title: Genome Organization Drives Chromosome Fragility [nsRNA-seq]

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

summary: In this study, we show that evolutionarily conserved chromosome loop anchors bound by CTCF and cohesin are vulnerable to DNA double strand breaks (DSBs) mediated by topoisomerase 2B (TOP2B). Polymorphisms in the genome that redistribute CTCF/cohesin occupancy concomitantly rewire DNA cleavage sites to novel contact domain boundaries. While transcription and replication coupled genomic rearrangements have been well documented, we demonstrate that DSBs at loop anchors are transcription-, replication-, and cell type- independent. DSBs are continuously formed throughout interphase, are enriched on both sides of strong topological domain borders, and frequently occur at breakpoint clusters commonly translocated in acute leukemias and prostate cancers.  Thus, loop anchors serve as preferred and promiscuous fragile sites that generate DSBs and chromosomal rearrangements.

overall_design: nascent RNA-seq profile in activated and resting B cells and T cells, with and without transcription inhibition drugs

first: Andres

last: Canela

first: Seolkyoung

last: Jung

first: Nancy

last: Wong

first: Amanda

last: Day

first: Elsa

last: Callen

first: Kyong-Rim

last: Kieffer-Kwon

first: Aleksandra

last: Pekowska

first: Hongliang

last: Zhang

first: Peter

last: Mckinnon

last: Aplan

first: Yves

last: Pommier

first: Erez

last: Lieberman Aiden

first: Rafael

last: Casellas

first: André

last: Nussenzweig


title: Identification of conserved and novel microRNAs in blueberry

status: Public on Jun 29 2017

city: Hefei

first: Junyang

last: Yue

state: Anhui

address: Tunxi Road

country: China

institute: Hefei University of Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: In the present study, we employed the high-throughput sequencing technology to profile miRNAs in blueberry fruits. A total of 9,992,446 small RNA tags with sizes ranged from 18 to 30 nt were obtained, indicating that blueberry fruits have a large and diverse small RNA population. Bioinformatic analysis has identified 412 conserved miRNAs, which belong to 20 families, and 57 predicted novel miRNAs likely unique to blueberries. Among them, expression profiles of 5 conserved miRNAs were validated by stem loop qRT-PCR. Furthermore, the potential target genes of the abundant conserved and novel miRNAs were predicted and subjected for Gene Ontology (GO) annotation. Enrichment analysis of the GO-represented biological processes and molecular functions revealed that these target genes were involved in a wide range of metabolic and developmental processes. This study is the first report on genome-wide miRNA profile analysis in blueberry and it provides a useful resource for further elucidation of the functional roles of miRNAs during fruit development and ripening.

overall_design: one ripening blueberry fruit

first: Yongsheng

last: Liu


title: Genome Organization Drives Chromosome Fragility

status: Public on Jun 28 2017

last: Maman

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus
Mus spretus

platform_organism:
Homo sapiens
Mus musculus
Mus spretus

overall_design: Refer to individual Series


title: Genome Organization Drives Chromosome Fragility [ChIP-seq]

sample_organism:
Mus musculus
Mus spretus

platform_organism:
Mus musculus
Mus spretus

overall_design: ChIP-seq profile in Activated and resting B cells, MEFs, pre-B cells, T cells, and Neurons

last: Canela

middle: J

middle: D


title: BET proteins bind the lytic origins of replication [MutuI ChIP-seq]

status: Public on Jun 30 2017

city: New York

first: JJ

last: Miranda

address: 3009 Broadway

country: USA

institute: Barnard College, Columbia University

summary: Lytic infection by the Epstein-Barr virus (EBV) poses numerous health risks, such as infectious mononucleosis and lymphoproliferative disorder. We demonstrate that JQ1 and other BET inhibitors block two different steps in the sequential cascade of the EBV life cycle: expression of the immediate-early gene BZLF1 and lytic genome replication. This represents a novel mode of action for antiviral drugs that may increase efficacy and decrease emergence of resistance. The ChIP-seq data below show that the BET proteins bind to both EBV lytic origins of replication.

sample_organism:
Homo sapiens
human gammaherpesvirus 4

platform_organism:
Homo sapiens
human gammaherpesvirus 4

overall_design: ChIP-seq and input from untreated and JQ1 treated MutuI cells

first: Kristin

middle: M

last: Keck

first: S

middle: A

last: Moquin

first: J

middle: L


title: Genome Organization Drives Chromosome Fragility [END-seq]

first: Yaakov

overall_design: END-seq profile in B, MEFs, pre-B, T, and Neurons

first: Andres

first: Seolkyoung

last: Jung

first: Nancy

last: Wong

last: Day

last: Callen


title: Hepatic transcriptomic alterations for N,N-dimethyl-p-toluidine (DMPT) and p-toluidine after 5-day exposure in rats

status: Public on Jun 27 2017

city: RTP

first: Keith

last: Shockley

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary:
To identify liver transcripts differentially expressed due to treatment with N, N-dimethyl-p-toluidine (DMPT) and p-toluidine, we collected RNA during the from male F344/N rats exposed to 0, 1, 6, 20, 60 or 120 mg/kg DMPT (or p-toluidine), 5 days after exposure for animals 5-6 weeks of age.  These samples were interrogated with the Affymetrix Rat Genome 230 2.0 GeneChip Array.
A total of 511 gene transcripts were differentially expressed due to DMPT treatment and 354 gene transcripts were differentially expressed due to p-toluidine treatment (false discovery rate (FDR) < 0.05).

overall_design: There were 6 groups and 5x replication for each group for each chemical, for 60 total samples. The groups were (1) DMPT-0mg/kg, (2) DMPT-1mg/kg, (3) DMPT-6mg/kg, DMPT-20mg/kg, DMPT-60mg/kg, DMPT-120mg/kg, ptoluidine-0mg/kg, ptoluidine-1mg/kg, ptoluidine-6mg/kg, ptoluidine-20mg/kg, ptoluidine-60mg/kg, ptoluidine-120mg/kg. We compared vehicle control (0mg/kg) vs dose within each chemical using ORIOGEN software. The permutation based p-values for each test were significant for FDR≤5%.

middle: R

first: June

middle: K

last: Dunnick


title: Promoter architecture determines cotranslational regulation of mRNA

first: Julia

last: Domingo

state: NY

address: 101 6th Av

institute: New York Genome Center

summary: Information that regulates gene expression is encoded throughout each gene but if different regulatory regions can be understood in isolation, or if they interact, is unknown. Here we measure mRNA levels for 10,000 open reading frames (ORFs) transcribed from either an inducible or constitutive promoter. We find that the strength of cotranslational regulation on mRNA levels is determined by promoter architecture. By using a novel computational genetic screen of 6402 RNA-seq experiments, we identify the RNA helicase Dbp2 as the mechanism by which cotranslational regulation is reduced specifically for inducible promoters. Finally, we find that for constitutive genes, but not inducible genes, most of the information encoding regulation of mRNA levels in response to changes in growth rate is encoded in the ORF and not in the promoter. Thus, the ORF sequence is a major regulator of gene expression, and a nonlinear interaction between promoters and ORFs determines mRNA levels.

overall_design: Library of random Open Reading Frames (ORFs). To generate the library, random fragments of the yeast genome were cloned under the expression of the same promoter and terminator.

first: Lorena

last: Espinar

first: Miquel

last: Shikora Tamarit

first: Júlia

first: Lucas

last: Carey


title: Transgenic expression of miR-32 in mouse dorsolateral prostate

city: Tampere

first: Mauro

last: Scaravilli

address: Arvo Ylpön katu 34 D253

department: BioMediTech

country: Finland

institute: University of Tampere

summary: Transcriptional profiling of dorsolateral prostate of mice with prostate-specific transgenic expression of miR-32 compared with wild type mice.

overall_design: RNA pool of 6 wild type mice was compared with RNA pool of 6 miR-32 transgenic mice at 6 months of age.

first: Leena

last: Latonen

first: Pekka

last: Ruusuvuori

first: Tapio

last: Visakorpi


title: Transgenic expression of miR-32 in mouse ventral prostate

summary: Transcriptional profiling of ventral prostate of mice with prostate-specific transgenic expression of miR-32 compared with wild type mice.


title: gene expression profile of hippocampus from offspring exposure to maternal excessive estradiol

city: Hangzhou

first: Chengliang

last: Zhou

state: Zhejiang

address: No. 866th, Yuhangtang Road

department: School of Medicine

institute: Zhejiang University

summary:
Accumulating researches suggest that exposure to abnormal environment in the uterus causes chronic diseases in future life. High intrauterine estradiol level is a major characteristic of in vitro fertilization.
Here, we explored the potential neurodevelopment harm and behavior disorder of prenatal high estradiol exposure.

overall_design: Hippocampus of five offspring from normal control offspring and five offspring from maternal excessive estradiol exposure group were included.

first: Zhou

last: Chengliang

first: Yang

last: Qian

first: Wang

last: Huihui


title: Transgenic expression of miR-32 in mouse ventral and dorsolateral prostate


title: High-resolution mapping of heteroduplex DNA formed in UV-induced and spontaneous mitotic recombination events in yeast

city: Los Angeles

first: Yi

last: Yin

state: CA

address: 695 Charles E. Young Dr. S.

department: Human Genetics

institute: University of California, Los Angeles

summary: In yeast, DNA breaks are usually repaired by homologous recombination (HR). An early step for HR pathways is formation of a heteroduplex, in which a single-strand from the broken DNA molecule pairs with a strand derived from an intact DNA molecule.  If the two strands of DNA are not identical, there will be mismatches within the heteroduplex DNA (hetDNA). In wild-type strains, these mismatches are repaired by the mismatch repair (MMR) system, producing a gene conversion event. In strains lacking MMR, the mismatches persist. Most previous studies involving hetDNA formed during mitotic recombination were restricted to one locus. Below, we present a global mapping of hetDNA formed in the MMR-defective mlh1 strain. We find that many recombination events are associated with repair of double-stranded DNA gaps and/or involve Mlh1-independent mismatch repair. Many of our events are not explicable by the simplest form of the double-strand break repair model of recombination.

overall_design: Using whole genome and chromosome-specific SNP microarray, we mapped heteroduplex DNA, a recombination intermediate, from all four granddaughter cells after spontaneous or UV-induced mitotic recombination events. We also determined linkage of SNPs by mapping spores derived from these granddaughter cells.

first: Thomas

last: Petes


title: mRNA sequencing of wild type Columbia and serrate-1 globular stage embryos of Arabidopsis thaliana

city: Irapuato

first: C.

middle: Stewart

last: Gillmor

state: Guanajuato

address: Km. 9.6 Libramiento Nte Carr Leon-Irapuato

country: Mexico

institute: National Laboratory of Genomics for Biodiversity

type: Expression profiling by high throughput sequencing

summary: Wild type Columbia and serrate-1 globular stage embryos were sequenced in order to profile miRNAs which are expressed in embryogenesis in Arabidopsis thaliana

overall_design: Two biological replicates, two conditions

first: Alma

last: Armenta-Medina

first: Daniel

last: Lepe-Soltero

first: Daoquan

last: Xiang

first: Raju

last: Datla

first: Cei

last: Abreu-Goodger

first: C

middle: S


title: Inhibition of RNA polymerase II allows controlled mobilisation of retrotransposons for plant breeding [Arabidopsis]

status: Public on Jun 26 2017

city: Beaucouzé

first: Etienne

last: Bucher

address: 42 rue Georges Morel

country: France

institute: IRHS

type: Methylation profiling by high throughput sequencing

summary: The main objective of this analysis was to investigate the methylome changes in Arabidopsis plants treated with drugs affecting DNA methylation.

overall_design: Four samples have been analyzed. Plants were treated as follows: no drugs, amanitin, zebularine, amanitin and zebularine. After DNA purification,Bisulfite treatment was applied to determine the cytosine methylation status. Illumina reads of the four libraries were generated using an Illumina Hiseq instrument.

first: Michael

last: Thieme

first: Nicolas

last: Daccord

first: Sandrine

last: Balzergue

first: Marie

last: Mirouze

first: Sophie

last: Lanciano


title: RNA editing by ADAR1 leads to context-dependent transcriptome-wide changes in RNA Secondary Structure

status: Public on Jun 25 2017

city: Haifa

first: Oz

last: Solomon

address: Technion

institute: Technion

summary: Adenosine deaminase acting on RNA 1 (ADAR1) is the master RNA editor, catalyzing the deamination of adenosine to inosine. RNA editing is vital for  preventing abnormal activation of cytosolic nucleic acid sensing pathways by self-double-stranded RNAs. Here we determine by parallel analysis of RNA secondary structure sequencing (PARS-seq), the global RNA secondary structure changes in ADAR1 deficient cells. Surprisingly, ADAR1 silencing resulted in a lower global double-stranded to single-stranded RNA ratio, suggesting that A-to-I editing can stabilize a large subset of imperfect RNA duplexes. The duplexes destabilized by editing are composed of vastly complementary inverted Alus found in untranslated regions of genes with vital biological processes, including housekeeping functions and type-I interferon responses. They are predominantly cytoplasmic and generally demonstrate higher ribosomal occupancy. Our findings imply that the editing effect on RNA secondary structure is context dependent and underline the intricate regulatory role of ADAR1 on global RNA secondary structure.

overall_design: Examination of control and ADAR1 KD HepG2 cells using PARSseq method in order to find changes in RNA 2D structure induced by A-to-I RNA editing. We used PARSseq for HepG2 control and ADAR KD cells in two replicates with S1/V1 nucleases treatment for each ((control+KD)*2*2= 8 PARSseq samples). We used RNAseq of HepG2 control and ADAR KD cells with additional Ribo-seq (control and ADAR KD in 2 replicates=4 Ribo-seq samples) to further confirm the changes we observed in the PARSseq experiment.

first: Ayelet

last: Di Segni

first: Karen

last: Cesarkas

first: Hagit

last: Porath

first: Victoria

last: Marcu-Malina

first: Orel

last: Mizrahi

first: Noam

last: Stern-Ginossar

first: Nitzan

last: Kol

first: Sarit

last: Farage Barhom

first: Efrat

last: Glick-Saar

first: Yaniv

last: Lerenthal

first: Erez

last: Levanon

first: Ninette

last: Amariglio

first: Ron

last: Unger

first: Itamar

last: Goldstein

first: Eran

last: Eyal

first: Gidi

last: Rechavi


title: Formin 2 Links Neuropsychiatric Phenotypes At Young Age To An Increased Risk For Dementia

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

country: Germany

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

summary: Age-associated memory decline is due to variable combinations of genetic and environmental risk factors. How these risk factors interact to drive disease onset is currently unknown. Here we begin to elucidate the mechanisms by which post-traumatic stress disorder (PTSD) at a young age contributes to an increased risk to develop dementia at old age. We show that the actin nucleator Formin 2 (Fmn2) is deregulated in PTSD and in Alzheimer’s disease (AD) patients. Young mice lacking the Fmn2 gene exhibit PTSD-like phenotypes and corresponding impairments of synaptic plasticity while the consolidation of new memories is unaffected. However, Fmn2 mutant mice develop accelerated age-associated memory decline that is further increased in the presence of additional risk factors and is mechanistically linked to a loss of transcriptional homeostasis. In conclusion, our data present a new approach to explore the connection between AD risk factors across life span and provide mechanistic insight to the processes by which neuropsychiatric diseases at a young age affect the risk for developing dementia.

overall_design: Role of Fmn2 gene for PTSD like phenotypes and impairments of synaptic plasticity.

first: Roberto

middle: C

last: Agís-Balboa

first: Andre

last: Fischer

first: Farahnaz

last: Sananbenesi


title: H3K4me3 Epigenetic remodelling after Dabrafenib treatment

status: Public on Jun 24 2017

city: Woolloongabba

first: Helmut

last: Schaider

state: Queensland

address: level 7, 37 Kent Street

department: Diamantina Institute

country: Australia

institute: The University Of Queensland

summary: The data depicts H3k4me3-CHIP SEQ results done on WM164 cells before treatment and after 50 days treatment with Dabrafenib

overall_design: Examination of H3K4me3 remodelling after drug treatment.


title: CUREfast: Accelerating research with families

city: Beaverton

first: Noah

last: Berlow

address: 12655 SW Beaverdam Rd

institute: CC-TDI

summary: RNA sequencing of tissue samples taken from pediatric cancer patients of varying disease type. Patients represented those with terminal disease with samples taken from resection or autopsy.

overall_design: snap frozen tumor tissue were processed to isolate DNA and RNA from resected or autopsy tissues. Tissues were generally acquired following therapeutic regimens

middle: E

first: Charles

last: Keller


title: Dynamic Maps of UV Damage Formation and Repair for the Human Genome

city: Istanbul

first: Ogun

last: Adebali

address: Orta Mah. Universite Cad No 27

department: Faculty of Natural Sciences and Engineering

country: Turkey

institute: Sabanci University

summary: UV-induced DNA damage is the major carcinogen of skin cancer. We developed HS-Damage-seq to map UV damage with unprecedented sensitivity and resolution in human cells.  While the distribution of UV-induced damage are mainly determined by sequence context and essentially uniform throughout the genome, transcription factors can affect damage formation at specific positions.  With time-course experiments, we observed changes in damage distribution at particular genomic loci and chromatin states, which reflects the nucleotide excision repair preferences and complements the repair maps by XR-seq. Our results demonstrated that while initial damage is uniformly distributed, they are heterogeneously repaired throughout the genome. The combination of damage and repair maps provides a holistic perspective of UV damage and repair in the human genome.

overall_design: 38 samples were analyzed for (6-4)PP and CPD. Two main experiments were performed: time-course (with NHF1 cell line) and cell vs naked DNA (with GM12878 cell line). Each sample has a biological replicate. We also have control samples which are the undamaged samples and reference genome samples for two cell lines.

first: Jinchuan

last: Hu

first: Sheera

last: Adar

first: Aziz

last: Sancar


title: Gene Expression Profile of ING5-knockdown Brain Tumor Initiating Cell Lines

city: Vancouver

first: Fangwu

last: Wang

address: 675 W 10th Ave

country: Canada

institute: UBC

summary:
Transcriptome analysis on ING5-knockdown brain tumor stem cell lines
Stem cell-like brain tumor initiating cells (BTICs) cause recurrence of glioblastomas, with BTIC "stemness" affected by epigenetic mechanisms. The ING family of epigenetic regulators (ING1-5) function by targeting histone acetyltransferase (HAT) or histone deacetylase (HDAC) complexes to the H3K4me3 mark to alter histone acetylation and subsequently, gene expression. Here we find that ectopic expression of ING5, the targeting subunit of HBO1, MOZ and MORF HAT complexes increases expression of the Oct4, Olig2 and Nestin stem cell markers, promotes self-renewal, prevents lineage differentiation and increases stem cell pools in BTIC populations. This activity requires the plant homeodomain region of ING5 that interacts specifically with the H3K4me3 mark. ING5 also enhances PI3K/AKT and MEK/ERK activity to sustain self-renewal of BTICs over serial passage of stem cell-like spheres. ING5 exerts these effects by activating transcription of calcium channel and follicle stimulating hormone (FSH) pathway genes. In silico analyses of The Cancer Genome Atlas (TCGA) data suggest that ING5 is a positive regulator of BTIC stemness, whose expression negatively correlates with patient prognosis, especially in the Proneural and Classical subtypes, and in tumors with low SOX2 expression. These data suggest that altering histone acetylation status and signaling pathways induced by ING5 may provide useful clinical strategies to target tumor resistance and recurrence in glioblastoma.

overall_design: The transcriptome of the shRNA cell line targeting ING5 and the control shRNA cells are compared using Affymetrix GeneChip Human Gene 2.0 ST arrays; two biological replicates for each group are performed.

first: Karl

last: Riabowol


title: Signaling strength determines proapoptotic functions of STING

city: Lausanne

first: Muhammet

middle: Fatih

last: Gulen

state: VD

address: Station 19

department: GHI

country: Switzerland

institute: EPFL

summary: T cells exhibit an intensified STING response, which leads to the expression of a distinct set of genes and results in the induction of apoptosis

overall_design: CD4+ T cells were stimulated either with DMSO or 10-carboxymethyl-9-acridanone (CMA) for 16 hours. RNA was isolated for analysis.

middle: F

first: Ute

last: Koch

first: Simone

last: Haag

first: Fabian

last: Schuler

first: Lionel

last: Apetoh

first: Andreas

last: Villunger

first: Freddy

last: Radtke

first: Andrea

last: Ablasser


title: Pharmacodynamics, Safety, and Clinical Efficacy of AMG 811, a Human Anti-Interferon-γ Antibody, in Patients With Discoid Lupus Erythematosus [blood]

status: Public on Jun 23 2017

city: Thousand Oaks

first: Dan

last: Baker

address: 1 Amgen Center Drive

department: Molecular Sciences

institute: Amgen Inc.

summary:
This is a phase I randomized, double-blind, placebo-controlled crossover study which sought to evaluate a single dose of AMG 811, an anti-IFNγ antibody, in patients with DLE.
The patients in sequence 1 received AMG 811 followed by placebo, while those in sequence 2 received placebo followed by AMG 811. Pharmacodynamic end points included global transcriptional analyses of lesional and nonlesional skin, IFNγ blockade signature (IGBS) transcriptional scores in the skin and blood, keratinocyte IFNγ RNA scores, and serum levels of CXCL10 protein

overall_design: Sixteen patients with DLE were enrolled in the study (9 in sequence 1 and 7 in sequence 2).  The patients in sequence 1 received AMG 811 (180mg) followed by placebo, while those in sequence 2 received placebo followed by AMG 811 (180 mg).  Blood draws were taken at D1 and multiple follow-up timepoints.

first: V

middle: P

last: Werth

first: D

last: Fiorentino

first: B

last: Sullivan

first: M

last: Boedigheimer

first: K

last: Chiu

first: C

first: G

last: Arnold

last: Damore

first: J

last: Bigler

first: A

last: Welcher

middle: B

last: Russell

last: Martin

last: Chung


title: Type I IFNs and TNF Cooperatively Reprogram Epigenomic Landscape of Human Macrophages to Promote Inflammatory Activation [ATAC-seq]

last: Ivashkiv

address: 535 E 70th St

institute: Hospital For Special Surgery

summary: Crossregulation of TLR responses by cytokines is essential for effective host defense, avoidance of toxicity, and homeostasis, but underlying mechanisms are not well understood. A comprehensive approach integrating RNA-seq, ChIP-seq and ATAC-seq digital footprinting showed that TNF and type I IFNs extensively remodel chromatin states in human macrophages to differentially regulate transcriptional induction of NF-κB, STAT, antiviral, and metabolic genes by LPS. IFN-α potentiated TNF inflammatory function by abrogating feedback silencing of inflammatory genes via priming of chromatin to enable robust transcriptional responses to weak upstream signals. Similar chromatin regulation occurred in human diseases. Our findings provide insights into epigenomic mechanisms by which cytokines reprogram inflammatory responses, and identify new functions and mechanisms of action of TNF and IFNs.

overall_design: Analysis of transcriptional changes in human macrophages stimulated with or without TNF and LPS

first: Sungho

last: Park


title: Pharmacodynamics, Safety, and Clinical Efficacy of AMG 811, a Human Anti-Interferon-γ Antibody, in Patients With Discoid Lupus Erythematosus [skin]

overall_design: Sixteen patients with DLE were enrolled in the study (9 in sequence 1 and 7 in sequence 2).  The patients in sequence 1 received AMG 811 (180mg) followed by placebo, while those in sequence 2 received placebo followed by AMG 811 (180 mg).  Biopsy specimens of lesional and nonlesional skin were collected at baseline, and biopsy specimens of lesional skin were collected on days 15 and 57 postdosing.

last: Wang


title: Highly purified human cord blood-derived CD34+/- hematopoietic stem cells

city: Hirakata

first: Yoshikazu

last: Matsuoka

address: 2-5-1 shinmachi

country: Japan

institute: Kansai Medical University

summary: Global gene expressions of human cord blood-derived 18Lineage-negative (18Lin-)CD34+CD38-CD133+GPI-80+ cells (CD34+ HSCs), 18Lin-CD34-CD133+GPI-80+ cells (CD34- HSCs) and 18Lin-CD34+CD133- cells (non-HSCs) were analyzed. Results provide an insight into the molecular mechanisms underlying the self-renewal, maintenance and differentiation of human cord blood-derived CD34+/- HSCs.

overall_design: Thirty-four to fifty thousand 18Lin-CD34+CD38-CD133+GPI-80+, 18Lin-CD34-CD133+GPI-80+ and 18Lin-CD34+CD133+ cells were isolated from human cord blood by FACS. The data were obtained from three independent experiments.

first: Keisuke

last: Sumide

first: Hiroshi

last: Kawamura

first: Ryusuke

last: Nakatsuka

first: Tatsuya

last: Fujioka

first: Hiroaki

last: Asano

first: Yoshihiro

last: Takihara

first: Yoshiaki

last: Sonoda


title: Pharmacodynamics, Safety, and Clinical Efficacy of AMG 811, a Human Anti-Interferon-γ Antibody, in Patients With Discoid Lupus Erythematosus

first: Dan

last: Baker

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

overall_design: Refer to individual Series


title: Type I IFNs and TNF Cooperatively Reprogram Epigenomic Landscape of Human Macrophages to Promote Inflammatory Activation

first: Lionel


title: Deep Sequencing Analysis of miRNAs Expression in leg muscle of Xinghua Chicken

status: Public on Jun 22 2017

city: Guangzhou

first: Endashaw

middle: Jebessa

last: Bekele

state: Guangduong

address: Wushan street,Tianhe district

department: Animal Genetics, Breeding and Reproduction

institute: South China Agricultural University

summary:
Purpose:We have used RNA-seq to examine of differentially expressed miRNAs  in chicken leg muscle of three different development stages (11 embryo ages, 16 embryo ages, and 1 day old post hatch chick).The aims of this study are characterization of miRNAs differentially expressed in different developmental stage of chicken embryo, using RNA sequence sample.

Methods: On this study we used two embryonic stage and one post hatch chick leg muscle of Xinghua chicken breed.  Total RNA from E11 day embryo, E16 day embryo and 1 day post hatch chick was isolated by TRIzol following the manufacturer’s protocol  (Invitrogen, CA, USA). Each stages were designed two samples, and the total samples were six (three group × two sample/group) and RNA samples of six individuals were pooled with equal amounts, and then were subjected to Illumina deep sequencing.

Results: After eliminating adaptor and low-quality reads, a total of 5,302,700, 6,556,747, 5,359,793, 4,213,112, 7,112,885 and 7,469,939 clean reads were obtained in group E11 (E11.1-E11.2), group E16 (E16.1-E16.2) and group P1 (P1.1–P1.2) libraries, respectively. The clean reads were aligned to the chicken genome databases, miRBase, Rfam, RepBase and mRNA.

Conclusions:To assess miRNA expression during chicken embryo skeletal muscle development, we sequenced and analyzed leg muscle at 11 day embryo age, 16 day embryo age, and 1 days post hatch.

overall_design: Skeletal leg muscle miRNA profile of two embryonic and one post hatch chick of Xinghua chicken were generated by deep sequencing, using Illumina Hiseq 2500.

last: Jebessa

first: Qinghua

last: Nie


title: Enterochromaffin cells are gut chemosensors that couple to sensory neural pathways

city: San Francisco

first: Duncan

last: Leitch

state: California

department: Physiology

institute: University of California - San Francisco

summary: Dietary, microbial, and inflammatory factors modulate the gut-brain axis and influence physiological processes ranging from metabolism to cognition. The gut epithelium is a principle site for detecting such agents, but precisely how it communicates with neural elements is poorly understood. Serotonergic enterochromaffin (EC) cells are proposed to fulfill this role by acting as chemosensors, but understanding how these rare and unique cell types transduce chemosensory information to the nervous system has been hampered by their paucity and inaccessibility to single cell measurements. Here, we circumvent this limitation by exploiting cultured intestinal organoids together with single cell measurements to elucidate intrinsic biophysical, pharmacological, and genetic properties of EC cells. We show that EC cells express specific chemosensory receptors, are electrically excitable, and modulate serotonin-sensitive primary afferent nerve fibers via synaptic connections, enabling them to detect and transduce environmental, metabolic, and homeostatic information from the gut directly to the nervous system

overall_design: Examination of mRNA expression in mouse intestinal organoids prepared from polyA+ RNA using SMARTer Ultra Low Input RNA kit and Low Input Library Prep Kit for Ilumina platform

first: Nicholas

middle: W

last: Bellono

first: James

last: Bayrer

first: Joel

last: Castro

first: Chuchu

last: Zhang

first: Tracey

last: O'Donnell

first: Stuart

last: Brierley

first: Holly

last: Ingraham

first: David

last: Julius


title: An erythroid-specific enhancer of ATP2B4 mediates red blood cell hydration and malaria susceptibility

city: Montreal

first: Guillaume

last: Lettre

state: Québec

address: 5000 rue Bélanger

institute: Montreal Heart Institute


title: HPIP controls osteoarthritis cartilage degeneration

city: Beijing

first: Quanbo

last: Ji

address: #28, Fuxing Road.

institute: The 301 hospital


title: CXCR3 signaling is required for restricted homing of parenteral TB vaccine-induced T cells to both the lung parenchyma and airway

city: Hamilton

first: Zhou

last: Xing

state: Ontario

address: 1280 Main street

department: Pathology and molecular Medicine

institute: McMaster University

summary: While most novel tuberculosis (TB) vaccines are designed for delivery via the muscle or skin for enhanced protection in the lung, it has remained poorly understood whether systemic vaccine-induced memory T cells can readily home to the lung mucosa prior to and shortly after pathogen exposure. We have investigated this issue by using a model of parenteral TB immunization and intravascular immunostaining. We find that systemically induced memory T cells are restricted to the blood vessels in the lung, unable to populate either the lung parenchymal tissue or the airway under homeostatic conditions. We further find that after pulmonary TB infection, it still takes many days before such T cells can enter the lung parenchymal tissue and airway. We have identified the acquisition of CXCR3 expression by circulating T cells to be critical for their entry to these lung mucosal compartments. Our findings offer new insights into mucosal T cell biology and have important implications in vaccine strategies against pulmonary TB and other intracellular infections in the lung.

overall_design: To identify the potential molecular determinants of lung mucosal homing of systemically induced T cells, difference in transcriptional signature of parenteral TB immunization-induced Ag-specific CD8 T cells collected when they were largely in lung vasculature and after they homed to lung mucosal tissue following pulmonary Mycobacterium tuberculosis infection were analyzed by using Affymetrix Mouse Gene 2.0ST microarray. We elected to focus on days 0, 7 and 21 timepoints post-infection to compare the T cells located in lung vasculature (d0 & d7- largely resting memory T cells) with those in lung mucosal tissue (d21-largely secondary effector T cells.   RNA from purified CD8 T cells was isolated using RNeasy® Mini Kit (Qiagen, Germantown, MD, USA). Quality of RNA and subsequent microarray was carried out by Center for Applied Genomics of The Hospital for Sick Children, Toronto, Ontario, Canada. Quality of RNA samples were analyzed using the Agilent 2100 bioanalyzer, which uses RNA 6000 Nano LabChip platform (Agilent Technologies Canada Inc., Mississauga, ON, Canada). On average RNA integrity number (RIN) for all the samples included in the study were above 7. RNA samples were then subjected to RNA Microarray expression analysis using Mouse Gene 2.0ST Affymetrix array. This array contains protein-coding regions. Triplicate sets of lung cell-derived RNA samples per timepoint was generated (8 mice/set; 24 mice/timepoint)

first: Mangalakumari

last: Jeyanathan

first: Sam

last: Afkham

first: Amandeep

last: Khera

first: Talveer

last: Mandur

first: Daniela

last: Damjanovic

first: Yushi

last: Yao

first: Rocky

last: Lai

first: Siamak

last: Haddadi

first: Anna

last: Dvorkin-Gheva

first: Manel

last: Jordana

first: Steven

last: Kunkel


title: Transcriptome analysis of conditional mutations in the genes encoding six different essential proteins that influence Sen1-dependent termination in Saccharomyces cerevisiae

city: Madison

last: Brow

state: WI

address: 420 Henry Mall, Room 1135

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

type: Expression profiling by genome tiling array

summary: The information stored in the DNA of a cell’s chromosomes is transmitted to the rest of the cell by transcribing the DNA into RNA copies or “transcripts”. The fidelity of this process, and thus the health of the cell, depends critically on the proper function of proteins that direct transcription. Since hundreds of genes, each specifying a unique RNA transcript, are arranged in tandem along each chromosome, the beginning and end of each gene must be marked in the DNA sequence. Although encoded in DNA, the signal for terminating an RNA transcript is usually recognized in the transcript itself. We examined the genome-wide functional targets of six proteins implicated in transcription termination by identifying transcripts whose structure or abundance is altered by a mutation that compromises the activity of each protein. For a small minority of transcripts, a mutation in any of the six proteins disrupts termination. Much more commonly, a transcript is affected by a mutation in only one or a few of the six proteins, revealing the varying extent to which the proteins cooperate with one another. We discovered affected transcripts that were not known to be controlled by any of the six proteins, including a cohort of genes required for meiosis.

overall_design: In total 9 samples with 2 duplicates for each sample

first: Xin

last: Chen

first: Kunal

last: Poorey

first: Melissa

last: Carver

first: Ulrika

last: Müller

first: Stefan

last: Bekiranov

last: Auble


title: Genome-wide single molecule footprinting reveals high RNA polymerase II turnover at paused promoters

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute for Biomedical Research

summary: Transcription initiation entails chromatin opening followed by pre-initiation complex formation and RNA Polymerase II recruitment. Subsequent polymerase elongation requires additional signals, resulting in increased residence time downstream of the start site, a phenomenon referred to as pausing. Here we harnessed single molecule footprinting to quantify distinct steps of initiation in vivo throughout the drosophila genome. This identifies the impact of promoter structure on initiation dynamics in relation to nucleosomal occupancy.  Additionally, perturbation of transcriptional initiation reveals an unexpected high turnover of polymerases at paused promoters--an observation confirmed at the level of nascent RNAs. These observations argue that absence of elongation is largely caused by premature termination rather than stable polymerase stalling. In support of this non-processive model, we observe that induction of the paused heat-shock promoter depends on continuous initiation. Our study provides a framework to quantify protein binding at single molecule resolution and refines concepts of transcriptional pausing.

overall_design: S2 and OSC cell lines. Flavopiridol inhibition, triptolide inhibition, and/or heat shock. McviPI and SssI footprints. Amplicon bisulfite sequencing, short RNA sequncing and whole-genome bisulfite sequencing.


title: Transcriptome analysis of virulence factors in Vibrio parahaemolyticus FORC_022, isolated from a soy sauce marinated crab

status: Public on Jun 21 2017

city: Seoul

first: Han Young

last: Chung

address: 1 Gwanak-ro, Gwanak-gu, Seoul 151-742

country: South Korea

institute: Seoul National University

summary: Crab is one of the major source for V. parahaemolyticus outbreak among aquatic products in Northeast Asian due to improperly cooking and wound infection by mishandling. However, there is no report on whole genome sequence of V. parahaemolyticus isolated from contaminated crab, thus no information is available for major virulence factors about V. parahaemolyticus obtained from crab. Therefore, the analysis of transcriptome of isolated V. parahaemolyticus from crab products are necessary to investigate potential risk of foodborne illness by contaminated products.

overall_design: The washed swimming crab added to FORC_022 inoculated minimal medium, and incubated for 4 h/Control group  (FORC_022 inoculated minimal medium, and incubated for 4 h), in biological duplication, using Illumina HiSeq2500.

first: Han-Young

first: Byungho

last: Lee


title: HPIP controls osteoarthritis cartilage degeneration  [ChIP-seq]

first: Quanbo

last: Ji

summary: To assess the direct downstream targets of HPIP, a genome-wide ChIP-seq profiling was performed. The ChIP-seq data was examined by the quality evaluation. The results demonstrated that of significant ChIP-seq peaks for HPIP, 59% of them occurred at intronic and intergenic sites We found HPIP was closely correlated with the cartilage development.

overall_design:
For ChIP assay, chondrocytes were fixed in 37% formaldehyde, pelleted, and resuspended in lysis buffer. The cells were sonicated and centrifuged to remove insoluble material. The supernatants were collected, and Pellet Protein G magnetic beads were added and incubated for 1 hour at 4°C with anti-HPIP (Proteintech, 1:50, 12102-1-AP). The chromatin was collected, purified, and de-crosslinked at 62°C for 2 h, followed by incubation at 95°C for 10 min. The DNA was isolated using the ChIP DNA Clean & Concentrator (Zymo Research Corp.) according to the manufacturer’s instructions. 100ng DNA fragments were used per ChIP. Sequencing libraries were prepared from collected HPIP ChIP and corresponding input DNA by blunting, A-tailing, adaptor ligation using NEXTFlex barcoded adapters (Bioo Scientific). Libraries were PCR-amplified for 16 cycles, fragments size of 300bp were processed using the Covaris Focused-ultrasonicators (Covaris, Inc. S220). Sequencing was performed using the Hi-Seq 2500 (Illumina) platform
contributor: Novel Bioinformatics Co, Ltd


title: IFN-gamma-dependent tissue immune homeostasis is co-opted in the tumor microenvironment

city: New York

first: James

last: Krueger

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

summary: Homeostatic programs maintain equilibrium between immune protection, and selftolerance. Such mechanisms impact autoimmunity and tumor formation, respectively. How tissue homeostasis is maintained, and impacts tumor surveillance is unknown. Here we identify that mononuclear phagocytes share conserved programming during homeostatic differentiation, and entry into tissue. IFNγ is necessary and sufficient to induce these transcripts, revealing a key instructive role. Remarkably, homeostatic and IFNγ-dependent programs enrich across primary human tumors, including melanoma, and stratify metastatic melanoma survival. Single-cell RNA-sequencing reveals enrichment of these modules in monocytes and DCs in human metastatic melanoma. Suppressor-of-cytokine-2 (SOCS2), a highly conserved transcript in this program is induced by IFNγ, and expressed in mononuclear phagocytes infiltrating primary melanoma. SOCS2 limits DC adaptive anti-tumoral immunity and T cell priming in vivo, indicating a critical regulatory role. Our findings link homeostasis in peripheral tissue to anti-tumoral immunity and escape, revealing coopting of tissue-specific immune development in the tumor microenvironment.

overall_design: Comparison Melanoma vs. Control

first: Niroshana

last: Anandasabapathy

first: Mayte

last: Suarezfarinas

first: Sandra

last: Garcet


title: Gene expression profile of ADM, ductal and acinar cells in the setting of pancreatitis

city: Kyoto

first: Takahisa

last: Maruno

state: Kyoto

address: 54 Syogoin-Kawahara-cho, Sakyo-ku

department: Gastroenterology and hepatology

institute: Kyoto university

summary: In order to compare the gene expression profile of acinar-to-ductal metaplasia (ADM), ductal and acinar cells in the setting of pancreatitis, which were obtained by laser-capture microdissection (LMD) from frozen sections of wild type mice pancreata 2 days after caerulein administration, we performed microarray analysis. ADM has an intermediate property between ductal and acinar cells in the setting of pancreatitis, and Cxcr4 mRNA which is expressed in multipotent pancreatic progenitors, were up-regulated in ADM compared with ductal cells or acinar cells. Notably, in consistent with our immunostaining data, Dclk1 mRNA was highly expressed in ADM cells compared with ductal and acinar cells.

overall_design: ADM, duct and acinar cells were collected from frozen pancreatic specimens of 3 WT mice two days after caerulein pancreatitis by the laser-microdissection method. Total RNA was extracted from each sample and gene expression profiles were compared.

first: Hiroshi

last: Seno


title: Provitamin A-enriched Golden Cassava generated through metabolic engineering has reduced dry matter, elevated oil content and enhanced shelf-life

city: St. Louis

first: Malia

last: Gehan

state: Missouri

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: In this study, β-carotene concentrations in cassava storage roots were enhanced by co-expression of transgenes for deoxyxylulose-5-phosphate synthase (DXS) and bacterial phytoene synthase (crtB), mediated by the patatin type-1 promoter. Storage roots harvested from field-grown plants accumulated carotenoids to ≤50 μg/g DW, a 15- to 20-fold increase relative to roots from non-transgenic plants. Approximately 85-90% of these carotenoids accumulated as all-trans-β-carotene, the most nutritionally efficacious carotenoid. β-carotene-accumulating storage roots displayed delayed onset of post-harvest physiological deterioration, a major constraint limiting utilization of cassava products. Significant metabolite changes were detected in β-carotene enhanced storage roots.  Most significantly, an inverse correlation was observed between β-carotene and dry matter contents, with reductions of 50% to 60% of dry matter content in the highest carotenoid accumulating storage roots of different cultivars. Further analysis confirmed concomitant reduction in starch content, and increased levels of total fatty acids, triacylglycerols, soluble sugars, and abscisic acid. Irish potato engineered to co-express DXS and crtB displayed a similar correlation between β-carotene accumulation, reduced dry matter and starch content, and elevated oil and soluble sugars in tubers. Transcriptome analyses revealed reduced expression of starch biosynthetic genes, ADP-glucose pyrophosphorylase genes, in transgenic, carotene-accumulating cassava roots relative to non-transgenic roots.  These findings highlight unintended metabolic consequences of provitamin A biofortification of starch-rich organs and point to strategies for redirecting metabolic flux to restore starch production.

overall_design: Transcriptom data was generated from cassava storage roots harvetsed at 12 months after planting from confined field trial conducted in Puerto Rico. Two transgenic cassava lines DXS//PS-20 and DXS//PS-37 and a non-tranegnic control cultivar 60444 were used for the study each replicated three-times

first: Getu

last: Beyene

first: Nigel

last: Taylor


title: Circulating mRNA Profiles Differ between Qi-Deficiency and Yin deficiency in Ischemic Stroke Rats with Blood Stasis Syndrome

city: Xi’an

first: Tianlong

last: Liu

address: No. 127 West Changle Road

department: Pharmacy

institute: Xijing Hospital

summary:
Qi deficiency blood stasis (QDBS) and Yin deficiency blood stasis (YDBS) are the two major subtypes of which according to the traditional Chinese medicine.
This study was conducted to distinguish these two syndromes at transcriptomics level and explore the underlying mechanisms.

overall_design: Male rats were randomly divided into three groups: sham group, QDBS/MCAO group and YDBS/MCAO group. Microarray and bioinformatics analyses with circulating mRNA were then performed to identify differential gene expression profile.


title: Transcriptional profiling of small intestinal lamina propria Dendritic cells by microarray

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

summary: CD103+CD11b+ dendritic cells (DC) are unique to the intestine, but the factors governing their differentiation are unclear. Here we show that transforming growth factor receptor 1 (TGF beta 1) has an indispensable, cell intrinsic role in the development of these cells. Deletion of Tgfbr1 results in markedly fewer intestinal CD103+CD11b+ DCs and a reciprocal increase in the CD103–CD11b+ DC subset. Transcriptional profiling identifies markers that define the CD103+CD11b+ DC lineage, including CD101, TREM1 and Siglec-F, and shows that the absence of CD103+CD11b+ DCs in CD11c-Cre.Tgfbr1fl/fl mice reflects defective differentiation from CD103–CD11b+ intermediaries, rather than an isolated loss of CD103 expression. The defect in CD103+CD11b+ DCs is accompanied by reduced generation of antigen-specific, inducible FoxP3+ regulatory T (Treg) cells in vitro and in vivo, and by reduced numbers of endogenous TH17 cells in the intestinal mucosa. Thus, TGF beta 1 mediated signalling may explain the tissue-specific development of these unique DCs.

overall_design: Dendritic cell and Macrophage subpopoulations were isolated from the Small Intestine of Healthy Steady State mice, RNA was isolated and sent for microarray analysis

first: C

last: Bain

first: J

last: Montgomery

last: Scott

last: Kel

first: M

middle: J

last: Girard-Madoux

first: L

first: T

last: Zangerle-Murray

last: Ober-Blöbaum

first: D

last: Lindenbergh-Kortleve

middle: N

last: Samsom

first: S

last: Henri

last: Lawrence

first: Y

last: Saeys

first: B

last: Malissen

last: Dalod

last: Clausen

first: A

last: Mowat


title: Rader HHDL and BioBank genotyping

city: Philadelphia

first: Sumeet

last: Khetarpal

address: 3400 Civic Center Blvd, 11-166 SCTR

institute: University of Pennsylvania

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

summary:
The presence of a coding variant affecting plasma high density lipoprotein cholesterol (HDLC) levels was evaluated in subjects with elevated or normal plasma levels of HDLC.
Carriers of the variant were further analyzed phenotypically

overall_design: 19 DNA samples from subjects with normal or high plasma HDLC levels were analyzed.

first: Daniel

last: Rader


title: Pervasive genetic interactions modulate neurodevelopmental defects of the autism-associated 16p11.2 deletion in Drosophila melanogaster

city: State College

first: Santhosh

last: Girirajan

state: PA

address: 205A Life Sciences Building

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: As opposed to syndromic CNVs caused by single genes, extensive phenotypic heterogeneity in variably-expressive CNVs complicates disease gene discovery and functional evaluation. Here, we propose a complex interaction model for pathogenicity of the autism-associated 16p11.2 deletion, where CNV genes interact with each other in conserved pathways to modulate expression of the phenotype. Using multiple quantitative methods in Drosophila RNAi lines, we identify a range of neurodevelopmental phenotypes for knockdown of individual 16p11.2 homologs in different tissues. We test 565 pairwise knockdowns in the developing eye, and identify 24 interactions between pairs of 16p11.2 homologs and 46 interactions between 16p11.2 homologs and neurodevelopmental genes that suppress or enhance cell proliferation phenotypes compared to one-hit knockdowns. These interactions within cell proliferation pathways are also enriched in a human brain-specific network, providing translational relevance in humans. Our study indicates a role for pervasive genetic interactions within CNVs towards cellular and developmental phenotypes.

overall_design: mRNA-sequencing of Drosophila neuron-specific knockdown model heads for six 16p11.2 homologs and wild-type control. Sequencing was performed using Illumina HiSeq 2000 on three biological replicates per sample, with three technical replicates per biological replicate.

first: Janani

last: Iyer

first: Mayanglambam

middle: D

last: Singh

first: Matthew

last: Jensen

first: Payal

last: Patel


title: Transcritome analysis of herbal extract WCE mediated gene signature in 22Rv1 cells

city: Taipei

first: Chin-Hsien

last: Tsai

state: Others

address: Nan-Kang

department: ABRC

country: Taiwan

institute: Academia Sinica

summary: Recurrences of hormone-refractory prostate cancer highly affect the therapeutic outcome. Although anti-androgen therapy prolongs survival in prostate cancer patients, resistance rapidly develops and is often associated with increased androgen receptor expression and upregulated HER2/3-AKT signaling pathway. However, single agent therapy targeting AR, HER2/3 or AKT usually failed due to the reciprocal feedback loop. Here, we demonstrated that herbal extract of Wedelia chinensis (WCE) effectively disrupted the androgen receptor, HER2/3, and AKT signaling network and therefore enhanced therapeutic efficacy of androgen ablation in PCa.

overall_design: To further study WCE effect, 22Rv1 prostate cancer cells were treated by vehicle control or 10 μg/mL of WCE for 16 hr. Total RNA expressions were analyzed in cDNA microarray.

first: Mong-Hsun

first: Pei-Wen

last: Hsiao


title: Integrative analysis of behavioral, syaptic, and genomic plasticity in the hippocampus

city: Davis

first: Rayna

middle: Michelle

last: Harris

address: 1 Shields Ave

institute: University of California Davis

summary: We examined the the effects of cognitive training on behavior, synaptic physiology, and gene expression in the hippocampus.

overall_design: Homecage, Yoked Control, Consistently Trained, Conflict Trained

middle: M

first: Hsin-Yu

last: Kao

first: Juan

last: Alarcon

first: Hans

last: Hofmann

first: Andre

last: Fenton


title: Mitochondrial complex I-perturbed muscle remotely affects gene expression in the fat body in Drosophila

status: Public on Jun 20 2017

city: Boston

first: Wei

last: Song

email: rocwsong@gmail.com, songw@whu.edu.cn

state: Massachusetts

address: 77 Ave Louis Pasteur, NRB 336

department: Department of Genetics

institute: Harvard Medical School

summary:
Purpose: Muscle injury caused by mitocondrial complex I disruption remotedly impairs mitochondrial activity and lipid homeostasis in the fat body . To gain insight into the corss talk between fat body  and muscle, we performed a transcriptomic analysis in fat bodies of 3rd instar larvae with complex I-perturbed muscles.
Methods: To extract total RNAs for RNA-Seq experiment, we used 10 fat bodies dissected out from both dMef2-Gal4/UAS-white-RNAi (Con) and dMef2-Gal4/UAS-ND-75-RNAi (ND-75-i) 3rd instar larvae. After assessing RNA quality with Agilent Bioanalyzer, mRNAs were enriched by poly-A pull-down. Then, sequencing libraries constructed with Illumina TruSeq RNA prep kit were sequenced using Illumina HiSeq2000 at the Columbia Genome Center (http://systemsbiology.columbia.edu/genome-center). We multiplexed samples in each lane, which yields targeted number of single-end 100 bp reads for each sample, as a fraction of 180 million reads for the whole lane. Sequence reads were Reads were mapped back to fly genome using flybase annotation r5.51  using Tophat with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). With the uniquely mapped reads, we quantified gene expression levels using Cufflinks (FPKM values) (version 2.0.2) with default settings. Next, we performed data normalization on the read counts and applied a negative binomial statistical framework using the Bioconductor package DESeq to quantify differential expression between experimental and control data.
Results: Gene list enrichment analysis of the differentially expressed genes in ND-75-i larval fat body revealed a striking enrichment of multiple metabolic processes impinging on carbohydrate metabolism, amino acid metabolism, and lipid metabolism. However, half of genes that encode mitochondrial proteins are up-regulated. Interestingly, target genes of TGF-beta signaling pathways, including activin signaling and BMP signaling,  are enriched in changed transcriptome in ND-75-i larval fat body . In particular, p-Mad and p-dSmad2, are validated with westenr blot or immunostaining.
Conclusions: Our study represents that complex I-perturbed muscle remotely decreases mitochondrial activity and subsequent lipid mobilization in the fat body via modulation of TGF-beta signaling. Our results show that RNA-seq offers a comprehensive evaluation of signaling network and biological process in organ communication.

overall_design: mRNA profiles of both dMef2-Gal4/UAS-white-RNAi (Con) and dMef2-Gal4/UAS-ND-75-RNAi (ND-75-i) 3rd instar arval fat bodies were  generated by deep sequencing, in replicate, using Illumina HiSeq2000.

first: Perrimon

last: Norbert


title: Expression analysis of Arabidopsis thaliana Col-0 and parg1 with and without PARP inhibitor (3AB, 3MB), with and without MAMP (flg22, elf18)

city: Beloit

first: Amy

middle: Graham

last: Briggs

address: 700 College St.

department: Biology

institute: Beloit College

summary:
Genome-wide gene expression analysis of the effects of PARP inhibitor (3AB) and, separately, a parg1 knockout, on early microbe-associate molecular pattern (MAMP)-induced gene expression in the plant basal defense response. Arabidopsis thaliana wild-type (Col-0), 3AB-treated and parg1-2 T-DNA knockout plants responding to the MAMP elicitors flg22 or elf18 were studied.
The mutant and PARP inhibitors analyzed in this study are further described in Adams-Phillips, L.,C., Briggs, A.,G., Bent, A., F.  2010. Disruption of poly(ADP-ribosyl)ation mechanisms alters responses of Arabidopsis to biotic stress. Planty Physiol. 152(1):267-80 DOI: 10.1104/pp.109.148049.

overall_design: A 27 chip study using total RNA recovered from three separate wild-type extracts of Arabidopsis Col-0 and three separate cultures of a parg1-2 knockout strain, in which a TDNA insertion has knocked out expression of At2g31870, treated for 1 hour with vehicle, flg22, elf28, 3AB, or 3MB.  Each chip measures the expression level of 30,387 genes from Arabidopsis thaliana Col-0 with 6 60-mer probe pairs (PM/MM) per gene, with two-fold technical redundancy and three-fold biological redundancy.

first: Andrew

last: Bent

middle: G

first: Lori

last: Adams-Phillips


title: Solanum dulcamara's response to insect eggs comprises ovicidal hydrogen peroxide production

city: Berlin

first: Tobias

last: Lortzing

state: Berlin

address: Haderslebener Str. 9

institute: Freie Universität Berlin

summary: Plants can respond to insect oviposition but little is known about which responses directly target the insect eggs and how. Here, we reveal a mechanism by which the bittersweet nightshade, Solanum dulcamara, kills the eggs of a generalist noctuid herbivore. The plant responded at the site of oviposition by Spodoptera exigua with neoplasm and chlorotic tissue formation, accumulation of reactive oxygen species and induction of defence genes and proteins. Transcriptome analysis revealed that these responses were reflected in the transcriptional reprogramming of the egg-laden leaf. The plant-mediated egg mortality on S. dulcamara was not present on a genotype lacking chlorotic leaf tissue at the oviposition sites on which the eggs are exposed to less hydrogen peroxide. As exposure to hydrogen peroxide increased egg mortality, while catalase supplementation prevented the plants from killing the eggs, our results suggest that ROS formation directly acts as an ovicidal plant response of S. dulcamara.

overall_design: The transcriptome of S. dulcamara leaves was analyzed in plants grown from seeds from two different locations in Germany (Erkner, Siethen) and from one loaction in The Netherlands (Friesland). Leaves were either untreated (control) or had carried an egg clutch from Spodoptera exigua moths for 3 days (eggs)

first: Daniel

last: Geuss

first: Sandra

last: Stelzer

first: Anke

last: Steppuhn


title: Germline Chd8 haploinsufficiency alters brain development in mouse

first: Alex

last: Nord

address: 1544 Newton Court

department: Neurobiology, Physiology, and Behavior

summary: We examined the impact of germline heterozygous frameshift Chd8 mutation on neurodevelopment in mice. Adult Chd8+/del5 mice exhibited cognitive impairment correlated with increased cerebral cortex, hippocampus, and amygdala volume, but displayed normal social interactions and no repetitive behaviors. Network analysis of neurodevelopmental gene expression revealed widespread transcriptional changes in Chd8+/del5 mice across pathways disrupted in neurodevelopmental disorders, including neurogenesis,  synaptic processes, and neuroimmune signaling. Among gene co-expression networks, we identified a module with peak expression in early brain development that featured dysregulation of genes enriched for promoter binding by Chd8 and associated with RNA processing, chromatin remodeling, and cell cycle. We validated increased neuronal proliferation and splicing alterations during Chd8+/del5 brain development. Our results show that Chd8+/del5 mice exhibit neurodevelopmental changes paralleling humans with CHD8 mutations and highlight widespread pathological consequences of Chd8 haploinsufficiency.

overall_design: We examined RNA expression (RNA-sequencing) and Chd8 binding to the genome (ChIP-seq) from whole forebrain dissections of WT and germline heterozygous Chd8 mutant mice.

first: Andrea

middle: L

last: Gompers

first: Linda

last: Su-Feher

first: Jacob

last: Ellegood

first: Nycole

middle: A

last: Copping

first: M

last: Riyadh

first: Tyler

last: Stradleigh

first: Michael

last: Pride

first: Melanie

last: Schaffler

first: A

last: Wade

first: Rinaldo

last: Catta-Preta

first: Iva

last: Zdilar

first: Shreya

last: Louis

first: Gaurav

last: Kaushik

first: Brandon

last: Mannion

first: Ingrid

last: Plajzer-Frick

first: Veena

last: Afzal

first: Axel

last: Visel

first: Len

last: Pennacchio

first: Diane

last: Dickel

first: Jason

last: Lerch

first: Jacqueline

last: Crawley

first: Konstantinos

last: Zarbalis

first: Jill

last: Silverman


title: Hilpda deficiency effect on brown adipose tissue

city: Columbus

first: Ioanna

last: Papandreou

state: OH

department: Radiation Oncology

institute: The Ohio State University Comprehensive Cancer Center

summary: Analysis of interscapular brown fat tissue of fasted mice to identify the possible impact of the lipid droplet protein Hilpda on thermogenesis. Tissues were isolated from genetically engineered mice with the Hilpda gene knocked out and Luciferase knocked in, and Hilpda WT counterparts.

overall_design: We analyzed brown adipose tissues from 4 HILPDA KO mice and 4 WT mice using the Affymetrix Clariom S solutions. Array data was processed by Affymetrix Expression Console and Transcriptome Analysis Console . No techinical replicates were performed.

first: Jinghai

last: Wu

first: Matthew

last: VandeKopple

first: Nicholas

last: Denko


title: Novel chimeric transcript RRM2-c2orf48 promotes metastasis in nasopharyngeal carcinoma

city: Guangzhou

first: Tianliang

last: Xia

address: Dongfeng Road East 651

institute: Sun Yat-sen University Cancer Center

summary:
A microarray analysis was performed on the vector and over-expressing RRM2-c2orf48 NPC cell samples(CNE2-PMSCV-Vector and CNE2-PMSCV-RRM2-c2orf48).
Total RNA was extracted from 1 × 106 cells using TRIzol reagent and was further purified using a Qiagen RNeasy Mini Kit according to the manufactures’ instructions. RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically. Total RNA was labeled and hybridized to the CapitalBio Corporation’s Affymetrix GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix). We applied a two class unpaired method available through the Significant Analysis of Microarray software (SAM) to identify significantly differentially expressed genes between vector and over-expression samples. Genes were deemed significantly differentially expressed based on a selection threshold of a false discovery rate of FDR<5% and a fold change level of ＞1.5 in the SAM output results.

overall_design: Micrarray analysis was preformed on the vector and RC of CNE2 cell line

first: Ping

last: Han

first: Ren-Hui

last: Chen

first: Fang

last: Wang

first: Jia-Yi

last: Zeng

first: Tian-Liang

first: Qian

last: Zhong

first: Xiao-Ming

last: Huang


title: Transcriptional Profiling Confirms the Therapeutic Effects of Mast Cell Stabilization in a Dengue Disease Model [spleen]

city: Riverside

first: Juliet

last: Morrison

state: CA

address: 900 University Avenue

department: Microbiology and Plant Pathology

institute: University of California, Riverside

summary:
In this study, we show that the host response to DENV infection in immunocompetent mice recapitulates transcriptional changes that have been described in human studies. We found that DENV infection induced metabolic dysregulation and inflammatory responses, and also affected the immune cell content of the spleen and liver.
Use of the mast cell stabilization drug, ketotifen, reversed many of these responses, and induced additional changes in the transcriptome and immune cell repertoire that contribute to decreased dengue disease.

overall_design: Gene expression in liver and spleen were measured on days 1 and 3 post mock infection or infection with DENV2 plus or minus ketotifen treatment. Three mice were profiled for each treatment category and timepoint. This dataset includes the data from spleen.

first: Ashley

last: St. John


title: Transcriptional Signature Associated with Early Rheumatoid Arthritis and Healthy Individuals at high risk to develop the disease.

city: Aguascalientes

first: Noe

last: Macias-Segura

state: Aguascalientes

address: Av. Universidad #940 ciudad universitaria cp20131

institute: Universidad Autonoma de Aguascalientes

summary: To identify biomarkers and transcriptomic pathways associated with the development of rheumatoid arhtritis, we performed a transcriptional analysis  using a hole genome microarray to demostrate that a specific transcriptional signature is associated with the development of RA, and it exists since the beginning and presence of auto-antibodies against citrulinated proteins.

overall_design: Whole blood total RNA was obtained from non-treated early RA patients with <1 year of evolution as well as from healthy first-degree relatives of patients with RA (FDR) classified as ACCP+ and ACCP- according to their serum levels of antibodies against cyclic citrullinated peptides. Cy3-labeled complementary RNA (cRNA) was synthetized and hybridized to high-density microarrays, analyzed in genespring and functional categories were assigned to a specific transcriptome identified in subjects with RA and FDR ACCP positive. Specific signaling pathways for genes associated to RA were identified.

first: N

first: J

last: Enciso-Moreno


title: Transcriptional Profiling Confirms the Therapeutic Effects of Mast Cell Stabilization in a Dengue Disease Model [liver]

overall_design: Gene expression in liver and spleen were measured on days 1 and 3 post mock infection or infection with DENV2 plus or minus ketotifen treatment. Three mice were profiled for each treatment category and timepoint. This dataset includes the data from liver.


title: Transcriptional Profiling Confirms the Therapeutic Effects of Mast Cell Stabilization in a Dengue Disease Model

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

overall_design: Refer to individual Series


title: Expression data from T-DM1 resistant clones

city: Salamanca

first: Sara

last: García-Alonso

state: Salamanca

address: Campus Miguel de Unamuno s/n

country: Spain

institute: Centro de Investigación del Cáncer

summary:
The mechanisms of resistance to the antibody-drug conjugate, T-DM1, were studied on clones derived from breast cancer cell line, BT474.
Microarray analyses were performed to explore potential transcriptomic differences among the distinct cell lines.

overall_design: RNA from parental cell line, BT474, and four resistant clones, C#1, C#2, C#3 and C#6, was purified and their gene expression profiles compared using the Affimetrix Transcriptome Analysis console. Three biological replicates were analyzed for each cell lines.

first: Carla

last: Ríos-Luci


title: Porcine oviductal epithelial cells (OECs) primary in vitro culture

city: Poznań

first: Marcin

last: Ruciński

state: Wielkopolska

address: Święcickiego 6

department: Histology and Embryology

country: Poland

institute: Poznań University of Medical Sciences

summary:
Recently a lot of experiment were developed based on primary cell culture models, including several species of mammals, organs and tissues. The results from these studies revealed the differences in cells proliferation ability in vitro, which is significantly related to the type of tissue originated cells.
In this study, we demonstrated the gene expression profile of long time primary cultured porcine oviductal epithelial cells.

overall_design: Oviductal epithelial cell (OECs) were obtained from 9 months old crossbred landrace glits. OECs were pooled and harvested 24h, 7days, 15 days and 30 days after begining of culture and submited to RNA isolation and microarray analisys.

first: Bartosz

last: Kempisty

first: Joanna

last: Budna

first: Piotr

last: Celichowski

first: Artur

last: Bryja


title: circRNA expression in renal cell carcinoma and mached non-tumor tissues

city: Shanghai

first: lv

last: qi

address: Xincun Road 389

institute: Tongji Hospital affiliated to Tongji university

summary: To determine the circRNA expression profile in CCRCC and matched non-tumor tissues, we uesed circRNA microArray analysis form Arraystar to examine the expression of circRNAs in CCRCC and matched non-tumor tissues.

overall_design: renal celar cell carcinoma tissues from CCRCC surgery were distributed into two experimental groups: tumor tissue group and normal tissue group, then perform circRNAs chips by Arraystar Human circRNAs chip (Arraystar)

first: Qi

last: Lv

first: Peijun


title: Sirt6 Deficiency Exacerbates Podocyte Injury and Proteinuria through Targeting Notch Signaling

city: Jinan

first: Min

last: Liu

state: Shandong

address: wen hua xi road 44

department: Department of Pharmacology

institute: Shandong University School of Medicine

summary: Podocyte injury is a major determinant in proteinuric kidney disease and identification of potential therapeutic targets for preventing podocyte injury has clinical importance. Here, we show that histone deacetylase Sirt6 protects against podocyte injury through epigenetic regulation of Notch signaling. Sirt6 is downregulated in renal biopsies from patients with podocytopathies and its expression negatively correlates withglomerular filtration rate. Podocyte-specific deletion of Sirt6 exacerbates podocyte injury and proteinuria in two independent mouse models including diabetic nephropathy and adriamycin-induced nephropathy. Sirt6 has pleiotropic protective actions in podocytes including anti-inflammatory and anti-apoptotic effects, is involved in actin cytoskeleton maintenance, and promotes autophagy. Sirt6 also reduces urokinase plasminogen activator receptor expression, which is a key factor for podocyte foot process effacement and proteinuria. Mechanistically, Sirt6 inhibits Notch1 and Notch4 transcription by deacetylating the histone H3K9. We suggest Sirt6 as a potential therapeutic target in proteinuric kidney disease.

overall_design: Overexpression of Sirt6 by a Sirt6-adenovirus transfection was used in this study. Cells were stimulated with high glucose for 24h (a final concentration of 40 mmol/l in culture medium).

first: Fan

last: Yi


title: Expression data comparing attached and spheroid cells of primary cervical cancer cell lines derived from cervical cancer tissue

city: Hong Kong

first: Thomas

middle: HY

last: Leung

address: Laboratory Block, FMB, 21 Sassoon Road, Pokfulam

department: Obstetrics and Gynaecology

country: Hong Kong

institute: The University of Hong Kong

summary:
To identify cell surface markers in cells with cancer stem-like cell properties
Affymetrix Human Gene 2.0 ST GeneChip

overall_design: Attached cells verse Spheroid cells

last: LEUNG


title: Gene expression profile of peroxisome proliferator-activated receptor delta (Ppard)-overexpressing RAW 264.7 macrophages treated vehicle, GW501516 or interleukin-4 (Il-4)

first: Lingling

last: Dai

state: MA

address: 665 Huntington Avenue

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

summary:
Investigation of whole genome gene expression level changes in GW501516 (a Ppard ligand) or Il-4 treated Ppard-overexpressing RAW 264.7 macrophages as compared to vehicle.
Alternative activation of adipose tissue resident macrophages inhibits obesity-induced metabolic inflammation. In the current study we profile genes regulated by two M2 inducers, Il-4 or Ppard agonists and find that alternative activation promotes the cell survival program, while inhibiting that of inflammation-related cell death.

overall_design: 9 samples; 3 treatments in triplicate (Ppard-overexpressing RAW 264.7 cells are treated with vehicle, GW501516 or Il-4 overnight in triplicatet).

first: Kristopher

last: Stanya

first: Sihao

first: Chih-Hao

last: Lee


title: Differential impact of Dicer deficiency on microglia of the developing and adult brain

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science


title: Differential impact of Dicer deficiency on microglia of the developing and adult brain (Agilent miRNA microarrays)

summary: Microglia seed the embryonic neuro-epithelium, expand and actively sculpt neuronal circuits in the developing CNS, but eventually adopt relative quiescence and ramified morphology in the adult. Here we probed the impact of post-transcriptional control by microRNAs (miRNAs) on microglial performance during development and adulthood by generating mice lacking microglial dicer expression at these distinct stages. RNA seq of conditional dicer ablation in adult microglia revealed that miRNAs were required to limit microglial responses to challenge but had only minor changes on non-challenged microglia. Specifically, following peripheral endotoxin exposure of the animals (LPS), Dicer-deficient microglia either from total brain or hippocampus overexpressed pro-inflammatory cytokines and as a result compromised hippocampal neuronal functions. In contrast, prenatal ablation resulted in spontaneous microglia activation and revealed Dicer involvement in DNA repair and preservation of genome integrity. Overall, our study shows miRNA and Dicer regulation of inflammatory response either following challenge in the adult or spontaneously in the newborn microglia. Moreover, Dicer is required for preservation of microglia DNA integrity required for their proliferation, longevity and radioresistance.

overall_design: Adult Microglia (defined as CD45intCD11b+F4/80+Ly6C-Ly6G- cells, n=2, each replicte is a pool of 4-6 mice), Colon MFs (defined as CD45+CD11b+CD11c+CD64+Ly6C-, n=2, each replicate is a pool of 4-6 mice), and Liver MFs (KCs) (defined as CD45+CD11b+F4/80+CD64+MHCII+, n=2, each replicate is a pool of 4-6 mice) were sorted from 6-8 weeks old WT mice.                                                                                miRNA microarray profiling was performed on the populations above in order to identify miRNAs enriched in steady state adult microglia.

first: Diana

last: Varol

first: Alexander

last: Mildner

first: Eyal

last: David


title: Transcriptomic analysis of Mtb H37Rv and MtbΔwhiB4 on treatment to 10X Augmentin (AG) i.e. combination of 100 µg/ml of Amoxicillin and 8 µg/ml of Clavulanate and lower Augmentin doses at 1X and 5X

city: New York

first: SAURABH

last: MISHRA

state: New York

address: 1300 York Ave, Box 62, New York

department: Microbiology and Immunology

country: USA

institute: Weill Cornell Medicine

summary: Amox-Clav combination downregulates the expression of WhiB4. Further, MtbΔwhiB4 survives better upon treatment with this combination. Therefore, to study the role of WhiB4 in regulating the response of Mtb to this combination, we carried out global transcriptome profiling of Wt Mtb and MtbΔwhiB4 strains after treatment.

overall_design: Mtb H37Rv and MtbΔwhiB4 were grown till early log phase and treated with 10X Augmentin at 100 µg/ml of Amoxicillin and 8 µg/ml of Clavulanate for 6 h at 37 degree at 150rpm. Wildtype Mtb H37Rv were treated with  1X Augmentin (10 µg/ml of Amoxicillin and 8 µg/ml of Clavulanate), or 5X Augmentin (50 µg/ml of Amoxicillin and 8 µg/ml of Clavulanate) for 6 or 12 h at 37 degree at 150rpm. Experiments were done in duplicate, triplicate, tetraplicate or pentaplicate.

first: Saurabh

last: Mishra

first: Amit

last: Singh


title: Circular RNAs expression profiles in human gastric cancer

status: Public on Jun 19 2017

city: Fuzhou

first: Lie

last: Wang

address: Xierhuan Road

country: China

institute: Fuzhou general Hospital

summary: The circRNAs expression profiles in 5 gastric cancer (GC) and their matched non-gastric cancer (non-GC) tissues were detected by human circRNA expression profile chips, and the differentially expression circRNAs between GC and matched non-GC tissues were then identified.  A total of 713 circRNAs were differentially expressed in GC tissues vs. non-GC tissues (fold change≥2.0, p<0.05) among all the candidate circRNAs (62998) detected in both GC and non-GC tissues according to the T-test. 191/713 circRNAs were significantly upregulated in GC tissues, whereas 522/713 circRNAs were significantly downregulated in GC tissues. GO and KEGG pathway analyses showed that many dysregulated circRNAs may be functionally GC-related, thereby contributing to the development of GC.

overall_design: To detect the circRNAs expression profiles in 5 gastric cancer (GC) and their matched non-gastric cancer (non-GC) tissues by human circRNA expression profile chips and to identify the differentially expressed circRNAs between GC and their matched non-GC tissues based on the chip data. In this way,  this study provided the basis for identifying novel GC biomarkers and further studying the roles and functions of differentially expressed circRNAs in GC.


title: Role of ERα in Mediating Female Uterine Transcriptional Responses to IGF1

status: Public on Jun 17 2017

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Estrogen (E2) signaling through its nuclear receptor, estrogen receptor α (ERα) increases insulin-like growth factor 1 (IGF1) in the rodent uterus, which then initiates further signals via the IGF1 receptor (IGF1R). Directly administering IGF1 results in similar biological and transcriptional uterine responses. Our studies using global ERα-null mice demonstrated a loss of uterine biological responses of the uterus to E2 or IGF1 treatment, while maintaining transcriptional responses to IGF1. To address this discrepancy in the need for uterine ERα in mediating the IGF1 transcriptional vs. growth responses, we assessed the IGF1 transcriptional responses in PgrCre+Esr1f/f (called ERαUtcKO) mice, which selectively lack ERα in progesterone receptor (PGR) expressing cells, including all uterine cells, while maintaining ERα expression in other tissues and cells that do not express Pgr. Additionally, we profiled IGF1-induced ERα binding sites in uterine chromatin using ChIP-seq. Herein, we explore the transcriptional and molecular signaling that underlies our findings to refine our understanding of uterine IGF1 signaling and identify ERα-mediated and ERα-independent uterine transcriptional responses. Defining these mechanisms in vivo in whole tissue and animal contexts provides details of nuclear receptor mediated mechanisms that impact biological systems and have potential applicability to reproductive processes of humans, livestock and wildlife.

overall_design: Three replicates for each treatment group.  In cases where two sample replicates are submitted, one of the three replicates was excluded as an outlier based on PCA analysis.

first: Sylvia

middle: C

last: Hewitt

first: Wipawee

last: Winuthayanon

first: Sydney

last: Lierz

first: Katherine

last: Hamilton

first: Lauren

last: Donoghue

first: J

middle: T

last: Ramsey

first: Sara

last: Grimm

first: Yukitomo

last: Arao

first: Kenneth

middle: S

last: Korach


title: Expression data of Arabidopsis thaliana Col-0 and mlo2 mlo6 mlo12 plants prior (0h) and after (8 and 12 h) Golovinomyces orontii inoculation

city: Aachen

first: Hannah

last: Kuhn

address: Worringerweg 1

department: Institute for Biology I

institute: RWTH Aachen University

summary: Comparative microarray-based transcriptome analysis of A. thaliana mlo2 mlo6 mlo12 mutants and wild type plants upon Golovinomyces orontii inoculation revealed an increased and accelerated accumulation of many defense-related transcripts. Despite the biotrophic nature of the interaction, this included the non-canonical activation of a jasmonic acid/ethylene-dependent transcriptional program.

overall_design: Microarray analysis was performed in triplicates with 4-week-old A. thaliana wt (Col-0) and mlo2 mlo6 mlo12 plants that were sampled either prior (0 h) or 8 and 12 h after inoculation with G. orontii.

first: Justine

last: Lorek

first: Emiel

last: Ver Loren van Themaat

first: Bruno

last: Hüttel

first: Ralph

last: Panstruga


title: Role of JunB in Th17 cell effector stability [ChIP-seq]

city: Durham

first: Maria

last: Ciofani

address: 207 Research Drive, 128 Jones Building

department: Integrative Immunobiology

institute: Duke University School of Medicine

summary: Here we identify the activator protein-1 (AP-1) factor JunB as an essential regulator of Th17 cell identity. JunB activates the expression of Th17 lineage-specifying genes, and coordinately represses genes controlling Th1 and Treg fate. Through regulatory analysis, we find that JunB is a core regulator of global transcriptional programs that promote Th17 cell identity and restrict alternative CD4+ T cell potential.

overall_design: Examination of JunB and JunD occupancy in Junb+/+CD4cre and Junbfl/flCD4cre 48 hour in vitro polarized Th17 cell cultures

first: Tiffany

last: Carr

first: Joshua

last: Wheaton


title: Chromosomal organization and genic expression in Apicomplexan parasites is critically dictated by a versatile acetylation-methylation switch at K31 on the lateral surface of histone H4

city: LA TRONCHE

first: Mohamed-ali

last: HAKIMI

state: Grenoble

address: Domaine de la Merci, Campus Santé

institute: CNRS

summary: A striking unusual genome architecture characterizes the two related human parasitic pathogens Plasmodium falciparum and Toxoplasma gondii. A major fraction of the bulk parasite genome is packaged as transcriptionally permissive euchromatin with few loci embedded in silenced heterochromatin. Primary chromatin shapers include histone modifications at the nucleosome lateral surface close to the DNA but their mode of action remains unclear. We identify versatile modifications at Lys31 within the globular domain of histone H4 as key determinants of genome organization and expression in Apicomplexa. H4K31 acetylation promotes a relaxed chromatin state at the promoter of active genes through nucleosome disassembly in both parasites. In contrast, monomethylated H4K31 is enriched in the core body of Toxoplasma active genes but inversely correlates with transcription while being astonishingly enriched at transcriptionally inactive pericentromeric heterochromatin in Plasmodium. This is the first evidence for a methylated residue of H4 associating with transcriptional regulation likely by reducing histone turnover hence slowing RNA polymerase progression across transcribed loci.

overall_design: We report genome-wide H3K9me3, H3K4me1, H3K4me3, H3K14ac, H4K31ac, H4K31me1, H4K20me3 profiles in Toxoplasma gondii using ChIP-seq

first: Fabien

last: Sindikubwabo

first: Shuai

last: Ding

first: Tahir

last: Hussain

first: Philippe

last: Ortet

first: Mohamed

last: Barakat

first: Sebastian

last: Baumgarten

first: Dominique

last: Cannella

first: Andres

last: Palencia

first: Alexandre

last: Bougdour

first: Lucid

last: Belmudes

first: Yohann

last: Coute

first: Isabelle

last: Tardieux

first: Cyrille

middle: Y

last: Botte

first: Artur

last: Scherf

last: Hakimi


title: Role of JunB in Th17 cell effector stability

first: Maria

last: Ciofani


title: 10X Genomics scRNA sequence Lacrimal Data set

status: Public on Jun 16 2017

city: San Francisco

first: Aaron

last: Tward

address: 505 Parnassus AVE

institute: UCSF

summary: Outputs from scRNA seq reads from isolated Mouse E16 and P4 lacrimal glands

overall_design: wildtype mice lacrimal glands were isolated and sequenced in the single cell pipeline

first: Kevin

last: Yu

first: Sarah

last: Knox


title: Unexpected bactericidal activity of caspofungin against Enterococcus faecium

city: Rennes

first: Vincent

last: Cattoir

address: 2 rue Henri Le Guilloux

institute: CHU de Rennes

summary: Enterococcus faecium has become a major opportunistic pathogen with the emergence of multidrug-resistant clones that are well-adapted to the hospital environment. As part of the vast diversity of gut microbiota, they are faced with different environmental stress, including antimicrobial pressure. By contrast, little is known about the effect of non-antibiotic molecules on bacterial physiology while numerous drugs are used in inpatients, especially those hospitalized in intensive care units (ICUs). The aim of this study was to investigate the impact of the most prescribed xenobiotics in ICUs on fitness, pathogenicity and antimicrobial resistance of E. faecium. Several phenotypic analysis was carried out and we rapidly brought to light that caspofungin, an antifungal agent belonging to the echinocandin family, seemed to have an important impact on E. faecium growth. Since the fungal target of caspofungin [beta-(1,3)-glucan synthase] is absent in enterococci, the mechanism of caspofungin action was investigated by several approaches. First, we decided to confirm this result by electronic microscopy and a peptidoglycan analysis by Ultra Performance Liquid Chromatography coupled with mass spectrometry (UPLC-MS/MS). Again, we highlighted that caspofungin even at subinhibitory concentrations (SICs) seemed to have an impact on cell wall organization especially in muropeptide precursors abundance. Then, a transcriptomic analysis was performed by RNA-seq (HiSeq 2500, Illumina) using the vanB-positive reference strain E. faecium Aus0004 in the presence or absence of caspofungin SIC (8 mg/L i.e., ¼ of the MIC). Transcriptomic analysis showed that the expression of 568 genes (19.9% of the genome) was significantly altered in the presence of caspofungin SIC, with 323 genes induced (fold change >2, p-value <0.1) and 245 genes repressed (fold change <-2, p-value <0.1). Regarding the repressed genes, the pdhABCD operon is largely downregulated (fold changes -4.3, -9.7, -6.9 and -6.4, respectively). This operon encoded components of the pyruvate deshydrogenase multienzyme complex involved in bacterial energetic pathway by the citrate cycle (i.e., TCA cycle). Moreover, it seemed that the glycerol metabolism pathway and in particular the glpOKF operon is downregulated too. The dramatic alteration of TCA seemed to have an drastic impact on bacterial cells viability indeed decrease of glycerol metabolism could explain the conformational modifications of peptidoglycan.

overall_design: Transcriptome analysis by RNA-seq to monitor the levels of all transcripts in bacterial cells grown in the absence or the presence of a subinhibitory concentration (8 mg/L) of caspofungin

first: Christophe

last: Isnard

first: Sara

last: Hernandez

first: Fanny

last: Joalland

first: Didier

last: Goux

first: François

last: Guérin

last: Gravey

first: Michel

last: Auzou

first: David

last: Enot

first: Pierrick

last: Meignen

first: Felipe

last: Cava


title: HIC2 regulates maturation of the cardiovascular system

city: liverpool

first: Iain

last: Dykes

state: Select...

address: James Parson Bl, Byrom Street,

department: Pharmacy & Biomolecular science

country: United Kingdom

institute: Liverpool John Moores University

summary: HIC2 is required for normal development of the heart. Loss of function mutants exhibit early embryonic lethality while heterozygous mutants have a partially penetrant ventricular septal defect. The aim of this study was to understand the function of HIC2 in early heart development by identifying potential transcriptional targets. We harvested whole hearts (which contain circulating erythrocytes) at embryonic day E9.5 and compared expression in a conditional loss of function mutant (Mesp1 Cre/+; Hic2 Fl/Fl) to controls (Hic2 Fl/Fl).

overall_design: All samples represent pools of isolated hearts from E9.5 mouse embryos. 3 replicates of each genotype were assayed. The genotypes are: "WT": Hic2FL/FL "KO": Mesp1Cre/+; Hic2 FL/FL


title: Ppm1f is regulated by stress and associated with anxiety and depression [amygdala]

city: Atlanta

first: Raul

last: Andero Gali

state: GA

address: 954 Gatewood Rd

department: Department of Psychiatry and Behavioral Sciences

institute: Emory University

summary: Ppm1f regulation in the amygdala after acute stress immobilization

overall_design: Male mice were exposed to 2 hours acute stress immobilization. Gene changes were evaluated 6 or 8 days after stress under basal conditions.

first: Raül

last: Andero Galí

first: Kerry

last: Ressler


title: Mycobacteria induce TPL-2 mediated IL-10 in IL4 generated alternatively activated macrophages

city: Baltimore

first: Anne

middle: E.

last: Jedlicka

state: MD

address: 615 N. Wolfe street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins University, School of Public Health

summary:
IL-4 drives expansion of Th2 cells that cause generation of alternatively activated macrophages (AAMs). Filarial infections are established early in life, induce increased IL-4 production are co-endemic with tuberculosis (TB). We sought to understand, therefore, how mycobacteria are handled in the context of IL-4-induced AAM. Comparing IL-4 generated in vitro monocyte derived human AAMs to LPS and IFN-γ generated classically macrophages (CAMs), both infected with mycobacteria (BCG), we demonstrated increased early BCG uptake and increased IL-10 production in AAMs compared to CAMs.  We further demonstrated that increased IL-10 production is mediated by upregulation of tumor progression locus 2 (TPL-2), an upstream activator of extracellular signal related kinases (ERKs) in AAMs but not in CAMs, both at the transcript as well as the protein level. Pharmacologic inhibition of TPL-2 significantly diminished IL-10 production only in BCG-infected AAMs. Finally, we validated our findings in an in vivo C57Bl/6 model of filarial infection, where an exaggerated Th2 induced lung-specific alternative activation led to TPL-2 and IL-10 upregulation on subsequent TB infection. These data show that in response to mycobacterial infection, IL-4 generated AAMs in chronic filarial infections have impaired immune responses to TB infection by increasing IL-10 production in a TPL-2 mediated manner.
Experimental rationale (microarray): To understand the effect of a pre-existing filiarial infection on the immune response of mice to Mycobacterium tuberculosis

overall_design: C57BL/6 mice were infected with B. malayi microfilaria by i.v. injection in the tail vein and/or M. tuberculosis by nose aerosol. At 7 weeks post infection, lungs were harvested and frozen for subsequent RNA extraction and gene expression profiling with Affymetrix microarrays.

first: Soumya

last: Chatterjee

first: Kawsar

middle: R

last: Talaat

first: Emily

middle: E

last: van Seventer

first: Carl

last: Feng

first: Alan

last: Scott

first: Amanda

last: Dziedzic

first: Thomas

middle: B

last: Nutman


title: 0-12 hour transcriptional response of mouse bone marrow-derived macrophages to stimulation by LPS

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

summary:
Innate immune response to pathogens is a complex, multi-staged process involving thousands of genes. While numerous transcription factors that act as master regulators of the response to LPS have been identified, the temporal complexity of gene expression changes strongly suggest that additional layers of regulation remain to be uncovered.
This study was done to examine response of mouse bone marrow-derived macrophages to stimulation with LPS over time. Bone marrow-derived macrophages from C57BL/6J mice were incubated in the presence of LPS for 1, 4 or 12 h, while the control group was incubated under same conditions for 4 h in the absence of the LPS. RNA isolated from these macrophages was analyzed using the Affymetrix Mouse Exon Array 1.0 ST.

overall_design: Two sets of three female mice (strain C57BL/6J) were sacrificed at 8-12 weeks of age, and macrophages were derived from the femoral bone marrow using rhM-CSF. On day six, macrophages were divided into two treatment groups per animal, for a total of 12 samples. LPS was introduced into the medium for nine samples (one from each animal) at 10 ng/mL on day seven, and after 1, 4 or 12 h of incubation, RNA was isolated using TRIzol. Three sets of un-stimulated macrophages were harvested at 4 h and RNA isolated with TRIzol. Labeled cRNA derived from the RNA samples was hybridized to Affymetrix Mouse Exon Array 1.0 ST GeneChips.  Microarray data were processed using Affymetrix power tools and brain-array CDFs (v 18.0)

first: Kathleen

last: Kennedy

first: Peter

last: Askovich

last: Aderem


title: Ppm1f is regulated by stress and associated with anxiety and depression

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

overall_design: Refer to individual Series


title: Ppm1f is regulated by stress and associated with anxiety and depression [mPFC]

summary: Ppm1f regulation in the medial prefrontal cortex (mPFC) after acute stress immobilization

overall_design: Male mice were exposed to 2 hours acute stress immobilization. Gene changes were evaluated 6 days after stress under basal conditions.

middle: J


title: The prefrontal cortex microRNA expression in mice offspring caused by glyphosate exposure during pregnancy and lactation

city: HangZhou City

first: Hua

last: Ji

state: Zhejiang

address: No.481 Bingwen road

department: Department of Basic Medicine

institute: Hangzhou medical college

summary:
In this study, the miRNAs expression pattern in prefrontal cortex (PFC) of postnatal day (PND) 28 mice offsprings which were exposured by glyphosate-based herbicide (GBH) during pregnancy and lactation was investigated.
MiRNA microarray had detected 55 upregulated and 19 downregulated miRNAs in the PND28 mice offsprings' PFC.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In this study, the isolated total RNA taken from two pooled samples of two groups, was used to acquire expression profiles, and the result shows 53 differentially-expressed miRNAs, some of them are known to be involved in brain development or the pathogenesis of neurodevelopmental disorders, indicate that dysregulated expression of miRNAs may be involved in the mechanism of glyphosate-induced neurotoxicity.

first: Xinli

last: Fan

first: Lihui

last: Wu


title: Effects of polychlorinated biphenyls (PCBs) and their hydroxylated metabolites (OH-PCBs) on Arabidopsis thaliana.

status: Public on Jun 15 2017

city: Philadelphia

first: Benoit

last: Van Aken

state: PA

address: 1947 N. 12th Street

department: CEE

institute: Temple University

summary: The transcriptomic response of A. thaliana to 2,5-dichlorobiphenyl (2,5-DCB) and its OH-metabolite, 4'-OH-2,5-DCB, was then examined using whole-genome expression microarrays (Affymetrix).

overall_design: A. thaliana plantlets were exposed for 21 days to 2,5-DCB (50 mg L-1) and 4'-OH-2,5-DCB (5 mg L-1). Control plantlets were grown in the presence of the solvent carrier only (acetone). Six boxes containing five plantlets each were used for each treatment.

first: Srishty

last: Subramanian

first: Jerald

last: Schnoor


title: ZEB1 binding sites in TGF-beta-stimulated MCF7 breast cancer cell line

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

institute: University of Tokyo

summary: We searched for roles of ZEB1 during EMT through genome-wide analysis of its binding sites in breast cancer cells.

overall_design: ZEB1 binding sites in TGF-beta-stimulated MCF7 cells were determined by ChIP-seq as a negative control of those obtained from the basal typle breast cancer cell lines.

first: Akihiro

last: Katsura

first: Yusuke

last: Tamura

first: Masato

last: Morikawa

first: Tsubasa

last: Sakurai

first: Anna

last: Mizutani

first: Yasuyuki

last: Morishita

first: Kohei

last: Miyazono


title: The first large-scale sequencing of M. javanica transcriptomes from salivary glands, liver and small intestine by using Illumina HiSeq technology

city: Guangzhou

first: Jing

last: Ma

state: Guangdong

address: xingangxi

institute: Guangdong Institute of Applied Biological Resources

summary: The Malayan pangolin (Manis javanica), an unusual mammal that is a scale-covered, toothless specialist myrmecophage, is maintained primarily through captive breeding in China. Maintaining this species in captivity is a significant challenge partly because little is known about its behavior and reproduction. The molecular mechanisms of its digestive system play a key role in the feeding and dietary husbandry of pangolins in captivity. Here, we performed the first large-scale sequencing of M. javanica transcriptomes from three digestive organs—the salivary glands, liver, and small intestine—by using Illumina HiSeq technology- to provides useful genetic resources for future functional work that may be relevant for the maintenance of captive pangolins.

overall_design: RNA-Seq analysis of three digestive organs: salivary glands, liver, and small intestine

first: Jin

middle: P

last: Chen


title: Transcriptional profiling of THP-1 cells on treatment with LL-37 and nano conjugated LL-37

city: Bhubaneswar

first: Biswaranjan

last: Pradhan

state: ODISHA

address: Jatni

department: Biological Sciences

country: India

institute: National Institute of Science Education and Research Bhubaneswar

summary: Gene expression in THP-1 cells treated for 6 hours with CNT and GNP conjugated with LL-37, LL-37 spiked as well as free LL-37: Reference (Total RNA Mixture of all samples) vs. treated cells

overall_design: Eight conditions of the expriment, Untreated THP-1 cells (NT) vs. treatment with free LL-37, nano conjugated LL-37, and nano materials spiked with LL-37 for 6 hours. Biological replicates: 3 in each case (Equal amount of total RNA from each replicate pulled together for microarray). Common reference for all groups.

first: Pradhan

last: Biswaranjan

first: Murmu

last: Krushna Chandra

first: Aich

last: Palok


title: Assessing the developmental and malignant potential of human pluripotent stem cells

city: Sheffield

first: Paul

last: Gokhale

address: Western Bank

department: Biomedical Science

institute: University of Sheffield