need for larger integrative studies to decipher the mechanisms that contribute to its various subtypes and provide opportunities to refine patient stratification and treatment.

overall_design: Whole exomes were captured in solution with Agilent’s SureSelect Human All Exon (38Mb or 50Mb), Nextera Rapid Capture Exome Enrichment kit (case 791) or SureSelectXT Clinical Research Exome (case 879) kits according to the manufacturer’s protocol and sequenced on the Life Technologies SOLiD 5500 System and for cases 791 and 879.

first: Jean-François

last: Spinella

first: Pauline

last: Cassart

first: Chantal

last: Richer

first: Virginie

last: Saillour

first: Manon

last: Ouimet

first: Sylvie

last: Langlois

first: Pascal

last: St-Onge

first: Thomas

last: Sontag

first: Jasmine

last: Healy


title: The genomic landscape of pediatric T-cell acute lymphoblastic leukemia reveals novel X-linked somatic mutations associated with apoptosis resistance. [RNA-Seq]

overall_design: Total RNA was extracted from bone marrow samples at diagnosis for patients 432, 437, 547, 693, 716, 743, 744, 748, 791 and 849 using the mirVana Isolation kit (Ambion) according to the manufacturer’s protocol. The Allprep DNA/RNA Mini kit (Qiagen) was used for relapse samples in patients 791 and 879. For patient 744, mature RNA was also purified using the Ambion's MicroPoly(A)Purist kit (Small Scale mRNA Purification Kit P/N AM1919). Following a DNAse I treatment, total or mature RNA samples were quantified by NanoDrop ND1000 (Thermo-Fisher Scientific) and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent). Ribosomal ribonucleic acid (rRNA) were depleted using the Invitrogen RiboMinus Eukaryote kit (Life Technologies). cDNA libraries were prepared using the SOLiD Total RNA-seq kit (diagnosis samples) and the Illumina TruSeq Stranded Total RNA kit (relapse samples) based on manufacturer’s protocol and sequenced on the Life Technologies SOLiD 5500 System or the Illumina HiSeq 2500 System.


title: Transcriptome analysis of Enterococcus faecalis towards its adaption to surviving in the mouse intestinal tract

city: Freising

first: Juergen

last: Behr

state: Bavaria

address: Weihenstephaner Steig 16

department: Technische Mikrobiologie

institute: TU Muenchen

summary: Enterococcus (E.) faecalis is a commensal in healthy humans, frequently found in a variety of fermented foods, and can serve as a probiotic. However, it has also been recognized as a pathogen causing diseases such as endocarditis, bacteremia and urinary tract infections. As known virulence factors are not limited to clinical isolates but widespread in many strains, additional fitness determinants should influence E. faecalis behavior in the host. We have performed a transcriptomic in vivo study with E. faecalis in the intestine of living mice to identify novel latent and adaptive fitness determinants within E. faecalis. The transcriptomic data derived from E. faecalis strain OG1RF monoassociated with wild type mice provide a first insight in the genes used to live as a commensal in the intestinal tract. Clear changes are observed as compared to growth under laboratory conditions (BHI broth) in the expression of genes involved in energy metabolism (e.g. dhaK and glpK pathway), transport and binding mechanisms (e.g. phosphoenolpyruvate carbohydrate PTS) as well as fatty acid metabolism (fab genes). This knowledge can be used to help explain its persistence in this environment, which is a prerequisite to cause infection in a compromised or inflamed host and possibly develop improved treatment strategies of the so far hard to cure infections.

overall_design: Comparison of transcriptome data from Enterococcus faecalis growing in BHI broth and monoassociated mice

first: Jürgen

first: Rudi

middle: F

last: Vogel


title: Comparison of the transcriptomes of a Pasteurella multocida VP161 wild-type strain with a Pasteurella multocida VP161 hfq mutant

city: Clayton

first: David

middle: Richard

last: Powell

address: Wellington Road

department: Bioinformatics Platform

institute: Monash University

summary: Objectives: To determine the transcripts that are differentially expressed in a hfq mutant. Hfq is an RNA chaperone that mediates many interactions between regultory RNAs and their mRNA targets. Analysis of the transcriptomes of the Pasteurella multocida wild-type strain and the Pasteurella multocida hfq mutant will allow for identification of genes controlled by hfq and the sRNAs with which it interacts.

overall_design: Methods: RNA sequencing was employed to determine the transcriptomes of a wild-type Pasteurella multocida strain and a hfq mutant strain. Comparison of these two transcriptomes allows for determination of differentially expressed genes and therefore those genes controlled by Hfq and sRNAs with which it interacts.

first: John

middle: D

last: Boyce


title: Comparative virulence studies and transcriptome analysis of Staphylococcus aureus strains isolated from animals

city: Shanghai

first: Hanqi

last: Yin

address: libing road 151

institute: shanghai biochip corporation

summary: Staphylococcus aureus can infect a wide range of animals and pose as a serious threat to public health by transferring via animals or animal-derived food stuff. Even more importantly, multiple drug resistance development in the bacteria has resulted in therapeutic failure of a number of antibiotics. Therefore by realizing the need of time, this study was designed to investigate the underlying mechanisms of virulence and resistance in S. aureus. After screening through in vivo and in vitro virulence assays and susceptibility test, a highly virulent and multidrug resistant MRSA strain was selected for differential analysis by RNA-seq technology and gene expression results were verified by RT-qPCR. Up-regulation of crucial regulators like sarA and KdpDE seemed to play role in decreased expression of many exotoxin genes while enhanced the adhesion and cell wall protein expression, leading to strong biofilm production in the presence of inactivated agr system. In addition to resistance genes like blaZ, ermC and femA, up-regulation of vraS and multidrug ABC transporter genes contributed to the multidrug resistance in MRSA. Fluoroquinolone resistance was attributed to mutational changes in gyrA and parC genes. Our findings suggested that many virulence and resistance determinants in S. aureus are controlled by complex network of various regulators, and sarA is the most important of those as it adds to pathogenicity of the bacteria and ensures its survival in diverse environment. Further investigations are required to unveil these mechanisms in S. aureus.

overall_design: Four samples were analysed including 2 MRSA1679a test strain and  2 reference strain ATCC1 samples with two replicates of each.

first: Zahid

last: Iqbal

first: Haihong

last: Hao

first: Haﬁz

middle: I

last: Hussain

first: Guyue

last: Cheng

first: Muhammad

middle: A

last: Shabbir

first: Menghong

last: Dai

first: Adeel

last: Sattar

first: Jun

last: Li

first: Awais

last: Ihsan

first: Zonghui

last: Yuan


title: Polycomb dysregulation in gliomagenesis targets a Zfp423-dependent differentiation network

city: Milano

first: Pasquale

last: Laise

address: Via Adamello,16

country: Italy

institute: IEO


title: Polycomb dysregulation in gliomagenesis targets a Zfp423-dependent differentiation network [ChIP-Seq]

summary: Malignant gliomas constitute one of the most significant areas of unmet medical need, due to the invariable failure of surgical eradication and their marked molecular heterogeneity. Accumulating evidence has revealed a critical contribution by the Polycomb axis of epigenetic repression. However, a coherent understanding of the regulatory networks affected by Polycomb during gliomagenesis is still lacking. Here we integrate transcriptomic and epigenomic analyses to define Polycomb-dependent networks that promote gliomagenesis, validating them both in two independent mouse models and in a large cohort of human samples. We found that Polycomb dysregulation in gliomagenesis affects transcriptional networks associated to invasiveness and de-differentiation. The dissection of these networks uncovers Zfp423 as a crtitical Polycomb-dependent transcription factor whose silencing negatively impacts survival. The anti-gliomagenic activity of Zfp423 requires interaction with the SMAD proteins within the BMP signaling pathway, pointing to a novel synergic circuit through which Polycomb inhibits BMP signaling.

overall_design: Analysis of H3K27me3 distribition in two different stages of gliomagenesis

first: Elena

last: Signaroldi

first: Silvia

last: Cristofanon

first: Arianna

last: Brancaccio

first: Elisa

last: Reisoli

first: Sina

last: Atashpaz

first: Maria

last: Terreni

first: Claudio

last: Doglioni

first: Giancarlo

last: Pruneri

first: Paolo

last: Malatesta

first: Giuseppe

last: Testa


title: RNA-SEQ on resting (R) and stimulated (S) B cells from several IgH 3'RR mutant models

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: We evaluated by RNA-seq obveral transcripts in B cells (resting and activated for 2 days with LPS) sorted from several KO mice models devoid of portion or all the IgH 3' Regulatory Region

overall_design: One RNA-seq point was realized per condition (resting or stimulated) and per genotype. Each point corresponds to a pool of equivalent number of B cells sorted from 4 animals

first: E

last: Pinaud

first: Y

last: Denizot

first: V

last: Magnone

first: K

first: P

last: Barbry