title: Antiviral Activity of BMPs and Activins

city: Oxford

first: Hal

last: Drakesmith

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: A microarray experiment was performed to investigate changes in gene expression induced in the Huh7.5 hepatoma cell line following treatment for 24 hours with recombinant human Bone Morphogenetic Protein 6 (BMP6) (18 nM).

overall_design: Total RNA extracted from HuH7.5 cells treated with 18nM BMP6 or Vehicle for 24 hours

first: Lucy

last: Eddowes

first: Eleni

last: Giannoulatou

first: Andrew

last: Armitage


title: Drug-induced change in gene expression across NCI-60 cell lines after exposure to 15 anticancer agents for 2, 6 and 24h (lapatinib)

status: Public on Oct 09 2018

city: Rockville

first: Anne

last: Monks

state: MD

address: 9609 Medical Center Dr

department: Developmental Therapeutics Program

country: USA

institute: National Cancer Institute

summary: To identify patterns of drug-induced gene modulation that occur across different cell types, we measured gene expression changes across NCI-60 cell lines after exposure to 15 anticancer agents.  The results were integrated into a database and set of interactive analysis tools, the NCI Transcriptional Pharmacodynamics Workbench (NCI TPW), intended to allow exploration of gene expression modulation, including by molecular pathway, drug target, and association with drug sensitivity.  We identified common transcriptional responses across drugs and cell types and uncovered cell signaling pathway–specific gene expression changes associated with drug sensitivity.  We also demonstrated the value of this tool for investigating clinically relevant molecular hypotheses, utilizing the NCI TPW to assess drug-induced expression changes in genes associated with immune function and epithelial-mesenchymal transition, and to identify candidate biomarkers for drug activity.  The NCI TPW provides a comprehensive resource to facilitate understanding of tumor cell characteristics that define sensitivity to anticancer drugs.

overall_design: To compare and contrast transcriptional responses over time, in the NCI-60 cell line panel after treatment with 15 anticancer agents.

first: Yingdong

last: Zhao

first: Curtis

last: Hose

first: Hossein

last: Hamed

first: Julia

last: Krushkal

first: Jianwen

last: Fang

first: Dmitriy

last: Sonkin

first: Eric

middle: C

last: Polley

first: Laura

middle: K

last: Fogli

first: Mariam

middle: M

last: Konate

first: Sarah

middle: B

last: Miller

first: Melanie

middle: A

last: Simpson

first: Andrea

middle: R

last: Voth

first: Ming-Chung

last: Li

first: Alida

last: Palmisano

first: Erik

last: Harris

first: Xiaolin

last: Wu

first: John

last: Connelly

first: Annamaria

last: Rapisarda

first: Beverly

last: Teicher

first: Richard

last: Simon

first: James

middle: H

last: Doroshow


title: Drug-induced change in gene expression across NCI-60 cell lines after exposure to 15 anticancer agents for 2, 6 and 24h (gemcitabine)

first: Anne

last: Monks

first: Yingdong

last: Zhao

first: Curtis

last: Hose

first: Hossein

last: Hamed

first: Julia

last: Krushkal

first: Jianwen

last: Fang


title: Drug-induced change in gene expression across NCI-60 cell lines after exposure to 15 anticancer agents for 2, 6 and 24h (geldanamycin)

first: Dmitriy

last: Sonkin

first: Eric

last: Polley

first: Laura

last: Fogli

first: Mariam

last: Konate

first: Sarah

last: Miller

first: Melanie

last: Simpson


title: Drug-induced change in gene expression across NCI-60 cell lines after exposure to 15 anticancer agents for 2, 6 and 24h (erlotinib)

first: Andrea

last: Voth

first: Ming-Chung

last: Li

first: Alida

last: Palmisano

first: Erik

last: Harris

first: Xiaolin

last: Wu

first: John

last: Connelly


title: Drug-induced change in gene expression across NCI-60 cell lines after exposure to 15 anticancer agents for 2, 6 and 24h (paclitaxel)

first: Anne

last: Monks

first: Yingdong

last: Zhao

first: Annamaria

last: Rapisarda

first: Beverly

last: Teicher

first: Richard

last: Simon

first: James

last: Doroshow


title: Drug-induced change in gene expression across NCI-60 cell lines after exposure to 15 anticancer agents for 2, 6 and 24h (doxorubicin)

first: Curtis

last: Hose

first: Hossein

last: Hamed

first: Julia

last: Krushkal

first: Jianwen

last: Fang

first: Dmitriy

last: Sonkin

first: Eric

last: Polley


title: Drug-induced change in gene expression across NCI-60 cell lines after exposure to 15 anticancer agents for 2, 6 and 24h (cisplatin)

first: Laura

last: Fogli

first: Mariam

last: Konate

first: Sarah

last: Miller

first: Melanie

last: Simpson

first: Andrea

last: Voth

first: Ming-Chung

last: Li


title: Drug-induced change in gene expression across NCI-60 cell lines after exposure to 15 anticancer agents for 2, 6 and 24h (bortezomib)

first: Anne

last: Monks

first: Yingdong

last: Zhao

first: Alida

last: Palmisano

first: Erik

last: Harris

first: Xiaolin

last: Wu

first: John

last: Connelly


title: Drug-induced change in gene expression across NCI-60 cell lines after exposure to 15 anticancer agents for 2, 6 and 24h (5-Azacytidine)

first: Curtis

last: Hose

first: Hossein

last: Hamed

first: Annamaria

last: Rapisarda

first: Beverly

last: Teicher

first: Richard

last: Simon

first: James

last: Doroshow


title: Transcriptomic profiling of S2/S3 proximal tubules in response to LPS treatment

status: Public on Oct 06 2018

city: Indianapolis

first: Takashi

last: Hato

state: IN

address: 950 W. Walnut St. R2 202

department: Medicine

institute: Indiana University

summary: To investigate the mechanisms of endotoxin-mediated kidney injury as well as renoprotective effects of endotoxin preconditioning, we performed manual microdissection of S2/S3 proximal tubules in mice as follows: 1) Non-preconditioned mice subjected to single-dose 5 mg/kg LPS (0111:B4) i.p. for 4 hrs. 2) Non-preconditioned mice subjected to single-dose 5 mg/kg LPS (0111:B4) for 24 hrs. 3) Preconditioned mice subjected to 0.25 mg/kg LPS followed 24 hour later by 5 mg/kg LPS for 4 hrs. 4) Preconditioned mice subjected to 0.25 mg/kg LPS followed 24 hour later by 5 mg/kg LPS for 24 hrs. 5) Control mice (untreated).

overall_design: S2/S3 proximal tubular segments from control, LPS-treated (non-preconditioned) and preconditioned C57BL/6J male mice

first: Pierre

last: Dagher


title: Histological, transcriptomic and in vitro analysis reveal an intrinsic activated state of myogenic precursors in hyperplasic muscle of trout

status: Public on Oct 01 2018

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

summary: The dramatic increase in myotomal muscle mass in fish is related to their ability to lastingly  produce new muscle fibres, a process termed hyperplasia. The molecular and cellular mechanisms underlying fish muscle hyperplasia largely remain unknown. In this study, we aimed to characterize intrinsic properties of myogenic cells originating from fish hyperplasic muscle. For this purpose, we compared in situ proliferation, in vitro cell behavior and transcriptomic profile of myogenic precursors originating from hyperplasic muscle of juvenile trout (JT) and from non-hyperplasic muscle of fasted juvenile trout (FJT) and adult trout (AT). For the first time, we showed that myogenic precursors proliferate in hyperplasic muscle from JTas shown by in vivo BrdU labeling. This proliferative rate was very low in AT and FJT muscle. Transcriptiomic analysis revealed that myogenic cells from FJT and AT displayed close expression profiles with only 64 differentially expressed genes (BH corrected p-val < 0.001). In contrast, 2623 differentially expressed genes were found between myogenic cells from JT and from both FJT and AT. Functional categories related to translation, mitochondrial activity, cell cycle, and myogenic differentiation were inferred from genes up regulated in JT compared to AT and FJT myogenic cells. Conversely, Notch signaling pathway, that signs cell quiescence, was inferred from genes down regulated in JT compared to FJT and AT. In line with our transcriptomic data  JT myogenic precursors displayed higher proliferation and differentiation capacities than FJT and AT myogenic precursors. The transcriptomic analysis and examination of cell behavior converge to support the view that myogenic cells extracted from hyperplastic muscle of juvenile trout are intrinsically more potent to form myofibres than myogenic cells extracted from non-hyperplasic muscle. The generation of gene expression profiles in myogenic cell extracted from muscle of juvenile trout may yield insights into the molecular and cellular mechanisms controlling hyperplasia and provides a useful list of potential molecular markers of hyperplasia.

overall_design: Myogenic precursors were isolated from juvenile trout (5g, JT), from 3-4 weeks fasted juvenile rainbow trout (5g, FJT) and from adult rainbow trout (1.5-2kg, AT) as previously described (Gabillard et al. 2010).

first: Sabrina

last: Jagot

first: Nathalie

last: Sabin

first: Aurélie

last: Le Cam

first: Jérôme

last: Bugeon

first: Pierre-Yves

last: Rescan

first: Jean-Charles

last: Gabillard


title: High density analysis of the tailing and trimming patterns of RISC-cleaved MYB33 and SPL13 transcripts in Arabidopsis heso1 and urt1 mutants

status: Public on Oct 05 2018

city: Strasbourg

first: Dominique

last: Gagliardi

address: 12, rue du General Zimmer

department: IBMP

institute: CNRS

summary: Using 3' RACEseq method, we compared the tailing and nibbling patterns of RISC-cleaved MYB33 and SPL13 transcripts between wild-type plants and mutant plants depleted for the terminal uridylyltransferases (TUTases) HESO1 and URT1. Our data reveal a major and minor role for HESO and URT1, respectively, in the uridylation of RISC-cleaved transcripts.

overall_design: 3’ RACE-seq method was used to analyze the 3’ ends of 5’ MYB33 and SPL13 RISC-cleaved transcripts  for urt1, heso1 and heso1 urt1 mutants. This protocol is based on the ligation of a primer at the 3’ end of RNA, and the subsequent targeted amplification by PCR of amplicons suitable for Illumina sequencing.

first: Hélène

last: Zuber

last: Scheer


title: Drug-induced change in gene expression across NCI-60 cell lines after exposure to 15 anticancer agents for 2, 6 and 24h (dasatinib)

first: Anne

last: Monks

first: Yingdong

last: Zhao

first: Curtis

last: Hose

last: Hamed

first: Julia

last: Krushkal

first: Jianwen

last: Fang

first: Dmitriy

last: Sonkin

first: Eric

last: Polley

first: Laura

last: Fogli

first: Mariam

last: Konate

first: Sarah

last: Miller

first: Melanie

last: Simpson

first: Andrea

last: Voth

first: Ming-Chung

last: Li

first: Alida

last: Palmisano

first: Erik

last: Harris

first: Xiaolin

last: Wu

first: John

last: Connelly


title: Development of Trypanosoma brucei EATRO 1125 in the host bloodstream

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

type: Expression profiling by high throughput sequencing

summary: Trypanosoma brucei EATRO 1125 parasites were grown in adult MF1 mice with parasites harvested on day 3 post-infection ('ascend/slender') or on day 6 post-infection ('peak/stumpy').

overall_design: Three replicates each of two conditions (ascending/slender, peak/stumpy) were analysed. 'Peak' samples were each derived from infections in three individual mice; 'ascend' samples were derived from 2 individual mice infections (replicate 1 and 2) and from a pool of four infections (replicate 3), to generate sufficient material for analysis. All samples were analysed for their cell cycle status by scoring the number of kinetoplasts and nuclei in parasites and were assayed for PAD1 expression, a marker of stumpy formation.

first: Eleanor

last: Silvester

first: Keith

last: Matthews


title: Gene expression profile of Human non-functional Pancreatic neuroendocrine tumors (PanNETs)

city: New Brunswick

first: SAURABH

middle: V

last: LADDHA

state: NEW JERSEY

address: 195 Little Albany Street

department: Center for Systems and Computational Biology

institute: Rutgers Cancer Institute of New Jersey

summary:
Gene expression profiling of PanNETs patients samples were performed to understand genotype to phenotype correlations, novel molecular subtypes and cell of origin
The most commonly mutated genes in pancreatic neuroendocrine tumors (PanNETs) are ATRX, DAXX, and MEN1. Little is known about the cells-of-origin for non-functional neuroendocrine tumors. Here, we genotyped 64 PanNETs for mutations in ATRX, DAXX, and MEN1 and found 37 tumors (58%) carry mutations in these three genes (A-D-M mutant PanNETs) and this correlates with a worse clinical outcome than tumors carrying the wild-type alleles of all three genes (A-D-M WT PanNETs). We performed RNA sequencing and DNA-methylation analysis on 33 randomly selected cases to reveal two distinct subgroups with one group consisting entirely of A-D-M mutant PanNETs. Two biomarkers differentiating A-D-M mutant from A-D-M WT PanNETs were high ARX gene expression and low PDX1 gene expression with PDX1 promoter hyper-methylation in the A-D-M mutant PanNETs. Moreover, A-D-M mutant PanNETs had a gene expression signature related to that of alpha cells (pval < 0.009) of pancreatic islets including increased expression of HNF1A and its transcriptional target genes. This gene expression profile suggests that A-D-M mutant PanNETs originate from or transdifferentiate into a distinct cell type similar to alpha cells.

overall_design: 47 PanNETs tumor specimens were obtained from MSKCC and samples were hybridized to HGU133A2 (Affymetrix) to profile gene expression

first: Saurabh

last: Laddha

first: Chang

middle: S

last: Chan

last: Tang


title: ZEB2, a master regulator of the epithelial-mesenchymal transition, mediates trophoblast differentiation

city: Maplewood

first: Nick

last: Illsley

state: NJ

address: Richmond Ave

institute: Placental Research Group LLC

summary: Comparison of genes associated with the EMT between trophoblast cell line (BeWo, JEG3) controls and cells overexpressing the ZEB2 gene (BeWo ZEB2oe, JEG_ZEB2oe).

overall_design: EMT-associated genes compared between lentivirally-transduced BeWo and JEG3 cells expressing an empty vector construct and stable clones of BeWo and JEG3 cells overexpressing ZEB2.

first: Nicholas

middle: P


title: TRIM28 protects TRIM24 from SPOP-mediated degradation and promotes prostate cancer progression [microarray]

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

summary: In this study, proteomic profiling of TRIM24 interactome in conjunction with shRNA screening of TRIM24 top-interactors nominated that   TRIM28 is indispensable for TRIM24 protein stability. We showed that TRIM28 stabilizes TRIM24 against SPOP-mediated ubiquitination and   degradation. TRIM28 promotes TRIM24 and AR transcription activity, androgen-dependent and -independent PCa growth.   In addition, we demonstrated that TRIM28 level in high in advanced PCa, which drives TRIM24/AR transcription activity in a similar manner   to SPOP mutation, which implies that TRIM28 potentially dictates the therapeutic outcome of TRIM24-targeted therapy.

overall_design: genetic modification design

first: Ka-wing

last: Fong


title: A Kelch domain-containing KLHDC7B and a long non-coding RNA ST8SIA6-AS1 act oppositely on breast cancer cell proliferation via the interferon signaling pathway (KLHDC7B knockdown)

city: Ilsan

first: Juyeon

last: Ham

address: 32, Dongguk-ro

country: South Korea

institute: Dongguk University

summary: Kelch domain-containing 7B (KLHDC7B) was revealed hypermethylated at promoter but upregulated in breast cancer. And we identified a long non-coding RNA, ST8SIA6-AS1 (STAR1), of which expression was highly associated with KLHDC7B in breast cancer (r = 0.5887).

overall_design: Control sample is transfected RNA using si negative control and Test sample is a knockdown using KLHDC7B's  siRNA. Both sample RNA is extracted from breast cancer cell MCF-7

first: Gookjoo

last: Jeong

first: Hansol

last: Bae

first: Sun

middle: J

last: Kim


title: A Kelch domain-containing KLHDC7B and a long non-coding RNA ST8SIA6-AS1 act oppositely on breast cancer cell proliferation via the interferon signaling pathway (LOC100128098 knockdown)

overall_design: Control sample is RNA from MCF-7 and the test sample is RNA obtain from  MCF-7  transfected siLOC100128098


title: Reprogramming normal human epithelial tissues to a common, lethal neuroendocrine cancer lineage (Whole Exome-seq)

city: Los Angeles

first: Owen

middle: N

last: Witte

state: CA

address: 675 Charles E Young Dr S, 5720 MRL Bldg; MC 729022

department: MIMG

institute: UCLA

summary: Small cell carcinomas from different tissues exhibit transcriptional and epigenetic convergence and suggest common vulnerabilities for therapies

overall_design: Convergent neuroendocrine cancer from distinct epithelial tissues

first: Jung

middle: W

last: Park


title: The response of the hypothalamus to leptin and a high-fat diet in mice

status: Public on Sep 30 2018

city: Aberdeen

first: Claus

last: Mayer

address: Greenburn Road

institute: Biomathematics & Statistics Scotland

summary: Energy homeostasis is regulated by the hypothalamus but fails when animals are fed a high-fat diet (HFD), and leptin insensitivity and obesity develops. We have used a microarray-based transcriptomics approach to identify novel genes regulated by HFD and leptin in the hypothalamus using mouse global arrays.

overall_design: For the transcriptomics studies male, 16 week old, C57BL/6J mice were obtained from Charles River laboratories (Maastricht, the Netherlands) and housed in pairs in the light and temperature-controlled animal facility of Wageningen University (12:12 h light/dark cycle at 22⁰C). Mice were maintained for 1 or 4 weeks on either a HFD (45% kCal from fat) or LFD (10% kCal from fat) (D12451 and D12450B respectively Research Diets, NJ, US). Please see http://www.researchdiets.com/opensource-diets/stock-diets/dio-series-diets for diet composition details. The fat source in this experiment was palm oil. Mice were then challenged with three intraperitoneal (IP) injections of recombinant mouse leptin (2 mg/kg body weight) (R&D Systems, Abingdon, UK) or vehicle at 24, 15 and approximately 3 hours prior to killing in the early morning (n=10). This experiment was part of the NuGO Proof of Principle studies

first: Lynda

last: Williams

first: Claus-Dieter

first: Michael

last: Muller

first: Baukje

last: de Roos

first: Eva-Maria

last: Bachmair


title: Affymetrix CytoScan 750K and HD data for developmental delay and/or physical disability phenotypes samples

status: Public on Sep 29 2018

city: Yongin-si

first: Junnam

last: Lee

address: Green Cross Genome, Green Cross Laboratories-3rd floor . 107 Ihyeon-ro 30 beon-g

institute: GreenCross genome

type: Genome variation profiling by genome tiling array

summary: Chromosomal copy number variations (CNV) have been associated with various neurological and developmental disorders and chromosomal microarray (CMA) is a method of choice to diagnose Copy Number Gain/Loss syndromes. Recently, next-generation sequencing (NGS)-based low-coverage whole genome sequencing (LC-WGS) has been applied to detect Copy Number Gain/Loss syndromes. This dataset is intended to be used as a “Golden standard data set” for development of LC-WGS analysis method. It consists of patients (n=63) who have a mental delay and/or physical disability phenotype and normal (n=20) phenotype.

overall_design: CNV analysis using Affymetrix 750K and HD array was performed on 63 samples with developmental delay and/or physical disability phenotype. There are also 20 samples who were not diagnostic of any CNV disease and normal phenotype.

first: Eun

last: Cho


title: A role for the Tgf-β/Bmp co-receptor Endoglin in the molecular oscillator that regulates the hair follicle cycle.

status: Public on Sep 28 2018

city: Madrid

first: Gema

last: Moreno-Bueno

state: Madrid

address: Arturo Duperier

department: Biochemistry

country: Spain

institute: IIB

summary:
The hair follicle is a biological oscillator that alternates growth, regression, and rest phases driven by the sequential activation of the proliferation/differentiation programs of resident stem cell populations. The activation of hair follicle stem cell niches and subsequent entry into the growing phase is mainly regulated by Wnt/β-catenin signalling, while regression and resting phases are mainly regulated by Tgf-β/Bmp/Smad activity. A major question still unresolved is the nature of the molecular switch that dictates the coordinated transition between both signalling pathways. Here we have focused on the role of Endoglin (Eng), a key co-receptor for members of the Tgf-β/Bmp family of growth factors.Using an Eng haploinsufficient mouse model, we report that Eng is required to maintain a correct follicle cycling pattern and for an adequate stimulation of hair follicle stem cell niches. We further report that β-catenin binds to the Eng promoter depending on Bmp signalling. Moreover, we show that β-catenin interacts with Smad4 in a Bmp/Eng-dependent context and both proteins act synergistically to activate Eng promoter transcription. These observations point to the existence of a growth/rest switching mechanism in the hair follicle that is based on an Eng-dependent feedback crosstalk between Wnt/β-catenin and Bmp/Smad signals.
Implication of Endoglin,  Wnt/β-catenin and Bmp/Smad signals in the growth/rest hair follicle

overall_design: Microarray experiments were performed using Mouse Gene Expression 4x44K Microarray Kit G4122F (Agilent technologies, Wilmington, DE). RNA was isolated using RNAesy Extraction Kit (QIAGen, Germany). RNA was labeled and array hybridized us ing the Low RNA Linear Amplification Kit and the In Situ Hybridization Kit Plus (Agilent technologies, Wilmington, DE) respectively. After hybridization and washing, the slides were scanned in an Axon GenePix Scanner (Axon Instruments Inc., Union City, CA) and analysed using Feature Extraction Software 10.1 (Agilent technologies, Wilmington, DE). Two different RNA samples obtained from each Eng modified cell line were labelled with Cy5-dUTP. The RNA samples extracted Downloaded from https://academic.oup.com/jmcb/advance-article-abstract/doi/10.1093/jmcb/mjy051/5101434 by Bukkyo University user on 23 September 2018 23from wild type cells were marked with Cy3-dUTP (Amersham, Sweden). Two additional hybridizations were performed using the reciprocal fluorochrome labelling . The genes whose expression was up or downregulated at least 2-fold in Eng+/-with respect to control cells were selected for analysis.

first: María

middle: I

last: Calvo-Sánchez

first: Sandra

last: Fernández-Martos

first: Elisa

last: Carrasco

first: Carmelo

last: Bernabéu

first: Miguel

last: Quintanilla

first: Jesús

last: Espada


title: A temporal transcriptome and methylome in human embryonic stem cell-derived cardiomyocytes identifies novel regulators of early cardiac development

city: los angeles

first: Matteo

last: Pellegrini

address: 675 Charles E Young Drive S

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

type: Methylation profiling by high throughput sequencing

summary: We generated reduced-representive bisulfite sequencing data to assess the epigenetic dynamics of cardiac differentiation from stem cells

overall_design: Examination of DNA methylation level in four developmental stages during cardiogenesis

first: Kai

last: Fu

first: Haruko

last: Nakano


title: Genome wide DNA 6mA methylome and transcriptome change upon mitochondrial stress in C.elegans

status: Public on Sep 27 2018

city: beijing

first: huang

last: tianxiao

address: yiheyuan

country: China

institute: peking university

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

overall_design: Refer to individual Series


title: miRNA profiling from C13K and OV2008 ovarian cancer cell lines

city: Wuhan

first: Zihui

last: Xu

address: Jiefang Road 238

institute: Renmin Hospital of Wuhan University

summary:
Cisplatin-resistance is a major cause of treatment failure in human ovarian cancer. Besides lots of genes involved, emerging evidences demonstrate that miRNAs contribute to cisplatin-resistance in cancer.
We measured the miRNA expression profiles of cisplatin-resistant C13K ovarian cancer cell line compared with its cisplatin-sensitive OV2008 parent cell line using miRNA microarrays.

overall_design: Total RNA of OV2008 or C13K cells was extracted and purified. miRNA-profiling was carried out by miRNA microarray using Affymetrix miRNA 4.0 and Affymetrix GeneChip. The random-variance model (RVM) F test was applied to filter differentially expressed genes for the two ovarian cancer cell lines. After the significance analysis and false discovery rate (FDR) analysis, differentially expressed genes were selected according to their p value threshold.

first: Xiaoyan

last: Shi


title: A Kelch domain-containing KLHDC7B and a long non-coding RNA ST8SIA6-AS1 act oppositely on breast cancer cell proliferation via the interferon signaling pathway

first: Juyeon

last: Ham


title: A Kelch domain-containing KLHDC7B and a long non-coding RNA ST8SIA6-AS1 act oppositely on breast cancer cell proliferation via the interferon signaling pathway (KLHDC7B overexpression)

overall_design: Control sample is RNA from MCF-7 and the test sample is RNA obtain from  MCF-7  transfected KLHDC7B ORF vector

first: Gookjoo

last: Jeong

first: Hansol

last: Bae

first: Sun

last: Kim


title: NONO detects the nuclear HIV capsid to promote cGAS-mediated innate immune activation

city: Paris

first: Nicolas

last: Manel

address: 12 rue Lhomond

department: INSERM U932

institute: Institut Curie

summary: Detection of viruses by innate immune sensors induces protective antiviral immunity. The viral DNA sensor cGAS is necessary for detection of HIV by human dendritic cells and macrophages. However, synthesis of HIV DNA during infection is not sufficient for immune activation. The capsid protein, which associates with viral DNA, has a pivotal role in enabling cGAS-mediated immune activation. We now find that NONO is an essential sensor of the HIV capsid in the nucleus. NONO protein directly binds capsid with higher affinity for weakly pathogenic HIV-2 than highly pathogenic HIV-1. Upon infection, NONO is essential for cGAS activation by HIV and cGAS association with HIV DNA in the nucleus. NONO recognizes a conserved region in HIV capsid with limited tolerance for escape mutations. Detection of nuclear viral capsid by NONO to promote DNA sensing by cGAS reveals an innate strategy to achieve distinction of viruses from self in the nucleus.

overall_design: Monocyte-derived dendritic cells from healthy donors or NONO-deficient patients were either untouched, infected by a HIV-1 reporter virus with Vpx, infected by a HIV-2 GFP-reporter virus, or treated by cGAMP with lipofectamin. After 24 hours, RNA was extracted for gene expression analysis.

first: Xavier

last: Lahaye

first: Francesca

last: Nadalin


title: Genome wide 6mA modification change upon mitochondial stress in C.elegans

summary: We discovered 364 peaks enrichment change in wild-type C.elegans genome by 6mA MeDIP-seq, which indicated those genes response to mitochondrial stress and may function in mitochondrial stress response.

overall_design: Wild-type worms was treated by mitochondrial inhibitor antimycin A from L1 to L4, then performed to 6mA MeDIP and NGS.

first: Chengchuan

last: Ma

first: Wanqiu

last: Ding

first: Tianxiao

last: Huang


title: Transcriptome wide change upon mitochondial stress in C.elegans

summary: We discovered 5446 genes expression change (4218 genes from P0 to F2) in wild-type C.elegans transcriptome compared to DAMT-1 mutant upon mitochondrial stress by RNA-seq, which indicated those genes response to mitochondrial stress and may function in mitochondrial stress response.

overall_design: Wild-type worms or damt-1 mutant were treated by mitochondrial inhibitor antimycin A from L1 to L4, then performed to NGS.


title: Drug-induced change in gene expression across NCI-60 cell lines after exposure to 15 anticancer agents for 2, 6 and 24h

city: Rockville

first: Anne

last: Monks

address: 9609 Medical Center Dr

institute: National Cancer Institute

summary: To identify patterns of drug-induced gene modulation that occur across different cell types, we measured gene expression changes across NCI-60 cell lines after exposure to 15 anticancer agents. The results were integrated into a database and set of interactive analysis tools, the NCI Transcriptional Pharmacodynamics Workbench (NCI TPW), intended to allow exploration of gene expression modulation, including by molecular pathway, drug target, and association with drug sensitivity. We identified common transcriptional responses across drugs and cell types and uncovered cell signaling pathway–specific gene expression changes associated with drug sensitivity. We also demonstrated the value of this tool for investigating clinically relevant molecular hypotheses, utilizing the NCI TPW to assess drug-induced expression changes in genes associated with immune function and epithelial-mesenchymal transition, and to identify candidate biomarkers for drug activity. The NCI TPW provides a comprehensive resource to facilitate understanding of tumor cell characteristics that define sensitivity to anticancer drugs.

first: Yingdong

last: Zhao

first: Curtis

last: Hose

first: Hossein

last: Hamed

first: Julia

last: Krushkal

first: Jianwen

last: Fang

first: Dmitriy

last: Sonkin

first: Eric

last: Polley

first: Laura

last: Fogli

first: Mariam

last: Konate

first: Sarah

last: Miller

first: Melanie

last: Simpson

first: Andrea

last: Voth

first: Ming-Chung

last: Li

first: Alida

last: Palmisano

first: Erik

last: Harris

first: Xiaolin

last: Wu

first: John

last: Connelly

first: Annamaria

last: Rapisarda

first: Beverly

last: Teicher

first: Richard

last: Simon

first: James

last: Doroshow


title: Expression of regulatory elements and targets in celiac disease

city: Leioa

first: Jose Ramon

last: Bilbao

state: Outside the US or Canada

address: Bº Sarriena

department: Genetics, Physical Anthropology and Animal Physiology

institute: University of the Basque Country (UPV/EHU)


title: Estrogen-dependent up-regulation of Adcyap1r1 expression in nucleus accumbens is associated with genetic predisposition of sex-specific QTL for alcohol consumption on rat chromosome 4

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: RNA-seq was performed on the nucleus accumbens of female (F) interval-specific congenic strain-B (P.NP-ISCS-B) and inbred alcohol preferring (iP) control rat

overall_design: Total RNA was isolated from nucleus accumbens (NA) of female alcohol naive interval-specific congenic (ISCS) and control iP rats. Illumina TruSeq RNA Sample Preparation was performed following manufacturer's protocol. Samples were run on an Illumina HiSeq 2000 in triplicate.

first: Yong

last: Weidong

first: Lai

last: Zhao

first: Zou

last: Yi

first: Liang

last: Tiebing


title: Bach Factors Operate Erythro-Myeloid Differentiation by Responding to Infection

status: Public on Sep 26 2018

city: Sendai

first: Kazuhiko

last: Igarashi

state: Miyagi

address: Seiryo 2-1

country: Japan

institute: Tohoku University

summary: Hematopoietic cell differentiation should be tightly regulated in accordance with environmental changes to keep homeostasis. Infection is one of the conditions that induce myelopoiesis to exclude pathogens and repress erythropoiesis, which might be beneficial for the restriction of nutritional iron for pathogens. While several transcription factors (TFs), including C/EBP family and Gata1, play central roles in erythro-myeloid differentiation, the precise mechanism which controls the differentiation for the adaptation to infection remains obscure. In this study, it was revealed that Bach factors induce erythropoiesis and repress myelopoiesis in the erythro-myeloid bifurcation step, and their expressions per se were suppressed by infectious stimuli. Hence, they work as balancers of the erythro-myeloid differentiation between steady state and infectious state. These findings give us new insight into the machinery which regulates the fate of hematopoietic cells by responding to surrounding environments.

overall_design: To investigate the transcriptomic phenotype of Bach1–/–Bach2–/– (double knock out; DKO) mice in common myeloid progenitor level, gene expression profiling by array using primary common myeloid progenitors from WT or DKO mice was performed.

first: Hiroki

last: Kato

first: Risa

last: Ebina-Shibuya

first: Ari

last: Itoh-Nakadai


title: single cell RNA-sequencing data from CD4+CD25+ human cells

city: Bethesda

first: Mehdi

last: Pirooznia

address: 12 SOUTH DR

institute: National Institutes of Health

summary: We carry out single cell RNA-sequencing of CD4+CD25+ human T cells

overall_design: CD4+CD25+ cells were isolated from peripheral blood of three healthy donors and the mRNA profiles were analyzed by single cell RNA-seq

first: Giovanni

last: Povoleri


title: Protein Syndesmos is a novel RNA binding protein that regulates primary cilia formation [Illumina array]

city: Napoli

first: Danilo

last: Swann Matassa

address: Via Sergio Pansini 5

department: Molecular Medicine and Medical Biotechnology

country: Italy

institute: University of Naples “Federico II”

summary: We show here that SDOS interacts with another important cancer-linked protein, the chaperone TRAP1, associates with actively translating polyribosomes and represses translation. Moreover, we demonstrate that SDOS binds directly RNA in living cells. Combining individual gene expression profiling, nucleotide cross-linking and immunoprecipitation (iCLIP), and ribosome profiling, we discover several crucial pathways regulated post-transcriptionally by SDOS.

overall_design: Evaluation of differentially expressed transcripts in inducible SDOS-eGFP over eGFP expressing HeLa cells

last: Calice

first: Valentina

last: Condelli

first: Pietro

last: Zoppoli


title: Human Bone Marrow Assessment by Single Cell RNA Sequencing, Mass Cytometry and Flow Cytometry

first: Laura

last: Dillon

state: Maryland

address: Room 10CRC 6-5142, 10 Center Drive

department: Hematology Branch

institute: National Heart Lung and Blood Institute, NIH


title: Human Bone Marrow Assessment by Single Cell RNA Sequencing, Mass Cytometry and Flow Cytometry [bulk]

summary: Bulk RNA Sequencing of Healthy Bone Marrow Mononuclear Cells

overall_design: Using standard operating procedures, mononuclear cells from bone marrow aspirates were isolated using Ficoll density gradient separation and cryopreserved in 90% FBS/ 10% DMSO for storage in liquid nitrogen. RNA was harvested from thawed cell vials of BMMCs using AllPrep kits (QIAGEN). Libraries were prepared using TruSeq Stranded Total RNA Sample Preparation Kit (Illumina) with 1ug of RNA input. Sequencing was performed by paired-end 75 nt on Illumina HiSeq 3000.

first: Karolyn

last: Oetjen

first: Christopher

last: Hourigan


title: Investigation of Bach2 function by regulating inflammatory response and heme-iron homeostasis of bone marrow macrophage.

summary: Macrophages are central in regulating iron homeostasis. Transcription repressor Bach2 regulates by heme. Here we investigated the relationship between heme-regulated Bach2 and macrophage in bone marrow. We identified RFP-positive and negative macrophage were in bone marrow. We found that RFP-positive macrophage related with iron-heme homeostasis maintenance and RPF-negative population related with immune response.  In RFP positive macrophage, we also found  the lysosomal heme transporter hrg-1 was Bach2 direct target gene. Our results suggest that the function of the bone marrow macrophage alters according to expression of Bach2.

overall_design: Gene expression in bone marrow macrophages cells of Bach2-td RFP reporter mice was measured. 3 independent mice ware used for each genotype.

first: Miki

last: Watanabe-Matsui


title: ChIP-seq from lung (ENCSR936FAH)

status: Public on Sep 21 2018

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

type: Genome binding/occupancy profiling by high throughput sequencing

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from lung (ENCSR617SRM)


title: ChIP-seq from lung (ENCSR813HFV)


title: ChIP-seq from lung (ENCSR413WJD)


title: ChIP-seq from lung (ENCSR454WZX)


title: Transcriptome analysis of CD8+ T cells from healthy controls and patients wth CD46 deficiency

status: Public on Sep 14 2018

summary: RNA-seq data from CD8+ T cells of healthy controls and patients with CD46-deficiency activated, or not, in vitro

overall_design: 400,000 freshly sioalted CD8+ T cells from peripheral blood of patients with CD46-deficieny or healthy age- and sex-matched controls were activated, or not, with anti-CD3+anti-CD46 in vitro for 6hours in the presence of IL-2 before RNA extraction and library construction for sequencing

first: Giuseppina

last: Arbore

first: Ilker

last: Tunc


title: ChIP-seq from lung (ENCSR111KKC)


title: Signal transduction-dependent small regulatory RNA is involved in glutamate metabolism of the human pathogen Bordetella pertussis

status: Public on Sep 20 2018

city: Lille

first: David

last: Hot

address: 1 rue du professeur Calmette

department: Center for Infection and Immunity of Lille

institute: Institut Pasteur de Lille

summary: Bordetella pertussis is the causative agent of human whooping cough, a highly contagious respiratory disease which despite vaccination programs remains the major cause of infant morbidity and mortality. The requirement of the RNA chaperone Hfq for virulence of B. pertussis suggested that Hfq-dependent small regulatory RNAs are involved in the modulation of gene expression. High-throughput RNA sequencing revealed hundreds of putative noncoding RNAs including the RgtA sRNA. Abundance of RgtA is strongly decreased in the absence of the Hfq protein and its expression is modulated by the activities of the two-component regulatory system BvgAS and another response regulator RisA. Whereas RgtA levels were elevated under modulatory conditions or in the absence of bvg genes, deletion of the risA gene completely abolished RgtA expression. Profiling of the ΔrgtA mutant in the ΔbvgA genetic background identified the BP3831 gene encoding a periplasmic amino acid-binding protein of an ABC transporter as a possible target gene. The results of site-directed mutagenesis and in silico analysis indicate that RgtA base-pairs with the region upstream of the start codon of the BP3831 mRNA and thereby weakens the BP3831 protein production. Furthermore, our data suggest that the function of the BP3831 protein is related to transport of glutamate, an important metabolite in the B. pertussis physiology. We propose that the BvgAS/RisA interplay regulates the expression of RgtA which upon infection, when glutamate might be scarce, attenuates translation of the glutamate transporter and thereby assists in adaptation of the pathogen to other sources of energy.

overall_design: Transcriptomic comparison of a Bordetella pertussis double mutant strain delta-bvgA&delta-s2013 to a simple mutant strain delta-bvgA.

first: Kristina

last: Keidel

first: Branislav

last: Vecerek


title: Human Bone Marrow Assessment by Single Cell RNA Sequencing, Mass Cytometry and Flow Cytometry [scRNA]

summary:
New techniques for single-cell analysis have led to insights into hematopoiesis and the immune system, but the ability of these techniques to cross-validate and reproducibly identify the biological variation in diverse human samples is currently unproven. We therefore performed a comprehensive assessment of human bone marrow cells using both single-cell RNA sequencing and multiparameter flow cytometry from twenty healthy adult human donors across a broad age range. These data characterize variation between healthy donors as well as age-associated changes in cell population frequencies. Direct comparison of techniques revealed discrepancy in the quantification of T lymphocyte and natural killer cell populations. Orthogonal validation of immunophenotyping using mass cytometry demonstrated good correlation with flow cytometry. Technical replicates using single-cell RNA sequencing matched robustly, while biological replicates showed variation. Given the increasing use of single-cell technologies in translational research, this resource serves as an important reference dataset and highlights opportunities for further refinement.

[Funding source]
Project Number: 1ZIAHL006163-05
Contact PI / Project Leader: HOURIGAN, CHRISTOPHER
Title: DETECTION, PREVENTION AND TREATMENT OF ACUTE MYELOID LEUKEMIA (AML) RELAPSE.
Awardee Organization: NATIONAL HEART, LUNG, AND BLOOD INSTITUTE

overall_design: Using standard operating procedures, mononuclear cells from 20 healthy donors' bone marrow aspirates were isolated using Ficoll density gradient separation and cryopreserved in 90% FBS/ 10% DMSO for storage in 72 liquid nitrogen. scRNAseq was performed using 10X Genomics Single Cell 3’ Solution, version 2 according to manufacturer’s instructions (protocol rev A). Libraries were sequenced on HiSeq3000. Droplet-based scRNAseq of bone marrow mononuclear cells for all donor samples was performed with goal minimum sequencing depth of 50,000 reads/cell and detected a mean of 880 genes/cells (range 575-1,390 gene/cell).

first: Gege

last: Gui


title: CD95L mRNA is toxic to cells

first: Markus

last: Hafner

address: 50 South Drive

department: NIAMS

institute: NIH

type: Non-coding RNA profiling by high throughput sequencing

summary: >80% of a large number of tested siRNAs and shRNAs targeting CD95 or CD95 ligand (CD95L) induce a form of cell death that is characterized by the simultaneous activation of multiple death pathways and preferentially affects transformed and cancer stem cells. We now show that these si/shRNAs kill cancer cells through canonical RNAi by targeting the 3’UTR of critical survival genes in a unique form of off-target effect.  We also provide evidence showing that the full length CD95L mRNA is also toxic and produces small Ago-associated RNAs.

overall_design: Pan Argonaute immunoprecipitation and small RNA cloning in HeyA8 and HCT116 wild-type and HCT116 Drosha KO cells treated with plenti or hFasL

first: William

middle: E

last: Putzbach

first: Ashley

last: Haluck-Kangas

first: Quan

middle: Q

last: Gao

first: Aishe

last: Sarshad

first: Elizabeth

last: Bartom

first: Austin

last: Stults

first: Abdul

last: Qadir

first: Denise

last: Scholtens

first: Marcus

last: Peter


title: Characterization of ST2+ and ST2- mTh cells in helminth infection

city: Chiba

first: Atsushi

last: Onodera

address: Chuo-ku Inohana 1-8-1

department: Immunology

institute: Chiba University

summary: CD4+T cells are differentiated into Th1, Th2, Th17 and Treg cells after Antigen presentation by other cell types such as dendritic cells, macrophages and B cells in Lymph nodes. Those differentiated CD4+T cells are subdivided into cell subsets by their producing cytokines and surface markers. We recently identified that ST2 expressing Th2 cells highly produced IL-5 comparing to ST2- Th2 cells in helminth infection. In this study, we investigated the RNAseq analysis to characterize these Th2 cells.

overall_design: Characterization of ST2+ and ST2- mTh cells are assessed by RNA-seq.

first: Kazushige

last: Obata-Ninomiya

first: Miki

last: Kato

first: Toshinori

last: Nakayama


title: RNA-sequencing of SsrB-dependent gene expression in S. Typhimurium and S. bongori

status: Public on Sep 18 2018

city: Hamilton

first: Brian

last: Coombes

state: ON

address: MDCL 2108. 1200 Main St W, McMaster University

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

summary: We generated S. Typhimurium and S. bongori strains that express SsrB (SsrB+) or not (SsrB-) in trans to evaluate the changes in gene expression upon SsrB expression. As S. bongori evolved in the absence of SsrB, this allows us to explore the evolution of gene regulation in S. Typhimurium following horizontal gene acquisition of the SsrB response regulator.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: SsrB+ and SsrB- strains from both species were grown in SsrB-inducing conditions and RNA was collected and sequenced. Reads were mapped to the respective genomes with Rockhopper and differential gene expression (SsrB+/SsrB-) was calculated for both species.

first: Bushra

last: Ilyas

first: David

middle: T

last: Mulder

first: Dustin

last: Little

first: Wael

last: Elhenawy

first: María

last: Banda

first: Deyanira

last: Pérez-Morales

first: Caressa

last: Tsai

first: Nhu

middle: Y

last: Chau

first: Victor

last: Bustamante


title: Opaque-2 regulates a complex gene network associated with cell differentiation and storage function of maize endosperm

city: Tucson

first: Ramin

last: Yadegari

state: Arizona

address: 1140 E. South Campus Dr.

department: Plant Sciences

institute: University of Arizona

summary: Development of the cereal endosperm involves cell differentiation processes that enable nutrient uptake from the maternal plant, accumulation of storage products and their utilization during germination. However, little is known about the regulatory mechanisms that link cell differentiation processes with those controlling storage product synthesis and deposition, including the activation of zein genes by the maize (Zea mays) bZIP transcription factor Opaque-2 (O2). In this study, we mapped in vivo binding sites of O2 in B73 endosperm, and compared the results with genes differentially expressed in B73 and B73o2. We identified 186 putative direct O2 targets and 1,677 indirect targets, encoding a broad set of gene functionalities. Examination of the temporal expression patterns of O2 targets using real-time RT-PCR experiments revealed at least two distinct modes of O2-mediated gene activation. We also showed that two O2-activated genes, bZIP17 and NAKED ENDOSPERM2 (NKD2) encoded transcription factors, which can in turn co-activate other O2-network genes with O2. NKD2 (with its paralog NKD1) was previously shown to be involved in regulation of aleurone development. Collectively, our results provide novel insights into the complexity of the O2-regulated network and its role in regulation of endosperm cell differentiation and function.

overall_design: RNAs were isolated from endosperm of a maize o2 mutant (in B73 background) and a wild-type B73 at 15 days after pollination (DAP). Chromatin immunoprecipitation (ChIP) was performed using an anti-O2 antibody on 15-DAP endosperm of B73 in comparison to B73o2. All the RNAs and immunoprecipitated DNA were sequenced using an Illumina HiSeq 2500 platform.

first: Junpeng

last: Zhan

first: Guosheng

last: Li

first: Choong-Hwan

last: Ryu

first: Chuang

last: Ma

first: Shanshan

last: Zhang

first: Alan

last: Lloyd

first: Brenda

middle: G

last: Hunter

last: Larkins

first: Gary

last: Drews

first: Xiangfeng

last: Wang


title: Physical basis for long-distance communication along meiotic chromosomes (ChIP-chip))

status: Public on Sep 17 2018

city: San Francisco

first: Kyle

last: Fowler

state: California

address: 600 16th Street

institute: University of California San Francisco

type: Genome binding/occupancy profiling by array

summary: Viable gamete formation requires segregation of homologous chromosomes connected, in most species, by crossovers.  DNA double-strand break (DSB) formation and the resulting crossovers are regulated at multiple levels to prevent overabundance along chromosomes.  Meiotic cells coordinate these events between distant sites, but the physical basis of long-distance chromosomal communication has been unknown.  We show that DSB hotspots up to ~200 kb (~35 cM) apart form clusters via hotspot-binding proteins Rec25 and Rec27 in fission yeast.  Clustering coincides with hotspot competition and interference over similar distances.  Without Tel1 (ATM tumor-suppressor homolog), DSB and crossover interference become negative, reflecting coordinated action along a chromosome.  These results indicate that DSB hotspots within a limited chromosomal region and bound by their protein determinants form a clustered structure that, via Tel1, allows only one DSB per region.  Such a “roulette” process among clusters explains the observed pattern of crossover interference in fission yeast.  Key structural and regulatory components of clusters are phylogenetically conserved, suggesting conservation of this vital regulation.  Based on these observations, we discuss variations on a model in which clustering and competition between DSB sites leads to DSB interference and in turn produces crossover interference.

overall_design: Meiotic DSBs (Rec12-DNA linkages) assayed in two strains that differ at two hotspots: one strain has the ade6-3049 hotspot but lacks mbs1, while the other has the ade6-3057 non-hotspot allele but has mbs1.

first: Randy

last: Hyppa

first: Gareth

last: Cromie

first: Gerald

last: Smith


title: THE DNA BINDING LANDSCAPE OF THE MAIZE AUXIN RESPONSE FACTOR FAMILY [DAP-seq]

city: Piscataway

first: Andrea

last: Gallavotti

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute

institute: Rutgers University

summary: DAP-seq was used to generate genome-wide DNA:TF interaction maps for fourteen maize ARFs from the evolutionarily conserved class A ‘activator’ and class B ‘repressor’ clades. Among the distinct binding sites that were identified, we observed a high degree of overlap for ARFs of the same class, but found substantial differences in motif sequence, spacing, site preference, and association with auxin induced genes among clade A and clade B ARFs.

overall_design: Genome-wide DNA binding events were determined for fourteen maize ARFs using DAP-seq. Purified genomic DNA from B73 was incubated with purified GST-ARF fusion proteins expressed in Ecoli.

first: Mary

last: Galli


title: DNA methylome of tea tree

status: Public on Sep 15 2018

city: Fuzhou

first: Haifeng

state: Fujian

address: Shangxia dian

institute: Fujian Agriculture and Forestry University

summary: Bisulfite treatment libraries were made to characterize the DNA methylome of tea tree

overall_design: Genome-wide methylome was done by Illumina TruSeq preparation kits followed by high-throughput sequencing with Illumina HiSeqX-ten


title: Microarray based gene expression profiling of RNA binding protein, RBM10 in HEK 293 cells

status: Public on Sep 13 2018

city: Trivandrum

first: Rakesh

last: Laishram

state: Kerala

address: Thycaud P O, Poojappura

department: Cardiovascular and Diabetes Biology Group

country: India

institute: Rajiv Gandhi Centre for Biotechnology(RGCB)

summary: To determine the target genes of RBM10,we have employed microarray based gene expression profiling by knocking down RBM10 in HEK 293 cells. Microarray analysis after RBM10 knockdown on HEK 293 cells showed that over 1000 genes were down regulated while another 800 genes up regulated as a result of the knockdown. Among the down regulated genes, we found the significant presence of cardiovascular disease related genes, especially cardiac hypertrophy and heart failure.

overall_design: HEK 293 cells was transfected with siRNA oligos (both control siRNA and RBM10 specific siRNA) using Oligofectamine reagent and cells were harvested 48-hours post-transfection. Three independent experiments were conducted for both control siRNA and RBM10 siRNA treatment.

first: Nimmy

last: Mohan


title: THE DNA BINDING LANDSCAPE OF THE MAIZE AUXIN RESPONSE FACTOR FAMILY [RNA-seq]

overall_design: RNA-seq was performed on young maize seedlings with and without exogenous application of 100mM IAA for 30 min.


title: Analysis of transcriptomes of healthy donor and CD46 deficient CD8 T cells

first: Mehdi

last: Pirooznia

state: MD

summary:
This SuperSeries is composed of the SubSeries listed below.
We analyze the transcriptomes of healthy donor and CD46 deficieint patients with and without in vitro activation by microarray and RNA-seq

overall_design:
Refer to individual Series
Freshly isolated CD8 cells were either activated or not in vitro before RNA extraction and transcriptome analysis


title: Transcriptomic analysis of Campylobacter jejuni grown in medium containing serine as a main energy source

city: Tsukuba

first: ayako

last: watanabe

state: Ibaraki

address: 3-1-5 Kannondai

department: National Institute of Animal Health

institute: National Agriculture and Food Research Organization

summary: Campylobacter jejuni is one of the most important causes of food-borne diseases in industrialized countries. It is known that amino acids are important nutrient source for this pathogen, because C. jejuni lacks enzymes related to glycolysis. However, the characteristics on metabolism of C. jejuni grown in the nutrient restricted medium with a specific amino acid is not fully elucidated. This study shows that C. jejuni NCTC11168 grew well in the nutrient restricted medium containing serine, aspartate, glutamate, and proline. The single subtraction of serine significantly reduced the growth, while three other amino acids did not, suggesting the priority of serine among the four amino acids. In the transcriptomic analysis of C. jejuni NCTC11168 grown in medium with serine as a main energy source. Serine seemed to be sensed by some chemoreceptors and the C. jejuni might reached an adaptation stage with active growth. That is, the expression of flagellar assembly components was downregulated and the biosynthesis of multiple amino acids and nucleotide sugars were upregulated. These data suggest the higher requirement of serine as a nutrient of C. jejuni NCTC11168.

sample_organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

overall_design: Serine induced gene expression in Campylobacter jejuni was measured at 8 hours after exposure to dose of 20mM.

first: Ayako

last: Watanabe-Yanai


title: Toxicogenomics directory of rat hepatotoxicants in vivo and in cultivated hepatocytes

city: Dortmund

first: Jan

middle: G.

last: Hengstler

address: Ardeystrasse 67

country: Germany

institute: Leibniz Research Centre for Working Environment and Human Factors at the TU Dortmund University (IfADo)

summary:
Transcriptomics is developing into an invaluable tool in toxicology. The aim of this study was, using a transcriptomics approach, to identify genes that respond similarly to chemicals (including drugs and industrial compounds) in both rat liver in vivo and in cultivated hepatocytes, which are up- or downregulated by many different test compounds. For this purpose, we analyzed Affymetrix gene array data from 162 compounds that were previously tested in a concentration-dependent manner in rat livers in vivo and rat hepatocytes cultivated in sandwich culture. These data were obtained from the Japanese Toxicogenomics (TGP) and North-Rhine-Westphalian (NRW) data sets, which consist of 138 and 29 compounds, respectively, and have 5 mutual compounds between them. The in vitro gene array data from the NRW data set were generated in the present study, while TGP is publicly available. For each of the data sets, the overlap between up- or down-regulated genes in vitro and in vivo was identified, further named in vitro-in vivo consensus genes. Interestingly, an overlap of in vivo-in vitro consensus genes was obtained between both data sets, which were 21-times (up-regulated genes) or 12-times (down-regulated genes) en-riched compared to random expectation. This is remarkable since the TGP and NRW data sets contained only five mutual compounds. Finally, the genes in the TGP and NRW overlap were used to identify the upregulated genes with the highest com-pound coverage, resulting in a 7-gene set of Cyp1a1, Ugt2b1, Cdkn1a, Mdm2, Aldh1a1, Cyp4a3, and Ehhad. This 7-gene set was then successfully tested with structural analogues of valproic acid that are not present in the TGP and NRW data sets. In conclusion, the 7-gene set identified in the present study responds similarly in vitro and in vivo and is induced by a wide range of different chemicals. Despite these results, transcriptomics with cultivated rat hepatocytes remains a challenge, because many genes are up- or downregulated by the culture conditions, respond differently to test compounds in vitro and in vivo, and shows a higher variability in the in vitro system compared to the corresponding in vivo data.

The raw data for the TGP study are available at https://toxico.nibiohn.go.jp/  For the normalization of the entire set of expression arrays, the RMA algorithm was used. The results are summarized in the publicly available toxicotranscriptomics directory (http://wiki.toxbank.net/toxicogenomics-map/).

overall_design:
29 compounds were tested in vitro using cultivated hepatocytes from male Wistar rats. Three concentrations were used. Each compound was analyzed following treatment of hepatocytes from three different rats, isolated on different experimental days (three biological replicates). Cultivation was performed using 6-well dishes where three wells were incubated with the same concentration of the test compound and the remaining three wells were used for solvent controls (*Ctrl).  T0 samples were collected at the beginning of the incubation period on the morning after hepatocyte isolation. No solvent or compound was applied to T0 samples.

The full name, abbreviation and class of the compounds used in this study are included in the file compounds.xlsx, available at the foot of this record.

Compound phenotype:
GT - Genotoxic
NC - Non-carcinogen
NG - Non-genotoxic

first: Marianna

last: Grinberg

first: Regina

middle: M

last: Stöber

first: Wiebke

last: Albrecht

first: Karolina

last: Edlund

first: Markus

last: Schug

first: Patricio

last: Godoy

first: Cristina

last: Cadenas

first: Rosemarie

last: Marchan

first: Alfonso

last: Lampen

first: Albert

last: Braeuning

first: Thorsten

last: Buhrke

first: Marcel

last: Leist

first: Axel

last: Oberemm

first: Hennicke

last: Kamp

first: Heidrun

last: Ellinger-Ziegelbauer

first: Iain

last: Gardner

first: Sylvia

last: Escher

first: Olivier

last: Taboureau

first: Alejandro

last: Aguayom

first: Agapios

last: Sachinidis

first: Jörg

last: Rahnenführer


title: Histone 3 (k14) acetilation in hyperbilirubinmia

city: Biella

first: Paola

last: Ostano

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

summary: Bilirubin toxicity to the CNS has been widely studied for decades, and shown impacting potential toxic/adaptation mechanisms by a significant modulation of gene expression, suggesting that mechanisms having crucial role on the regulation of gene expression, such as epigenetic mechanisms, should have a strong impact in unconjugated bilirubin toxicity. In this work, we followed the levels of histone 3 acetylation (H3K14Ac) in the cerebellum (Cll) of the developing (2, 9, 17 days after the birth and in adult age) Gunn rat (the natural model for neonatal hyperbilirubinemia and kernicterus) by Western blot, discovering an age specific alteration of the H3K14Ac in the hyperbilirubinemic animals. Then, the H3K14Ac linked chromatin was immune-precipitated and submitted to sequencing (ChIP-Seq). The GeneOntology analysis revealed that almost the 45% of H3K14Ac ChiP-Seq TSS-promoter genes were involved in the CNS development.

overall_design: ChIP-Seq of the H3K14ac chomatin in hyperbilirubinmic (jj) and cotrols cerebella from P9 Gunn rats. 4 jj (2 runs) and 3 ctrl (1 run) were used.

first: Eleonora

last: Vianello

first: Stefania

last: Zampieri

first: Thomas

last: Marcuzzo

last: Bottin

first: Andrea

last: Dardis

first: Fabrizio

last: Zanconati

first: Cluadio

last: Tiribelli

first: Fabio

last: Tordini

first: Silvia

last: Gazzin


title: Genome-wide changes in OGT-depleted mouse adipose tissue

status: Public on Sep 12 2018

city: Chongqing

first: Min-Dian

last: Li

state: China

address: 30 Gaotanyan Main Street

department: Department of Cardiovascular Medicine

institute: Southwest Hospital, Army Medical University

summary: Appetite control is key to combat obesity in an over-nutritious environment. Whether and how over-nutrition induces hyperphagia and obesity through the adipose-to-brain axis is unclear. O-linked beta-D-N-acetylglucosamine (O-GlcNAc) transferase (OGT) couples nutrient cues to O-GlcNAcylation of intracellular proteins at serine/threonine residues. Here we show that adipocyte OGT is essential for high fat diet-induced hyperphagia, but is dispensable for baseline food intake. Adipocyte OGT stimulates hyperphagia by transcriptional activation of de novo lipid desaturation and accumulation of anandamide (AEA), an endogenous appetite-inducing cannabinoid (CB). Pharmacological manipulation of peripheral CB1 signaling regulates hyperphagia in an adipocyte OGT-dependent manner. These findings define adipocyte OGT as a fat sensor that regulates peripheral lipid signals, and uncover an unexpected adipose-to-brain axis that induces hyperphagia and obesity.

overall_design: Total RNA obtained from dissected OGT-deleted perigonadal white adipose tissue compared to control tissues from littermate mice. Young male mice (adipocyte-specific OGT knockout and littermate OGT flox wildtype) were fed high-fat diet for three days.

first: Mindian

first: Xu

last: Zhou

first: Xiaoyong

last: Yang


title: Comparison of enteroendocrine cells and pancreatic β-cells using gene expression profiling and insulin gene methylation

status: Public on Sep 11 2018

city: Seoul

first: Ki-Ho

last: Song

state: Korea

address: Yeouido St. Mary’s Hospital,10,63-ro,Youngdeungpo-gu

department: Department of Internal Medicine

institute: Catholic University

summary:
In this study, similarities between EECs and β-cells were evaluated in detail. To obtain specific subtypes of EECs, cell sorting by flow cytometry was conducted from STC-1 cells (a heterogenous EEC line), and each single cell was cultured and passaged. Five EEC subtypes were established according to hormone expression, measured by quantitative RT-PCR and immunostaining: L, K, I, G and S cells expressing glucagon-like peptide-1, glucose-dependent insulinotropic polypeptide, cholecystokinin, gastrin and secretin, respectively.
Global microarray gene expression profiles revealed a higher similarity between each EEC subtype and MIN6 cells (a β-cell line) than between C2C12 cells (a myoblast cell line) and MIN6 cells, and all EEC subtypes were highly similar to each other. Genes for insulin secretion-related proteins were mostly enriched in EECs.

overall_design: A total of 100 ng of RNA from each sample was amplified to make cDNA using the GeneChip Whole Transcript Amplification kit according to the supplied protocol. The sense cDNA was then fragmented and biotin-labeled with terminal deoxynucleotidyl transferase using the GeneChip Whole Transcript Terminal Labeling kit. A 5500-ng sample of each cDNA was hybridized to the Affymetrix GeneChip Mouse 2.0 ST Arrays at 45°C for 16 h. Hybridized arrays were scanned using a GSC3000 Scanner.

first: Gyeong

last: Ryu

first: Esder

last: Lee

first: Jong

last: Kim

first: Sung-Dae

last: Moon

first: Seung-Hyun

last: Ko

first: Yu-Bae

last: Ahn


title: Effects of exosomes from T lymphocytes of NOD mice on pancreatic islet-cell gene expression

city: Lausanne

first: Claudiane

last: Guay

state: Vaud

address: Du Bugnon 9

department: DNF

country: Switzerland

institute: University of Lausanne

summary: During Type 1 diabetes development, T lymphocytes infiltrate pancreatic islets and induce the destruction of the insulin-producing cells within the islets, the beta-cells. T lymphocytes are known to secrete pro-inflammatory cytokines but also exosomes that could contribute to the mechanisms leading to beta-cell death. In this project, we wanted to investigate the effect of exosomes released from T lymphocytes on beta-cell gene expression.

overall_design: Dispersed C57Bl/6N mouse islet cells were incubated for 72h in the absence (Ctl) or presence of 50 µg/ml of exosomes isolated from the culture media of CD4+CD25- T lymphocytes of NOD mice (exoNOD), prior to RNA extraction and gene expression profiling. Three independent experiments were performed, using different islet and exosome preparations.

first: Romano

last: Regazzi


title: Small RNA libraries

city: Rosario

first: Uciel

middle: Pablo

last: Chorostecki

address: Ocampo y Esmeralda

country: Argentina

institute: IBR

summary:
Many evolutionarily conserved miRNAs in plants regulate transcription factors with key functions in plant development. Hence, mutations in core components of the miRNA biogenesis machinery causes strong growth defects. An essential aspect of miRNA biogenesis is the precise excision of the small RNA from an arm of the fold-back precursor. Defects in the selection of the correct miRNA sequence will ultimately affect miRNA target specificity, plant development and other processes controlled by these small RNAs. Intriguingly, plant miRNA precursors are largely variable in size and shape and can be processed by different modes.

Here, we optimized genomic approaches to detect processing intermediates during miRNA biogenesis. We identified and characterized an endogenous miRNA whose processing is triggered by a terminal branched loop. Plant miRNA processing can be initiated by internal bubbles, small terminal loops or branched loops followed by dsRNA segments of 15-17 bp. Interestingly, precision and efficiency vary with the processing modes suggesting intrinsic differences between miRNA biogenesis pathways. Despite the various potential structural determinants present in a single a miRNA precursor, we found that DCL1 is mostly guided by a predominant structural region in each precursor in wild-type plants. However, genomic studies of miRNA processing intermediates in fiery1, hyl1 and se mutants revealed the existence of cleavage signatures consistent with the recognition of alternative or cryptic processing determinants in miRNA precursors. The results provide a general view of the mechanisms underlying the specificity of miRNA biogenesis in plants.

overall_design: We identified small RNA sequences in wild-type seedlings and link them to their biogenesis pathway

first: Javier

middle: F

last: Palatnik

first: Blake

last: Meyers

first: Belén

last: Moro


title: Small RNA-seq analysis shows reduced tRNA levels in cdk1-as1 mutants

status: Public on Sep 10 2018

city: Oslo

first: Jorrit

last: Enserink

address: Montebello

department: Molecular Cell Biology

country: Norway

institute: Oslo University Hospital

summary: Purpose: Determine whether Cdk1 only regulates a specific subset of tDNAs, or whether Cdk1 has a more global impact on tDNA expression; Method: We study the expression of tRNA genes in WT cells and cdk1-as1 mutants during S phase by small-RNAseq; Result: We found that expression of at least 77% of all tDNAs is significantly downregulated in S-phase in the cdk1-as1 mutant compared with the WT strain; Conclussions: Cdk1 promotes transcription of the majority of tRNA genes during the cell cycle.

overall_design: Examination of tRNA expression in CDK1 and cdk1-as1 mutant in S phase during the cell cycle

first: Carmen

last: Herrera


title: Specific Parallel Analysis of RNA Ends

overall_design: Processing intermediates are indentified on wt and mutant plants


title: Specific Parallel Analysis of RNA End and Small RNA libraries

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

overall_design: Refer to individual Series


title: Dynamics and functional interplay of histone lysine butyrylation, crotonylation, and acetylation in rice under starvation and submergence

status: Public on Sep 08 2018

city: Wuhan

first: Yue

last: Lu

state: Hubei

address: No.1 Shizishan street

department: national key lab of crop genetic improvement

institute: Huazhong Agriculture University

summary: In this work, we detected lysinebutyrylation (Kbu) and crotonylation(Kcr) sites in rice histone proteins by mass spectrometry, and found both similar and specific acylation patterns compared with that in mammalian cells. Comparative analysis of genome-wide histone Kbu, Kcr, and H3K9ac in combination of RNA-sequencing revealed that a large number of rice genes are marked by both Kbu and Kcr, most of which overlap with H3K9ac and are active genes. Under starvation and submergence, Kbu andKcr appeared to be less dynamic than H3K9ac and the three marks displayed changes in different sets of genes. Kbu and Kcr seemed to have a function to poise stress-induced gene activation. The results suggest that histone Kbu and Kcr provide a platform for histone acetylation during gene activation and that the proportional mixture of distinct histone lysine acylations which are regulated by environmental cues and has functionally consequence in chromatin modification and gene expression in plants.

overall_design: RNA-seq and H3K9ac, Kbu, and Kcr ChIP-seq of rice seedlings under normal conditions and starvation and submergence treatments; RNA-seq and H3K9ac ChIP-seq of rice leaf in 4 diurnal times.

first: Qiutao

last: Xu


title: nCounter analysis of mRNAs associated with occupational benzene exposure using a Nanostring custom assay

status: Public on Sep 06 2018

city: Berkeley

first: Cliona

last: McHale

state: CA

address: 384 Li Ka Shing Center

department: School of Public Health

institute: University of California Berkeley

summary: Previously, using microarrays and mRNA-Sequencing (mRNA-Seq) we found that occupational exposure to a range of benzene levels perturbed gene expression in peripheral blood mononuclear cells. In the current study, we sought to identify gene expression biomarkers predictive of benzene exposure below 1 part per million (ppm), the occupational standard in the U.S. First, we used the nCounter platform to validate altered expression of 30 genes in 33 unexposed controls and 57 subjects exposed to benzene (<1 to ≥5 ppm). Second, we used SuperLearner (SL) to identify a minimal number of genes for which altered expression could predict <1 ppm benzene exposure, in 44 subjects with a mean air benzene level of 0.55±0.248 ppm (minimum 0.203ppm). nCounter and microarray expression levels were highly correlated (coefficients >0.7, p<0.05) for 26 microarray-selected genes. nCounter and mRNA-Seq levels were poorly correlated for 4 mRNA-Seq-selected genes. Using negative binomial regression with adjustment for covariates and multiple testing, we confirmed differential expression of 23 microarray-selected genes in the entire benzene-exposed group, and 27 genes in the <1 ppm-exposed subgroup, compared with the control group. Using SL, we identified 3 pairs of genes that could predict <1 ppm benzene exposure with cross-validated AUC estimates >0.9 (p<0.0001) and were not predictive of other exposures (nickel, arsenic, smoking, stress). The predictive gene pairs are PRG2/CLEC5A, NFKBI/CLEC5A, and ACSL1/CLEC5A. They play roles in innate immunity and inflammatory responses. Using nCounter and SL, we validated the altered expression of multiple mRNAs by benzene and identified gene pairs predictive of exposure to benzene at levels below the US occupational standard of 1ppm.

overall_design: We used the nCounter platform and a custom assay to validate altered expression of 30 mRNAs in total RNA from peripheral blood mononuclear cells from 57 subjects occupationally exposed to benzene (<1 to ≥5 ppm) and 33 non-occupationally-exposed controls. A custom probeset comprising genes previously detected as differentially expressed by microarray and mRNA-Seq and 3 reference genes was designed. Six randonly selected technical replicates were included in the assay.

first: Alan

last: Hubbard


title: Transcriptome-stable isotope probing provides targeted functional and taxonomic insights into hypoxic pollutant-degrading aquifer microbiota

status: Public on Sep 07 2018

city: Bayreuth

first: Tillmann

last: Lueders

state: Bayern

address: Dr.-Hans-Frisch-Straße 1-3

department: Lehrstuhl Ökologische Mikrobiologie (ÖMIK)

institute: Universitaet Bayreuth

summary: We investigated a contaminant-degrading microbial community by sequencing total RNA (without rRNA depletion) from microcosms containing sediment from a hypoxic contaminated aquifer fed with isotopically labeled toluene.

overall_design: Microcosms were made using sediment from a hypoxic, hydrocarbon-contaminated aquifer in Siklos, Hungary. They were incubated under hypoxic/microoxic conditions and provided with isotopically-labeled toluene as a substrate. RNA was extracted and subjected to isopycnic centrifugation to separated heavy (isotopically labeled) and light (unlabeled) RNA, representing microbes which did or did not metabolize toluene, respectively. Total RNA was sequenced to provide both taxonimic (16S) and functional (mRNA) data on this microbiota, the first instance of total-RNA-stable isotope probing used to investigate a contaminated environment.

first: Lauren

last: Bradford


title: A longitudinal gene expression microarray analysis of skeletal muscle resistance training

city: São Paulo

first: Carlos

last: Ugrinowitsch

state: SP

address: Av. Prof. Mello Moraes, 65. Cidade Universitária, Butantã.

department: Departamento de Esporte

country: Brazil

institute: Escola de Educação Física e Esporte - USP

summary: Skeletal muscle adapts to resistance exercise (RE) performance acutely and chronically. An important regulatory step of muscle adaptation to RE is gene expression. Microarray analysis can be used as an exploratory method to investigate how genes and gene clusters are modulated acutely and chronically by RE. The purpose of the present study was to investigate the effect of training status in the basal (rested) and pre- to 24h post-RE on the global transcriptome in vastus lateralis muscle biopsies of young men. Muscle biopsies of nine young men who undertook RE training for 10-wks were collected pre and 24h post-RE at the first (W1) and last (W10) weeks of training and analysed using microarray. An unaccustomed RE bout (at W1) up-regulated muscle gene transcripts related to stress (e.g., heat shock proteins), damage and inflammation, structural remodelling, protein turnover and increased translational capacity. Trained muscles (at W10) became more efficient metabolically, as training favoured a more oxidative metabolism, refined response to stress, showed by genes suppression related to RE-induced stress and inflammation, and up-regulated genes indicating greater muscle contractile efficiency and contribution to promote muscle growth and development. These data highlight that chronic repetition of RE increases muscle efficiency and adapt muscles to respond more specifically and accurately to RE-induced stress.

overall_design: A total of 36 skeletal muscle biopsies of nine young men who undertook RE training for 10-wks were collected pre and 24h post-RE at the first and last weeks of training and analysed using microarray.

first: Felipe

last: Damas

first: Cleiton

middle: A

last: Libardi

first: Paulo

middle: R

last: Jannig

first: Amy

last: Hector

first: Chris

last: McGlory

first: Manoel

last: Lixandrão

middle: C

last: Vechin

first: Horacio

last: Montenegro

first: Valmor

last: Tricoli

first: Hamilton

last: Roschel

first: Stuart

last: Phillips


title: Strain-specific differences in brain gene expression in a hydrocephalic mouse model with motile cilia dysfunction

city: Sioux Falls

first: Lance

last: Lee

state: SD

institute: Sanford Research

summary: Analysis of strain-specific differences in gene expression in brains from a hydrocephalic mouse model of primary ciliary dyskinesia. The results identify genes that are differentially expressed between C57BL6/J and 129S6/SvEvTac brains. These genes encode proteins that function in a variety of cellular processes and include some that are relevant to hydrocephalus and cilia function, providing insight into the mechanisms underlying susceptibility to hydrocephalus.

overall_design: Total RNA was isolated from whole brains from wild type and nm1054 mutant mice on the C57BL6/J and 129S6/SvEvTac backgrounds at postnatal day 1 for microarray analysis.

first: Casey

last: McKenzie

first: Claudia

last: Preston

first: Rozzy

last: Finn

first: Kathleen

last: Eyster

first: Randolph

middle: S

last: Faustino


title: Minipuberty and Thymic Sexual Dimorphism in the Infant Human Thymus [non-puberty miRNA]

status: Public on Sep 05 2018

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

institute: Faculdade de Medicina da Universidade de Sao Paulo

summary: AIRE expression in thymus is downregulated by estrogen after puberty, what probably renders women more susceptible to autoimmune disorders. Here we investigated the effects of minipuberty on male and female infant human thymic tissue in order to verify if this initial transient increase in sex hormones - along the first six months of life - could affect thymic transcriptional network regulation and AIRE expression. Gene co-expression network analysis for differentially expressed genes and miRNA-target analysis revealed sex differences in thymic tissue during minipuberty, but such sex differences were not detected in thymic tissues from donors aged 7-18 moths of age, the non-puberty group. AIRE expression was essentially the same in both sexes in minipuberty and in non-puberty groups, as assessed by genomic and immunohistochemical assays. However, AIRE-interactors networks showed several differences in all groups regarding gene-gene expression correlation. Therefore, minipuberty and genomic mechanisms interact in shaping thymic sexual dimorphism along the first six moths of life.

overall_design: Thymus miRNA transcriptomic profiles of patients undergoing non-puberty (aged 7 to 30 months) comparing male versus female infants in order to identify differentially expressed transcripts.

first: Silvia

last: Bando

first: Fernanda

middle: B

last: Bertonha

first: Leandro

last: Ferreira

first: Christiana

last: Vinhas

first: Lucila

middle: H

last: Oliveira

first: Maria

last: Zerbini

first: Glaucio

last: Furlanetto

last: Chacur

first: Antonio

last: Coutinho

first: Madga

last: Carneiro-Sampaio


title: Differences in gene expression profiles for subcutaneous adipose, liver, and skeletal muscle tissues between Meishan and Landrace pigs with different backfat thicknesses

first: Masaaki

last: Taniguchi

address: 2 Ikenodai

department: Division of Animal Breeding and Reproduction Research

institute: Institute of Livestock and Grassland Science National Agriculture Food Research Organization

summary: Backfat thickness is one of the most important traits of commercially raised pigs. Meishan pigs are renowned for having thicker backfat than Landrace pigs. To examine the genetic factors responsible for the differences, we first produced female crossbred pig lines by mating Landrace (L) × Large White (W) × Duroc (D) females (LWD) with Landrace (L) or Meishan (M) boars (i.e., LWD × L = LWDL for Landrace offspring and LWD × M = LWDM of the Meishan offspring). We confirmed that LWDM pigs indeed had a thicker backfat than LWDL pigs. Next, we performed gene expression microarray analysis (in both genetic lines) to examine differentially expressed genes (DEGs) in energy metabolism-related tissues, subcutaneous adipose (fat), liver, and longissimus dorsi muscle tissues. We analyzed the annotation of DEGs (2-fold cutoff) to functionally categorize them by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. The number of DEGs in muscle tissues of both lines was much less than that in fat and liver tissues, indicating that DEGs was much lesser in muscle tissues (in both genetic lines) than in fat and liver tissues, thus indicating that DEGs in muscle tissues may not contribute much to differences in backfat thickness. In contrast, several genes related to muscle (in fat tissue) and fatty acid and glucose metabolism (in the liver) were more upregulated in LWDM pigs than LWDL pigs, indicating that those DEGs might be responsible for differences in backfat thickness. The different genome-wide, gene expression profiles in the fat, liver, and muscle tissues between breeds can provide useful information for pig breeders.

overall_design: Comparative gene expression analysis between two pig breeds at 3-time-points in 3 tissues consisting of 102 samples.

first: Misaki

last: Kojima

first: Ikuyo

last: Nakajima

first: Yuki

last: Nakamura

first: Toshimi

last: Matsumoto

first: Hirohide

last: Uenishi

first: Satoshi

last: Mikawa

first: Aisaku

last: Arakawa


title: Minipuberty and Thymic Sexual Dimorphism in the Infant Human Thymus [non-puberty]

first: Carlos

last: Moreira-Filho

overall_design: Thymus transcriptomic profiles of patients undergoing non-puberty comparing male versus female infants in order to identify differentially expressed transcripts.

first: Silvia

last: Bando

last: Bertonha

last: Furlamento

first: Paulo


title: LncRNA and mRNA changes during postnatal islet maturation

status: Public on Sep 04 2018

first: Clara

last: Sanchez-Parra

address: Rue de Bugnon 9

department: Department of Fundamental Neurosciences

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

summary: To elucidate the mechanisms involved in the acquisition of a fully differentiated beta-cell phenotype, we compared by microarray the mRNAs and the long non-coding RNAs expressed in newborn and adult rat islets.

overall_design: Pancreatic islets from 3 adult male rats and from 3 pools of 10 days old rats were isolated by collagenase digestion. Total RNA was extracted and lncRNA and mRNA profiling was performed using the rat lncRNA Agilent array.

first: Cécile

last: Jacovetti

first: Romano

last: Regazzi


title: ELONGATED HYPOCOTYL 5 mediates blue light signalling to the Arabidopsis circadian clock

first: Balazs

last: Balint

state: Csongrad

address: Vallalkozok street

country: Hungary

institute: Seqomics Ltd

summary: Circadian clocks are gene networks producing 24-h oscillations at the level of clock gene expression that is synchronized to environmental cycles via light signals.   The ELONGATED HYPOCOTYL 5 (HY5) transcription factor is a signalling hub acting downstream of several photoreceptors and is a key regulator of photomorphogenesis.   Here we describe a mechanism by which light quality could modulate the pace of the circadian clock through controlling abundance of HY5. We show that hy5 mutants display   remarkably shorter period rhythms in blue but not in red light or darkness and blue light is more efficient than red to induce accumulation of HY5 at transcriptional and   post-transcriptional levels. We demonstrate that the pattern and level of HY5 accumulation modulates its binding to specific promoter elements of majority of   clock genes, but only a few of these show altered transcription in the hy5 mutant. Mathematical modelling suggests that the direct effect of HY5 on the apparently non-responsive   clock genes could be masked by feed-back from the clock gene network. We conclude that the information on the ratio of blue and red components of the white light spectrum is   decoded and relayed to the circadian oscillator, at least partially, by HY5.

overall_design: Study was carried out on two treatment groups (blue light vs red light) containing 3-3 biological replicates each. As a common reference point, a single pooled mock sample was used. Total number of samples is seven.

first: Anita

last: Hajdu

first: Orsolya

last: Dobos

first: Mirela

last: Domijan

first: Balázs

last: Bálint

first: István

last: Nagy

first: Ferenc

first: László

last: Kozma-Bognár


title: Minipuberty and Thymic Sexual Dimorphism in the Infant Human Thymus [minipuberty]

summary: AIRE expression in thymus is downregulated by estrogen after puberty, what probably renders women more susceptible to autoimmune disorders. Here we investigated the effects of minipuberty on male and female infant human thymic tissue in order to verify if this initial transient increase in sex hormones - along the first six months of life - could affect thymic transcriptional network regulation and AIRE expression. Gene co-expression network analysis for differentially expressed genes and miRNA-target analysis revealed sex differences in thymic tissue during minipuberty, but such sex differences were not detected in thymic tissues from donors aged 7-18 months of age, the non-puberty group. AIRE expression was essentially the same in both sexes in minipuberty and in non-puberty groups, as assessed by genomic and immunohistochemical assays. However, AIRE-interactors networks showed several differences in all groups regarding gene-gene expression correlation. Therefore, minipuberty and genomic mechanisms interact in shaping thymic sexual dimorphism along the first six moths of life.

overall_design: Thymus transcriptomic profiles of patients undergoing minipuberty comparing male versus female infants in order to identify differentially expressed transcripts.

first: Fernanda

first: Leandro

last: Ferreira

first: Christiana

last: Vinhas

first: Lucila

last: Oliveira

first: Maria

last: Zerbini

first: Glaucio

last: Chacur

first: Antonio

last: Coutinho

first: Madga

last: Carneiro-Sampaio


title: Differential gene expression between TCR-activated CD4+ T cells from control and Gch1;Lck mice

status: Public on Sep 03 2018

city: Wien

first: Shane

last: Cronin

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institut für Molekulare Biotechnologie GmbH

summary: To identify differences in gene transcription in the absence of Gch1 in T cells early after activation

overall_design: Two-condition experiment with common reference design with 3 biological replicates. Common reference is used in Cy5 channel labeling, and each sample is compared with the same common reference

middle: J

first: Josef

last: Penninger


title: Expression data of different types of OSAHS patients

first: Xiuping

last: Yang

address: No. 1277 Jiefang Road

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary:
OSAHS is a complex,synthetical disease that can lead to multiple system and multiple organ damage as the disease progresses.Metabolic syndrome is the most common complication, but the symptoms at different stages of the disease are different.It is known that miRNAs can be stably in the serum and changes during the development of the disease.Therefore, we speculate that serum miRNAs could biomarkers for OSAHS diagnosis and progression judgment.
We used microarrays to detail the miRNA expression of simple OSAHS patients, OSAHS patients with hypertension and healthy controls, and screened out the miRNAs that were differentially expressed between the two groups.

overall_design: Participants were divided into three groups: simple OSAHS patients and OSAHS patients with hypertension and healthy controls.Five serum from each group were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Xiong

last: Chen


title: Small RNA-Seq reveals novel miRNAs shaping the transcriptomic identity of rat brain structures

city: Bordeaux

first: Alexandre

last: FAVEREAUX

address: 146 rue leo saignat

institute: CNRS UMR 5297

summary: In the central nervous system (CNS), the microRNAs (miRNAs), small endogenous RNAs exerting a negative post-transcriptional regulation on mRNAs, are involved in major functions, such as neurogenesis, and synaptic plasticity. Moreover, they are essential to define the specific transcriptome of the tissues and cell types. However, few studies were performed to determine the miRNome of the different structures of the rat CNS, even through rat is a major model in neuroscience. We determined the miRNome profile of the hippocampus, the cortex, the striatum, the spinal cord and the olfactory bulb, by small RNA-Seq. We found a total of 365 known miRNAs' and 90 novel miRNAs expressed in the CNS of the rat. Novel miRNAs seemed to be important in defining structure-specific miRNomes. Differential analysis showed that several miRNAs were specifically enriched/depleted in these CNS structures. Then, we correlated miRNAs' expression with the expression of their mRNA targets by mRNA-Seq. This analysis suggests that the transcriptomic identity of each structure is regulated by specific miRNAs. Altogether, these results suggest the critical role played by these enriched/depleted miRNAs in the functional identities of CNS structures.

overall_design: miRNA and mRNA profile of 5 structures of the central nervous system of rat, for each structurewe analyzed three biological replicates

first: Anaïs

last: Soula

first: Mélissa

last: Valere

first: Maria-Jose

last: Lopez-Gonzalez

first: Vicky

last: Ury-Thiery

first: Alexis

last: Groppi

first: Marc

last: Landry

first: Macha

last: Nikolski

last: Favereaux


title: Ubiquitin-specific protease USP34 controls osteogenic differentiation and bone formation by regulating BMP2 signaling

status: Public on Sep 01 2018

city: Chengdu

first: Quan

last: Yuan

state: Sichuan

address: 14 Third section, Renmin Nan Road

institute: West China Hospital of Stomatology, Sichuan University

summary: The aim is to analyze the transcriptome profiling (RNA-seq) of Mettl3 knockout mesenchymal stem cells (MSCs) and identify m6A modified mRNThe aim is to analyze the transcriptome profiling (RNA-seq) of USP34 knockdown mesenchymal stem cells (MSCs). Total RNAs from  human MSCs of siCTRL and siUSP34 were extracted using an RNeasy mini kit (Qiagen). Libraries were prepared using the Illumina TrueSeq mRNA sample preparation kit according to manufacturer’s instruction, and single-end sequenced on an Illumina HiSeq 3000 machine. The reads were aligned to hg19 genome using Tophat. Analysis of RNA-seq data was done using Cufflinks with Refseq mRNAs to guide assembly and the cummeRbund package in R. Transcripts, which were regulated greater than 2-fold were considered significant difference.

overall_design: The mRNA profiles of siCTRL and siUSP34 MSCs were generated by deep sequencing, in duplicate, using Illumina HiSeq 3000.


title: tp53 deficiency causes a wide tumor spectrum and elevates embryonal rhabdomyosarcoma metastasis in zebrafish

city: Boston

first: Sowmya

last: Iyer

state: MA

department: Pathology

country: USA

institute: Massachusetts General Hospital

summary: We generated tp53 deletion mutant zebrafish that spontaneously develop malignant peripheral nerve-sheath tumors, angiosarcomas, germ cell tumors, and an aggressive Natural Killer cell leukemia not previously reported in zebrafish. Each tumor type efficiently engrafted into syngeneic recipient zebrafish and shared gene expression signatures with predicted cells of origin.

overall_design: We generated a complete-null tp53 deletion allele in syngeneic CG1 strain zebrafish using TALEN endonucleases. The list of tumors spontaneously developed in these tp53del/del animals included malignant peripheral nerve-sheath tumors (MPNSTs), angiosarcomas, germ cell tumors, and Natural Killer cell leukemia. We obtained 3 MPNSTs samples (MPNST_1, MPNST_2 and MPNST_3), 2 angiosarcoma samples (Angiosarcoma_1 and Angiosarcoma_2), 3 leukemia samples (Leukemia_1, Leukemia_2 and Leukemia_3), and 1 sample of germ cell tumor (GermCell_1). We also assessed the role of tp53 in kRASG12D-induced human embryonal rhabdomyosarcoma (ERMS) using large-scale cell transplantation assays and live fluorescent imaging over time. We obtained 3 ERMS samples (ERMS_1, ERMS_2 and ERMS_3). All these tumor samples were compared to 3 background CG1 samples (samples WholeFish_1, WholeFish_2 and WholeFish_3).

first: Myron

last: Ignatius

first: Madeline

middle: N

last: Hayes

first: David

last: Langenau


title: RNA expression in the chick embryonic heart and sino-atrial node

first: Jonathan

last: Seidman

address: 77 ave louis pasteur

institute: Harvard Medical School

summary: We describe early stages in differentiation of the sino-atrial node or pacemaker cells of the chicken heart.

overall_design: We compare RNA expression of pooled samples from the early chick embryo including ventricular right inflow region, atria and ventricle.

first: Michael

last: Bressan


title: RNA-seq of Nicotiana tabacum BY-2 cells treated with the chitin oligomer NAG6 and with the Moniliophthora perniciosa effector MpChi

city: Piracicaba

first: Paulo

last: Teixeira

address: Av. Pádua Dias, 11

department: Biology

institute: University of São Paulo (ESALQ/USP)

summary: This study evaluates the ability of MpChi, an effector protein from the fungus Moniliophthora perniciosa, in suppressing the transcriptional reprogramming associated with MTI (MAMP-triggered immunity) in Nicotiana tabacum cells exposed to the chitin oligomer NAG6.

overall_design: Nicotiana tabacum BY-2 cells were treated with 10 nM NAG6, 100 nM MpChi, 10 nM NAG6 + 100 nM MpChi or H2O (Mock treatment). Samples were harvested immediately before the start of the experiment (Time 0, untreated cells) and at four time points after the treatment (15 min, 60 min, 120 min and 180 min). The experiment was performed in triplicate.

first: Gabriel

last: Fiorin

first: Gonçalo

last: Pereira


title: The circadian gene Nr1d1 in the mouse nucleus accumbens modulates social reward and anxiety-related behavior

city: Madison

first: Stephen

middle: Coull

last: Gammie

state: WI

address: 430 Lincoln Drive

department: Zoology

institute: University of Wisconsin

summary:
Nuclear receptor subfamily 1, group D, member 1 (Nr1d1) (also known as Rev-erb alpha) has been linked to circadian rhythm regulation, mood-related behavior, and disorders associated with social deficits. Recent work from our laboratory found striking decreases in Nr1d1 in nucleus accumbens (NAc) in the maternal condition and indirect evidence that Nr1d1 was interacting with numerous addiction and reward-related genes to modulate social reward. In this study, we applied our insights from the maternal state to non-parental adult mice to determine whether decreases in Nr1d1 expression in NAc via adeno-associated viral (AAV) vectors and short hairpin RNA (shRNA)-mediated gene knockdown were sufficient to modulate social reward and mood-related behaviors. We also used microarray analysis of to identify gene expression alterations induced by the lowering of Nr1d1 expression.
We used microarrays to evalute the effects of knockdown of mRNA for Nr1d1 in nuclues accumbens on gene expression.

overall_design: In total, 23 total RNA samples derived from micropunched nucleus accumbens were used for microarray analysis: For females, there were 5 control and 6 Nr1d1 knockdown samples. For males, there were 6 control and 6 Nr1d1 knockdown samples. All samples are biological replicates.

first: C

last: Zhao

first: S