title: Nitrated meat products are associated with mania in humans and altered behavior and brain gene expression in rats

status: Public on Aug 18 2018

city: Baltimore

first: Robert

last: Yolken

address: 600 N Wolfe st

department: Pediatrics

institute: Johns Hopkins

summary: Mania is a serious neuropsychiatric condition associated with significant morbidity and mortality. Previous studies have suggested that environmental exposures can contribute to mania pathogenesis.  We measured dietary exposures in a cohort of individuals with mania and other psychiatric disorders as well as in control individual without a psychiatric disorder. We found that a history of eating nitrated dry cured meat, but not other meat or fish products, was strongly and independently associated with current mania (adjusted odds ratio 3.49, 95% confidence interval (CI) 2.24-5.45, p<8.97x 10-8). Lower odds of association were found between eating nitrated dry cured meat and other psychiatric disorders. We further found that the feeding of meat preparations with added nitrate to rats resulted in alterations in behavior and changes in intestinal microbiota. Rats fed diets with added nitrate also showed alterations of brain pathways dysregulated in mania. These findings may lead to new methods for preventing mania and for developing novel therapeutic interventions

overall_design: A group of N=10 control Rats were fed a diet consisting of research diet AIN93M with 35% beef added (Chow+Beef), and another group of N=10  the same diet containing sodium nitrate at cocentration of 33/.9 mg/kg (Chow+Beef+Nitrate) . Following a period of 4 weeks the rats were euthenized and the hippocampus region of the brain was extracted, and RNA was isolated for microarray analysis comparing the two groups.

first: Seva

last: Khambadkone

first: C

last: Talbot Jr


title: Gene Expression of PS19 Tau transgenic mice

status: Public on Aug 28 2018

city: Irvine

first: Vivek

last: Swarup

state: CALIFORNIA

address: 3400 Bio Sci 3

department: Neurobiology and Behavior

country: USA

institute: University of California Irvine

summary:
Expression of PS19 Tau Transgenic mice from hippocampus at different ages 3, 6, 9, and 12 months
We used Affy arrays to understand the global expression profile of PS19 Tau transgenic mice

overall_design: Total RNA from hippocampi samples of PS19 Tau transgenic and wild-type littermates were isolated at various ages and affymetrix microarray were run. Gene expression at the probe ID levels were collapsed using collapseRows function in WGCNA package, R and trajectory of salmon and turquoise modules were evaluated using module eigengene function, WGCNA package, R

first: Daniel

middle: H

last: Geschwind


title: Expression profile of adult mouse POA/BF regions

status: Public on Aug 17 2018

city: Suita

first: Hiroki

middle: R

last: Ueda

state: Osaka

address: 1-3 Yamadaoka

department: QBiC

country: Japan

institute: RIKEN

summary:
The adult mammalian brain is composed of distinct regions that have specialized roles. The BF/POA regions are thought to have an important role in the regulation of sleep/wake behavior. However, genetic markers of the responsible cells for the regulation of sleep/wake behavior are largely unknown. To identify the molecular markers of the BF/POA regions, we sampled the BF/POA regions and compared gene expression in the BF/POA regions with those of other brain regions which we previously reported in the BrainStars (B*) project, in which we sampled ~50 small brain regions, including sensory centers and centers for motion, time, memory, fear, and feeding.
We sampled each region every 4 hours for 24 hours, and pooled the sample sets for DNA-microarray assays. We then used informatics to identify candidates for genes with high or low expression in the BF/POA regions. We used our findings to develop an integrated database (http://poabf.brainstars.org/) for exploring genome-wide expression in the adult mouse brain including the BF/POA regions.

overall_design: For the BF/POA regions, slices (0.5-mm thick) of mouse brain were cut on a Mouse Brain Matrix, frozen, and the BF/POA regions were punched out bilaterally with a microdissecting needle (gauge 0.5 mm) under a stereomicroscope. We took samples every 4 hours, starting at ZT0 (Zeitgaber time 0; the time of lights on), for 24 hours (6 time-point samples for each region), and we pooled the samples from the different time points. We independently sampled each region twice (n=2).

first: Yasutaka

last: Niwa

first: Genki

middle: N

last: Kanda

first: Rikuhiro

middle: G

last: Yamada

first: Shoi

last: Shi

first: Genshiro

middle: A

last: Sunagawa

first: Maki

last: Ukai-Tadenuma

first: Hiroshi

last: Fujishima

first: Naomi

last: Matsumoto

first: Koh

last: Masumoto

first: Takeya

last: Kasukawa

first: James

last: Galloway

first: Dimitri

last: Perrin

first: Yasufumi

last: Shigeyoshi

first: Hideki

last: Ukai

last: Kiyonari

first: Kenta

last: Sumiyama


title: Lungs from mice infected with S. pneumoniae and treated with Nemiralisib

status: Public on Aug 13 2018

city: Stevenage

first: Glyn

last: Bradley

address: Medicines Research Centre

department: Computational Biology

country: United Kingdom

institute: GSK

summary: Bacterial infections cause exaserbations in COPD. Study conducted to asses the effect of Nemiralisib, a PI3Kdelta inhibitor, on S. pneumoniae infected mice

overall_design: 48 samples in total from infected mice +/- Nemiralisib. 4 point timecourse (0hr, 3hr, 6hr, 24hr), 6 reps per group

first: Anne-Katrien

last: Stark

first: Anita

last: Chandra

first: Krishnendu

last: Chakraborty

first: Rafeah

last: Alam

first: Valentina

last: Carbonaro

first: Jonathan

last: Clark

first: Srividya

last: Sriskantharajah

first: Alex

last: Richter

first: Edward

last: Banham-Hall

first: Menna

last: Clatworthy

first: Sergey

last: Nejentsev

first: Nicole

last: Hamblin

first: Edith

last: Hessel

first: Alison

last: Condliffe

first: Klaus

last: Okkenhaug


title: Next Generation Sequencing Facilitates Quantitative Analysis of control of Pseudomonas aeruginosa PAO1 and diallyl disulphide-treated P. aeruginosa PAO1 Transcriptomes

status: Public on Aug 21 2018

city: Guangzhou

first: Wenru

last: Li

address: No.100, Xianliezhong Road

country: China

institute: Institute of Microbiology, Guangdong Academy of Sciences

type: Expression profiling by high throughput sequencing

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling of control of P. aeruginosa PAO1 (RNA-seq) to transcriptome profiling of diallyl disulphide-treated P. aeruginosa PAO1 and to evaluate protocols for optimal high-throughput data analysis.
Methods: Every 50 mL LB medium was inoculated exponential growth phase of P. aeruginosa PAO1, with the bacterial concentration of 108 CFU/mL. Then DDS was added, with its concentrations were 0 (as control, three biological repeats numbered A1, A2, and A3) and 0.64 mg/mL (three biological repeats numbered B1, B2, and B3) separately, both with a triplicate. All the six experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate at 150 rpm for 5 hours. The cells were then sampled and centrifuged from the three control groups and three DDS treatment groups, respectively. The cell precipitates in the control and DDS-treated groups were quickly separately frozen at -80 ºC. Total RNA was isolated from cells using Trizol (Life Technologies, USA) according to the manufacturer’s protocol.
Results: The RNA sequencing results revealed that a large number of genes in P. aeruginosa PAO1 were differentially expressed after DDS treatment. More than three thousands of genes were differentially expressed, with either up regulated (1649 genes) or down regulated (1725 genes) more than two-fold.
Conclusions:

overall_design: The mRNA profiles of P. aeruginosa PAO1 (ck) and DDS-treated P. aeruginosa PAO1 (sample1) were generated by deep sequencing, in triplicate, using Illumina Higseq 2000.

first: Rui-Qiang

first: Wen-Ru


title: Bulk RNA-seq of foamy and non-foamy intimal macrophages from ApoE -/- mouse

status: Public on Aug 30 2018

city: St. Louis

first: Maxim

last: Artyomov

state: Missouri

address: 425 S Euclid Ave

department: Pathology & Immunology

institute: WASHINGTON UNIVERSITY IN ST LOUIS

summary: Macrophages in atherosclerotic aorta are major population in lesion and contributes to lesion formation by becoming foam cells. To investigate in vivo transcriptome profiles of those macrophages, we extracted foamy and non-foamy macrophages from atherosclerotic aorta using lipid probe-based flow cytometry sorting. Our data indicates that intima non-foamy and foamy macrophages show different mRNA expressions. Rather than non-foamy macrophages, foamy macrophages expressed more genes related to cholesterol metabolism, oxidative phosphorylation, lysosome and so on. The non-foamy macrophages expressed more genes related to immune response (Il-1b related pathways, TNF, TLR signaling pathways) than foamy macrophages.

overall_design: Comparison of transriptional profiles from two cell types: Intimal foamy and non-foamy macrophages in atherosclerotic ApoE-/- mice (n=6, WD for 28 wks), triplicate, using Illumina HiSeq-3000.

first: Kyeongdae

last: Kim

first: Dahee

last: Shim

first: Jun

middle: S

last: Lee

first: Konstantin

last: Zaitsev

first: Jesse

middle: W

last: Williams

first: Gwendalyn

middle: J

last: Randolph

first: Cheolho

last: Cheong

first: Jae-Hoon

last: Choi


title: Quantitative analysis of Escherichia coli sigma factor alleles wildtype rpoS, rpoS819 and rpoS92 transcriptomes in stationary-phase (16 hours)

status: Public on Aug 25 2018

city: Bangalore

first: Savita

last: Chib

state: Karnataka

address: Bellary Road

country: India

institute: National Centre For Biological Sciences

summary: The goal of this study was to compare system level changes in gene-expression in naturally isolated alleles of stationary-phase sigma factor rpoS and two variants of it isolated during evolution under prolonged stationary-phase. We show that while rpoS819 was an attenuated form of wild type rpoS, rpoS92 partially reverses rpoS819 expression compensating rpoS819.

overall_design: Two biological replicates for each strain were grown in Lysogeny Broth culture for sixteen hours and further processed for RNASeq sample preparation. Total RNA was isolated using Trizol method and treated with DNase to remove any genomic DNA contamination. Finally, total RNA was depleted of ribosomal RNA using Microbe express kit from Ambion.

first: Aswin

last: Seshasayee


title: Casp8- and Casp11-dependent gene expression in ileal mucosa of LPS-challenged male mice

status: Public on Aug 07 2018

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: The execution of shock following high dose E. coli lipopolysaccharide (LPS) or bacterial sepsis in mice required pro-apoptotic caspase-8 in addition to pro-pyroptotic caspase-11 and gasdermin d. Hematopoietic cells produced MyD88- and TRIF-dependent inflammatory cytokines sufficient to initiate LPS shock independent of caspase-8 or caspase-11. Both proteases had to be present to support tissue injury, dependent upon TNF and interferon , first observed in the small intestine and later in spleen and thymus. Caspase-11 enhanced the activation of caspase-8 and extrinsic cell death machinery within the lower small intestine. Neither caspase-8 nor caspase-11 was individually sufficient for shock, but collaborated to amplify the inflammatory signals associated with tissue injury. Therefore, combined pyroptotic and apoptotic signaling mediated endotoxemia independent of RIPK1 kinase activity and RIPK3 function. These observations bring to light the relevance of tissue compartmentalization during inflammatory signaling in vivo where cytokines execute diverse cell death pathways and tissue damage.

overall_design: Ileum was harvested from Wt (C57BL/6), Casp8-RIPK3-deficient and Casp11-deficient mice (5 male for each group) at 1.5 h post challenge with high dose LPS (54 mg/kg). Excised tissues were maintained in RNAlater solution for 24 h and RNA was harvested from mucosa.

first: Pratyusha

last: Mandal

first: Edward

last: Mocarski

first: Steven

middle: E

last: Bosinger

first: Nirav

last: Patel


title: The Effect of PRMT5 deficiency on thymic iNKT cells

status: Public on Aug 06 2018

city: Tokyo

first: Maia

last: Inoue

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

institute: The university of Tokyo

summary: Protein arginine methylation is a post-translational modification catalyzed by protein arginine methyltransferase (PRMT).  To elucidate the role of PRMT5 in T cells, we generated T-cell specific PRMT5-deficient mice (Prmt5 flox/d Cd4-Cre mice) and found a severe loss of thymic iNKT cells as well as a reduced number in peripheral CD4+ and CD8+ T cells.  As iNKT cells were significantly decreased in the stage 1, 2 and 3 of developmental stages, RNA-seq was performed using stage 1 iNKT cells of control and PRMT5-deficient mice.  This transcriptome analysis will provide mechanistic insight into how PRMT5 contributes to thymic iNKT cell development.

overall_design: Stage 1 iNKT cells were sorted from thymus of control and Prmt5 flox/D Cd4-Cre mice. Total RNA was extracted and RNA-seq was performed by Ion Proton.

first: Kazuo

last: Okamoto

first: Asuka

last: Terashima

first: Takeshi

last: Nitta

first: Ryunosuke

last: Muro

first: Takako

last: Negishi-Koga

first: Toshio

last: Kitamura

first: Tomoki

last: Nakashima

first: Hiroshi

last: Takayanagi


title: Placenta and uterus transcriptomes from transgenic mice expressing human corticotropin-releasing hormone in placenta

status: Public on Aug 09 2018

city: Cincinnati

first: Caitlin

last: Dunn

state: Ohio

address: 3333 Burnet Avenue

department: Division of Human Genetics

institute: Cincinnati Children's Hospital Medical Center

summary:
Purpose:  Parturition is delayed by approximately 12 hours in transgenic mice expressing human corticotropin-releasing hormone (CRH) in placenta. The goal of the study was to identify the pathways in reproductive tissues (uterus and placenta) altered by placental expression of human CRH.
Methods:  Human BAC RP11-366K18 (CHORI) containing human CRH and cis-regulatory region was inserted into the mouse genome by microinjection and random integration to create the BAC1 line. The CRISPR/Cas9 system was used to delete a CRH regulatory element from the BAC1 line to create the CR1 line, eliminating expression of CRH in placenta. Total expression of uterus and placenta by RNA-seq at embryonic day 18.5 were compared between BAC1, CR1, and nontransgenic mice.
Results: Genes known to be associated with luteolysis and initiation of parturition (Cav1, Gja1, Oxtr, Ptgs1, Ptgs2) were not differentially expressed in uterus of this model.
Conclusions: CRH-mediated delay of parturition is likely independent of luteolysis.

overall_design: mRNA-seq was performed on uterus and placenta harvested at embryonic day 18.5 from nontransgenic mice, Tg(BAC1) mice, and Tg(CR1) mice.

last: Dunn-Fletcher

first: Louis

last: Muglia


title: Quantitative analysis of Id1 Wild Type and Id1 knockout  hematopoietic stem cells transcriptome

city: Frederick

first: Jack

last: Chen

state: MD

address: SAIC-Frederick Miller Dr

institute: NIH

summary: To explore the molecular basis by which Id1 loss promotes HSC quiescence under stress we compared the transcriptome of Id1-/- and Id1+/+ HSCs isolated from primary BMT recipient mice by RNA-seq. We found 179 upregulated and 1476 downregulated genes in Id1-/- HSCs compared to Id1+/+ HSCs using a fold-change cut-off of 2 . Collectively, the IPA analysis shows that Id1-/- HSCs have gene expression profiles consistent with reduced response to stress, reduced cycling and proliferation, and reduced ribosomal biogenesis and protein synthesis, which is consistent with our hypothesis that Id1-/- HSCs have molecular signature of quiescent HSCs compared to Id1+/+ HSCs.

overall_design: RNA was isolated from HSCs FACS purified from mice transplanted with Lin- Id1-/- and Id1+/+ BMCs after 6 weeks for RNA-seq  analysis.

first: Satyendra

last: Singh

first: Shweta

first: Stephen

last: Gadomski

first: Lei

last: Sun

first: Jonathan

last: Keller


title: Expression data from mouse bone marrow sinusoidal endothelial cells (SECs) before and after the ablation of classical dendrtic cells (cDCs)

status: Public on Aug 02 2018

first: Daniel

middle: C

last: Link

state: MO

address: 660 South Euclid Avenue

department: Internal Medicine

institute: Washington University in St Louis

summary: The function of bone marrow sinusoidal endothelial cells may change upon the ablation of classical dendritic cells to promote vascular permeability and angiogenesis

overall_design: Zbtb46dtr bone marrow were transplanted into irradiated wild-type recipients. After 8 weeks, these mice were treated with diphtheria toxin (DT) to ablate cDCs, or PBS as control. Sinusoidal endothelial cells were sorted from the bone marrow of these mice, and their RNA expression was analyzed using RNA-sequencing

first: Jingzhu

last: Zhang


title: Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq [RNA-Seq]

status: Public on Aug 11 2018

city: Boston

first: Simona

last: Cristea

state: Massachusetts

address: 450 Brookline Ave.

department: Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute

summary: Triple-negative breast cancer (TNBC) is an aggressive subtype characterized by extensive intratumoral heterogeneity. To investigate the underlying biology, we conduct single-cell RNA- sequencing (scRNA-seq) of >1500 cells from six primary TNBC. Intercellular heterogeneity of gene expression programs within each tumor was variable and largely correlated with clonality of inferred genomic copy number changes, suggesting that genotype drives the gene expression phenotype of individual subpopulations. Clustering of gene expression profiles identified distinct subgroups of malignant cells shared by multiple tumors, including a single subpopulation associated with multiple signatures of treatment resistance and metastasis, and characterized functionally by activation of glycosphingolipid metabolism and associated innate immunity pathways. A novel signature defining this subpopulation was predictive of long-term outcomes for TNBC patients in a large patient cohort. Collectively, this analysis reveals the functional heterogeneity and its association with genomic evolution in TNBC, and uncovers unanticipated biological principles dictating poor outcomes in this disease.

overall_design: Single cell RNA sequencing of 1,534 cells in six fresh triple negative breast cancer tumors.


title: Single-cell RNA sequencing of zebrafish beta-cells from various stages

city: Greater Noida

first: Sumeet

middle: Pal

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

institute: Shiv Nadar Institution of Eminence

summary: Age-associated deterioration of cellular physiology leads to pathological conditions, and detection of premature aging could provide a window for preventive therapies against age-related diseases. For this, methods that accurately evaluate cellular age are required. However, such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age, and its modifiers, requires a framework that can robustly handle the noise associated with single-cell sampling protocols. Here, we implement GERAS (GEnetic Reference for Age of Single-cell), a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes.  GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta-cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise, as evaluated by its performance on independent samplings of single-cells. Additionally, GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells, respectively.  We further harnessed the predictive power of GERAS to identify genome-wide molecular factors that correlate with aging. We show that one of these factors, junb, which declines in expression with aging, is necessary to maintain the proliferative state of juvenile beta-cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro-aging factors, and uncovering candidate genes associated with premature aging.

overall_design: We used fluorescence-activated cell sorting (FACS) coupled with next generation RNA-Sequencing to profile beta-cells from various stages. Cells were sorted into a 96-well plates and single-cell library prepared using SMART-Seq v4 Ultra Low Input RNA Kit . Sequencing was performed on llumina Nextseq500 aiming at an average sequencing depth of 0.5 million reads per cell. Reads were splice-aligned to the zebrafish genome, GRCz10, using HISAT2. htseq-count was used to assign reads to exons thus eventually getting counts per gene.

middle: P

first: Nikolay

last: Ninov


title: Long noncoding RNAs could act as vectors for paternal heredity of high fat diet-induced obesity

status: Public on Aug 03 2018

city: Beijing

first: Sihua

last: Gao

address: No. 11, Bei San Huan Dong Lu, Chaoyang District, Beijing100029

institute: Beijing University of Chinese Medicine

summary: To investigate whether lncRNAs are involved in intergenerational inheritance of obesity and obesity-induced decline in fertility, we divided mice into obesity (F0 mice fed a high-fat diet, F0-HFD) and non-obese (F0 mice fed normal chow, F0-NC) model groups and their male offspring (F1-HFD and F1-NC, respectively). We examined the differences in the expression levels of lncRNAs and mRNAs in the F0-HFD/F0-normal and F1-HFD/F1-normal groups. The results revealed similar expression patterns in the F1-HFD/F0-HFD groups at both the lncRNA and mRNA levels. The maximum difference in the lncRNA expression was observed between the F0-HFD and F0-NC groups. The differentially expressed lncRNA targets and mRNAs identified in our study are mainly involved in GnRH signalling pathway, metabolic process, and Hippo signalling pathway; similarly expressed lncRNAs and mRNAs in F1-HFD/F0-HFD are closely linked with G-protein coupled receptor signalling pathway, pancreatic polypeptide receptor activity, and lysine biosynthesis, which may play an important role in the molecular mechanism of intergenerational inheritance of obesity. Furthermore, potential genes that might play important roles in the pathogenesis of obesity-related low fertility were revealed by lncRNA-and mRNA-interaction studies based on the microarray expression profiles. In conclusion, we found that lncRNA could be involved in obesity-induced infertility by expressing abnormalities, which could act as genetic vectors of paternal inheritance of obesity.

overall_design: The  sperm of C57bl/6J Obesity (F0 mice fed a high-fat diet, F0-HFD) and non-obese (F0 mice fed normal chow, F0-NC) model groups and their male offspring (F1-HFD and F1-NC, respectively) were used in this study for the detection of gene expression. Three independent experiments were performed at each group using different donors for each experiment.

first: Tian

last: An


title: Role of Fragaria FaDOF2 in fruit ripening by transiently silencing

status: Public on Jul 31 2018

city: CÓRDOBA

first: Francisco

middle: Javier

last: Molina-Hidalgo

state: Cordoba

address: Edif. Severo Ochoa (C6.) Planta Baja-Ala Norte Campus de Rabanales

department: Biochemistry and molecular biology

country: Spain

institute: University of Cordoba

summary:
The role played by transcription factors in the regulation of strawberry fruit ripening process is scant. We have identified and functionally characterized FaDOF2, a DOF-type transcription factor.
FaDOF2 is a ripening-related transcription factor that regulates key genes involved in eugenol biosynthesis in strawberry fruit receptacles.

overall_design: We have analyzed three control samples fruits agroinjected with the empty vector, a three samples fruits agroinjected with the RNAi construct

first: Juan

last: Muñoz-Blanco

first: Enriqueta

last: Moyano


title: Expression data from OVA-induced allergic mice [Affymetrix]

status: Public on Aug 01 2018

first: LI

middle: Yong

last: Ning

address: 7 Panjiayuan Nanli

institute: China National Center for Food Safety Risk Assessment

summary:
IgE antibodies are key mediators of food allergy, and the production of IgE is tightly regulated at the moleculaer and cellular level in the germinal center of lymph glands where specific sets of genes are up-regulated.
We used microarrays to detail the global programme of gene expression underlying ovalbumin-induced allergy and identified distinct classes of  up-regulated genes during this process.

overall_design: Peyer's Patches of control and  OVA-induced allergic mice  were harvested for RNA extraction and hybridization on Affymetrix microarrays.

first: Nanan

first: Hui

last: Yang


title: Prevalence of long RNA Duplexes in Human Model Cell Lines

status: Public on Jul 28 2018

first: Bruce

last: Shapiro

state: Maryland

address: Building 560/Room 11-83

institute: National Cancer Institute

summary: We present a novel transcriptome-wide experimental approach based on sequencing RNA fragments longer than 18 nts in order to detect accessible RNA duplexes

overall_design: The prevalence of RNA duplexes that are not degraded by single-strand cutting enzymes is ascertained for 4 human model cell lines with respect to different treatments.

first: Lisheng

last: Dai

first: Eckart

last: Bindewald

first: Wojciech

last: Kasprzak

first: Taejin

last: Kim

first: Shuo

last: Gu


title: Expression data from murine colon

status: Public on Jul 26 2018

city: ROME

first: FEDERICA

last: LAUDISI

address: VIA MONTPELLIER, 1

department: SYSTEMS MEDICINE

country: Italy

institute: UNIVERSITY OF ROME "TOR VERGATA"

summary: Expression data from colon samples isolated from mice exposed to drinking water in the presence or absence of 5% Maltodextrin for 45 days

overall_design: contributor: Microarray Unit of COGENTECH Scarl (Consortium for Genomic Technologies, Milan, Italy)

first: Federica

last: Laudisi


title: ChIP-seq from lung (ENCSR254NDP)

status: Public on Sep 21 2018

city: Stanford

first: ENCODE

last: DCC

state: CA

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: Krox20 hindbrain regulation in Zebrafish [ATAC-seq]

city: Paris

first: samuel

last: Collombet

address: 46 rue d'Ulm

department: Biology

country: France

institute: Ecole Normale Superieure

summary: In the present study, we have identified six enhancers located within the zebrafish krox20 locus, using accessibility data generated by ATAC-seq and characterized their activity profiles as well as their functions and interactions in the zebrafish hindbrain . We also investigated the orthologues in six evolutionary distant vertebrates of one of these element, showing a great variety of activity profiles demonstrating the striking evolutionary flexibility of this element .

overall_design: Chromatin accessibility assessed by ATAC-seq from Zebrafish embryonic samples at different time points and anatomical positions.

first: Patrick

last: Torbey

first: Samuel

last: Charnay

first: Pascale

last: Gilardi-Hebenstreit


title: Somatic piRNA pathway prevents transgenerational germline transposition [circularDNA-seq]

city: MONTPELLIER

first: SEVERINE

last: CHAMBEYRON

address: 141, rue de la Cardonille

department: Institute of Human Genetics

institute: CNRS

summary: Transposable elements (TEs) are genomic parasite that threat genome integrity. One major strategy organisms evolved to balance TE activity in the germline is the Piwi-interacting RNAs (piRNAs) pathway. It prevents transposition by repressing TE at transcriptional and/or post-transcriptional level. However, evidence that TE derepression caused by piRNA pathway impairment is actually followed by bursts of transposition is still lacking. Here we present a genome-wide TE-analyses of the replicative TE life cycle (their expression, their translation to their transposition in the germline) after  piRNA pathway impairment in the somatic follicle cells. We observed a high transposition-rate in the germline, leading to a 10-fold increase in genomic TE-load after 70 successive generations of piRNA pathway impairment. Moreover, we demonstrate that siRNAs co-regulate TE activity at post transcriptional level in follicle cells. These observations demonstrate that the small RNA-mediated TE repression in follicle cells contribute to genome homeostasis.

overall_design: Analysis of effects of conditional piwi knock down in somatic follicle cells on TE behaviour and progeny genome.

first: Bridlin

last: Barckmann

first: Marianne

last: El-Barouk

first: Alain

last: Pelisson

first: Blaise

last: Li

first: Bruno

last: Mugat

first: Anna-Sophie

last: Fiston Lavier

first: Marie

last: Mirouze

first: Klaus

last: Föstermann

last: Fablet

first: Severine

last: Chambeyron


city: Cambridge

first: Renato

last: Umeton

state: MA

address: 77 Massachusetts Avenue

institute: Massachusetts Institute of Technology

summary: Whole transcriptome analysis of circulating B cells from multiple sclerosis (MS) patients and healthy donors (HD).

overall_design: We studied CD19+ B cell subsets obtained from peripheral blood of 10 MS patients, 10 HD. All affected individuals were treatment-naïve and all the investigations were performed at least three months after the last steroid therapy. Microarray data was performed using GeneChip® Human Exon 1.0 ST Arrays  Affymetrix’s GeneChip


title: Expression profiling of mechanical stretched interfollicular epidermal stem cells (IFESCs)

city: shanghai

first: Jing

last: Wang

address: 639 Zhizaoju Road

department: Depart of Plastic & Reconstructive Surgery

institute: Shanghai 9th People's Hospital, School of Medicine, Shanghai JiaoTong University

summary: The renewing human epidermis constantly senses and adapts to a wide range of mechanical cues that are ubiquitous throughout life. The mechanisms of how mechanical forces are responded by interfollicular epidermal stem cells (IFESCs) and are transmitted directly into nucleus to modify gene expression remain incompletely defined. In vitro, human IFESCs were cultured on the collagen I coated silicon rubber membrane and then subjected to the mechanical stretched. Cyclic mechanical tension at 0.5 Hz sinusoidal curve at 10% elongation was applied using an FX-5000T™ Flexercell® Tension Plus™ unit (Flexcell International Corporation). In mechanical unloading groups, cells were cultured on the same plates in the same incubator with the mechanical stretched groups but not subjected to stretch. Combining genome-wide microarray and functional analyses, we made transcriptome analysis of samples from the mechanical unstretched or stretched isolated human IFESCs.

overall_design: We analyzed 6 samples (3 sampled of mechanical stretched and 3 samples of unstretched IFESCs) using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. Three techinical replicates were performed (exon-level expression value was analysed. ).

first: Qingfeng

first: Xiaoling

last: Zhang

first: Jiao

first: Yifan


title: Persistent transcriptomic alterations in medial prefrontal cortex after prenatal exposure to maternal inflammation

city: Palo Alto

first: John

last: Huguenard

address: 1050A Arastradero Rd., Room A250

institute: Stanford University

summary: Infection during pregnancy is strongly implicated as an environmental risk factor for autism spectrum disorder (ASD), with activation of the maternal immune system (MIA) identified in the causative pathway. Maternal exposure to viral and bacterial mimics at midgestation leads to the development of core ASD behaviors in rodent offspring. However, the fundamental pathogenic mechanisms coupling MIA to persistent changes in brain function and behavior are incompletely understood.The medial prefrontal cortex (mPFC) is a major locus of pathology in ASD and highly associated with behaviors dysregulated by MIA. Transcriptomic profiling of the mPFC from adult MIA and control offspring provides insight into molecular pathways persistently disrupted by prenatal exposure to maternal inflammation.

overall_design: Pregnant dams received a single intraperitoneal injection of saline (control) or the viral mimic polyinosinic:polycytidylic acid (poly(I:C)) to induce MIA at embryonic day 12.5 (E12.5). Brains were removed from saline and poly(I:C) offspring at 4 months of age and medial prefrontal cortices were dissected for RNA extraction (Stanford TASC) and hybridization onto Affymetrix Clariom S Mouse microarrays (Stanford PAN facility).

first: Tanya

last: Weerakkody

first: Chris

middle: D

last: Makinson

first: Jordan

middle: M

last: Sorokin


title: Folliculin deficiency effect on Raw264.7 cells

status: Public on Jul 30 2018

city: Kumamoto

first: Masaya

last: Baba

state: Kumamoto

address: 1-1-1 Honjo, Chuo-ku

department: Urology

institute: Kumamoto University

summary: Osteoclast differentiation is a dynamic differentiation process, which is accompanied by dramatic changes in metabolic status as well as in gene expression. Recent findings have revealed an essential connection between metabolic reprogramming and dynamic gene expression changes during osteoclast differentiation. However, the upstream regulatory mechanisms that drive these metabolic changes in osteoclastogenesis remain to be elucidated. We demonstrate that induced deletion of a tumor suppressor gene, Folliculin (Flcn), in mouse osteoclast precursors causes severe osteoporosis in 3 weeks through excess osteoclastogenesis. Flcn deficient osteoclast precursors (Raw264.7 cells) reveal cell autonomous accelerated osteoclastogenesis. For the purpose of elucidating the molecular mechanism of accelerated osteoclastogenesis in Flcn deficient Raw264.7 cells, we performed DNA microarray analysis.

overall_design: Raw264.7 cells were transfected with scramble or Flcn targeting siRNA, followed by a medium change at 24hr after transfection. Cells were cultured after an additional 48hr and total RNA was collected and purified using the RNeasy Micro kit. cDNA preparation and hybridization of the probe arrays were performed according to the manufacturer's instructions. Affymetrix GeneChip Mouse Genome 430 2.0 arrays were applied.

first: Mitsuhiro

last: Endoh

first: Wenjuan

last: Ma

first: Hirofumi

last: Toyama

first: Akiyoshi

last: Hirayama

first: Keizo

last: Nishikawa

first: Keiyo

last: Takubo

first: Hiroyuki

last: Hano

first: Hisashi

last: Hasumi

first: Terumasa

last: Umemoto

first: Michihiro

last: Hashimoto

first: Nobuko

last: Irie

first: Chiharu

last: Esumi

first: Miho

last: Kataoka

first: Naomi

last: Nakagata

first: Tomoyoshi

last: Soga

first: Masahiro

last: Yao

first: Tomomi

last: Kamba

first: Takashi

last: Minami

first: Masaru

last: Ishii

first: Toshio

last: Suda


title: In vivo replacement of damaged bladder urothelium by Wolffian duct epithelial cells

status: Public on Jul 19 2018

city: Madison

first: Chad

middle: Michael

last: Vezina

state: WI

address: 1656 Linden Drive

department: Comparative Biosciences

institute: University of Wisconsin-Madison

summary: The bladder’s remarkable regenerative capacity in response to  injury had been thought to reside exclusively in its basal and  intermediate cells. While examining consequences of DNA methyltransferase  1 (Dnmt1) inactivation in mouse embryonic bladder  epithelium, we made the surprising discovery that Wolffian duct  epithelial cells also support bladder regeneration. Conditional inactivation  of Dnmt1 in mouse urethral and bladder epithelium  triggered widespread apoptosis, depleted basal and intermediate  bladder cells and disrupted Uroplakin protein expression. These  events coincided with recruitment of Wolffian duct epithelial cells  into Dnmt1 mutant urethra and bladder where they were reprogrammed  to express bladder markers including FOXA1, Keratin 5,  P63 and Uroplakin. This is the first evidence that Wolffian duct  epithelial cells can be summoned in vivo to replace damaged  bladder epithelium and function as a cell reservoir for bladder  regeneration.

overall_design: Bladder urothelium were separated from stroma tissues and profiled by RNA-seq. Total 14 samples, from E15.5 embryos with three different genotypes ( including conditional Dnmt1 KO in the bladder urothelium, detailed in sample list characteristics: genotypes)

first: Diya

middle: B

last: Joseph

first: Li-Fang

last: Chu


title: Genome-wide Map of R-Loop-Induced Damage Reveals How a Subset of R-Loops Contributes to Genomic Instability

status: Public on Jul 16 2018

city: Berkeley

first: lorenzo

last: costantino

address: 16 Barker Hall # 3202

department: MCB

institute: university of california, berkeley

summary: Chromatin immuno-precipitation (ChIP) of Rad52-bound to ssDNA that was compatible with next-generation sequencing to map sites of DNA damage induced by accumulation of genomic DNA-RNA hybrids.

overall_design: Examination of RAD52 signal in strains defective for DNA-RNA hybrid removal. Cells possess different DNA-RNA hybrid removal machineries like the RNases-H (RNH1 and RNH201 in yeast), DNA-RNA helicases (the essential Sen1 gene in yeast) and Topoisomerases (Top1 gene used in this study). We removed the activity of those enzymes and analyzed the pattern of Rad52 localization by Rad52-ChIPseq as a readout to DNA damage induced by DNA-RNA hybrids.

first: Lorenzo

last: Costantino

first: Douglas

last: Koshland


title: Expression data from OVA-induced allergic mice

first: LI

last: Ning

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

overall_design: Refer to individual Series


title: Limited macrophage dynamics in progressing or regressing murine atherosclerotic plaques

status: Public on Jul 13 2018

city: Saint Louis

first: Gwendalyn

last: Randolph

address: 425 S Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: Previous studies using particle labeled monocytes to assess recruitment into tissues have demonstrated that bead labeling did not affect the ability of monocytes to enter tissues (Tacke et al., 2007), and particle uptake did not activate p38/MAPK or NFκB pathways (Yates and Russell, 2005). However, the possibility remains that bead labeling could have effects on global gene expression profiles. To address this prospect, we performed gene expression profiling of classical and non-classical monocytes that had taken up latex particle in vivo against cells from the same mouse that had not taken up particles.

overall_design: 8 samples were analyzed with two biological replicates per condition: Gr1 high monocytes with or without beads and Gr1 low monocytes with or without beads. C57bl/6 mice were injected i.v. with latex beads (diluted 1:4 in PBS) three days following chodonate liposome mediate monocyte depletion, then four days later classical and nonclassical blood monocytes were FACS sorted (FACSAria, BD Biosciences) for presence or absence of latex beads. RNA was extracted from sorted cells by TRIzol and RNeasy mRNA isolation kit (Qiagen). RNA amplification, direct labeling, hybridization, and chip scanning were performed as previously described (Grabner et al., 2009). Microarray was performed on an Affymetrix GeneChip 430 2.0. R packages 'oligo' and 'limma' were used to read, normalize, access QC and perform DE from the microarray expression data. Gene set enrichment analysis with fgsea package was used to identify pathway enrichments in hallmark and canonical pathways. Benjamini-Hochberg correction was used to correct p-value for multiple comparisons.

first: Jesse

last: Williams

first: Catherine

last: Martel

first: Stephane

last: Potteaux

first: Ekaterina

last: Esaulova

first: Molly

last: Ingersoll

first: Andrew

last: Elvington

first: Brian

middle: T

last: Saunders

first: Li

middle: H

last: Huang

first: Rainer

last: Sparbroek

first: Andreas

last: Habenicht

first: Bernd

last: Zinselmeyer


title: Persistent Bordetella bronchiseptica carriage is associated with broad phenotypic alterations of peripheral CD4+CD25+ T cells and differentially affects immune responses to secondary non-infectious and infectious stimuli in mice

status: Public on Jul 12 2018

city: Braunschweig

last: Jeron

state: Nierdersachsen

address: Inhoffenstraße 7

department: Viral Immunology

country: Germany

institute: Helmholtz Center for Infection Research

summary: The respiratory tract is constantly exposed to the environment and displays a favorable niche for colonizing microorganisms. However, the effects of respiratory bacterial carriage on the immune system and its implications for secondary responses remain largely unclear. We have employed respiratory carriage with Bordetella bronchiseptica (Bb) as the underlying model to comprehensively address effects on subsequent immune responses. Persistent carriage was associated with the stimulation of Bordetella-specific CD4+, CD8+ and CD4+CD25+Foxp3+ T cell responses and broad transcriptional activation was observed in CD4+CD25+ T cells. Importantly, transfer of lymphocytes from persistent carriers to acutely B. bronchiseptica infected mice resulted in a significantly increased bacterial burden in the recipient’s upper respiratory tract. In contrast, we found that B. bronchiseptica carriage resulted in a significant benefit for the host in systemic infection with Listeria monocytogenes. At the same time, vaccination and influenza A virus infection were unaffected. These data demonstrate that there are significant immune modulatory processes triggered by persistent B. bronchiseptica carriage that differentially affect subsequent immune responses. Thereby our results demonstrate the complexity of immune regulation induced by persistent bacterial carriage in the respiratory tract that can be beneficial or detrimental to the host, depending on the pathogen and the considered compartment.

overall_design: In total 8 sampels were analyzed. 7 and 42 days post Bb infection splenocytes from n = 6 BALB/c mice per group were pooled and CD4+CD25+ and CD4+CD25- T cells were FACS sorted. As controls the same cell subsets were isolated from age-matched uninfected control mice. For analysis each cell subset from Bb-infected mice was compared to the according uninfected control subset.

first: Julia

last: Boehme

last: Volckmar

first: Marcus

last: Gereke

first: Tetyana

last: Yevsa

first: Robert

last: Geffers

first: Carlos

middle: A

last: Guzmán

first: Jens

last: Schreiber

first: Sabine

last: Stegemann-Koniszewski

first: Dunja

last: Bruder


title: Gene Expression Profiles of Atxn3-WT and Atxn3-KO mouse embryonic fibroblasts

city: Ann Arbor

first: Henry

middle: L

last: Paulson

state: MI

address: 1500 E Medical Center Dr

department: Department of Neurology

institute: University of Michigan

summary: Spinocerebellar ataxia type 3 (SCA3) is a dominantly inherited neurodegenerative disorder caused by a polyglutamine-encoding CAG repeat expansion in the ATXN3 gene, which encodes a deubiquitinating enzyme, ATXN3, implicated in numerous quality control pathways. Several mechanisms have been proposed to explain the pathogenic role of mutant polyQ-expanded ATXN3 in SCA3 including disease protein aggregation, impairment of ubiquitin-proteasomal degradation and transcriptional dysregulation. A better understanding of the normal functions of this protein may shed light on SCA3 disease pathogenesis.  To assess the potential normal role of ATXN3 in regulating transcription, we compared gene expression profiles in wildtype (WT) versus Atxn3 knockout (KO) mouse embryonic fibroblasts (MEFs).

overall_design: A total of six microarray slides were hybridized for gene expression profiling in Atxn3-WT (3 replicates) and Atxn3-KO (3 replicates) MEFs.

last: Zeng

first: Dapeng

last: Zhang

first: Hayley

middle: S

last: McLoughlin

first: Annie

last: Zalon

first: Johnvesly

last: Basappa

first: L

last: Aravind


title: Expression data of the kidney tissues from wildtype and Tet2 KO mice

city: Shanghai

first: Hao

last: Wang

address: 180 Fenglin Road

institute: Fudan University

summary:
Our previous study has showed Ten-eleven translocation (Tet2) gene expression as well as the global 5-hydroxymethylcytosine (5hmC) level were reduced significantly in mouse kidney insulted by ischemia reperfusion (IR). Here, we investigate the functional role of Tet2 in renal IR injury. We constructed renal IR injury model in wild type and Tet2 knockout (KO) mice. Serum creatinine (SCr) and blood urea nitrogen (BUN) were examined to evaluate renal function. HE staining and renal injury biomarkers were tested to confirm the degree of injury.  Microarray analysis of mRNA expression levels was carried out to gain mechanistic insightinto the role of Tet2.
We used microarrays to profile the transcriptomes of the kidneys from wildtype and Tet2 KO mice.

overall_design: Wildtype and Tet2 KO mice were subjected to sham surgery or renal ischemia reperfusion. The kidney tissues of these mice were collected for RNA extraction and microarray analysis.

first: Li

last: Tan


title: Identification of differentially expressed genes between control and PIK3CD GOF human activated transitional B cells

city: Darlinghurst

first: Stuart

last: Tangye

state: NSW

address: 384 Victoria St

department: Immunology

country: Australia

institute: Garvan Institute of Medical Research

summary:
IL-21 induces B cell activation, and differentiation into antibody-secreting plasmblasts in vitro. This process is compromised in transitional B cells to gain of function mutations in PIK3CD
We used microarrays to identify genes that are differentiatlly expressed following CD40L/IL-21 stimulation of human transitonal B cells from healthy donors and patients with GOF mutations in PIK3CD

overall_design: Sort-purified transitional B cells from 3 healthy donors and 3 patients with APDS due to heterozygous activating gain of function PIK3CD mutations were cultured for four days with CD40L +/-  IL-21 (50ng/ml). RNA was then extracted from the harvested cells and the genetic profile  analysed by microarray.


title: p53 ChIP-seq in PHA-stimulated human T-lymphocytes

status: Public on Jul 24 2018

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: ChIP-seq profiles of p53 binding in PHA-stimulated human T-lymphocytes treated with either Doxorubicin, Nutlin-3, or DMSO

overall_design: Individual ChIP-seq profiles of p53 binding in PHA-stimulated human T-lymphocytes (from four healthy volunteers) treated ex vivo with either Doxorubicin, Nutlin-3, or DMSO. Input sequences were used as controls.

first: Thuy-Ai

last: Nguyen

first: Daniel

last: Menendez


title: Gene expression array of brain, mandible and maxilla tissues from P0 FoxO6-/- and wildtype mice

city: Iowa City

first: Brad

last: Amendt

state: Iowa

address: 100 Bowen Science Building

department: Anatomy and Cell Biology

institute: University of Iowa

summary:
FoxO6 is expressed in the brain, craniofacial region and somite, but the precise role of FoxO6 in craniofacial development remain unknown. We found that FoxO6 is expressed specifically in craniofacial tissues and FoxO6-/- mice undergo expansion of the face, frontal cortex, olfactory component and skull.
Our gene expression array data demonstrated that Lats1, an important component of Hippo signaling pathway, was decresed in FoxO6-/- mice. Our in vitro and in vivo data further validated that FoxO6 activates Lats1 expression, thereby increasing Yap phosphorylation and activation of Hippo signaling.

overall_design: The brain, mandible and maxilla tissues from P0 FoxO6-/- and wildtype mice were used for Affymetrix microarrays

first: Zhao

last: Sun


title: Study of vascular endothelial-specific and inducible vascular endothelial-specific deletion of Major Facilitator Superfamily Domain containing 2a (Mfsd2a) in mice.

status: Public on Jul 11 2018

city: Singapore

first: Bernice

last: Wong

address: 8 College Road, Level 8

department: Cardiovascular and Metabolic Disorders

country: Singapore

institute: Duke-NUS Medical School, Singapore

summary:
Brain development requires a massive increase in brain lipogenesis and accretion of the essential omega-3 fatty acid docosahexaenoic acid (DHA). Brain acquisition of DHA is primarily mediated by the transporter Major Facilitator Superfamily Domain containing 2a (Mfsd2a) expressed in the endothelium of the blood-brain barrier. Mfsd2a transports DHA and other polyunsaturated fatty acids esterified to lysophosphatidylcholine (LPC-DHA). However, the function of Mfsd2a and DHA in brain development is incompletely understood. Using vascular endothelial-specific (2aECKO) and inducible vascular endothelial-specific (2aiECKO) deletion of Mfsd2a in mice, we found Mfsd2a to be uniquely required postnatally at the blood-brain barrier for normal brain growth and DHA accretion, with DHA deficiency preceding the onset of microcephaly. Gene expression profiling analysis of these DHA deficient brains indicated that Srebp-1 and Srebp-2 pathways were highly elevated.
Affymetrix gene arrays were used to determine differences in gene expression between 2aECKO or 2aiECKO relative to their respective controls in the developing brain.

overall_design: RNA was extracted from half cerebrums of postnatal day 8-9 2aECKO, 2aiECKO or Mfsd2afl/fl mice. Equal amounts of RNA was pooled from five to six half cerebrums per genotype. Microarray profiling was done on pooled samples with a RIN cut-off of 8.0 using Mouse 430 2.0 arrays (Affymetrix).

first: David

last: Silver

first: Jia Pei

last: Chan


title: Functional annotation of transcriptional factors transactivation domains

status: Public on Jul 10 2018

city: Vienna

first: Alexander

last: Stark

address: Campus-Vienna-Biocenter 1

country: Austria

institute: The Research Institute of Molecular Pathology (IMP)

summary: The goal of this study is to identify transactivation domains within transcription factor body with high-throughput NGS sequencing methods

overall_design:
Examination of transcription factor's trans-activation domain activity between GFP+ and GFP- cells
Please note that raw reads from each replicates (*rep1*_R1* , *rep1*_R2*) and (*rep2*_R1*, *rep2*_R2*) were mapped independently into custom genome (TFbb_list180_linear*). Mapped reads from two replicates were merged for downstream analysis. Genome coverage files were made for six reading frames (+1, +2, +3, -1, -2, -3) and are linked to the corresponding *rep1 sample records. For example, file short-library_GFP-_3-.bw represent coverage for GFP- sample from short library in '-3' reading frame.

first: Cosmas

last: Arnold

first: Filip

last: Nemčko

first: Ashley

middle: R

last: Woodfin

first: Sebastian

last: Wienerroither

first: Anna

last: Vlasova

last: Schleiffer

first: Michaela

last: Pagani

first: Martina

last: Rath


title: Combined systemic disruption of MET and EGFR signaling causes liver failure in normal mice

status: Public on Jul 09 2018

city: Pittsburgh

first: George

middle: K

last: Michalopoulos

state: Pennsylvania

address: 411 SBST, 200 Lothrop Street

institute: University of Pittsburgh

summary:
MET and EGFR receptor tyrosine kinases are crucial for liver regeneration and normal hepatocyte function. Recently we demonstrated that in mice, combined inhibition of these two signaling pathways abolished liver regeneration following hepatectomy, with subsequent hepatic failure and death at 15-18 days post-resection. Morbidity was associated with distinct and specific alterations in important downstream signaling pathways that led to a decrease in hepatocyte volume, reduced proliferation, and shutdown of many essential hepatocyte functions such as fatty acid synthesis, urea cycle, and mitochondrial functions. In the present study we explore the role of MET and EGFR signaling in resting mouse livers that are not subjected to hepatectomy. Mice with combined disruption of MET and EGFR signaling (Delta MET + EGFRi) were noticeably sick by 10 day and died at 12-14 days. Delta MET + EGFRi mice showed decreased liver to body weight ratios, increased apoptosis in non-parenchymal cells, impaired liver metabolic functions, and activation of distinct, downstream signaling pathways related to inflammation, cell death, and survival. Conclusion: The present study demonstrates that in addition to controlling the regenerative response, MET and EGFR synergistically control baseline liver homeostasis in normal mice in such a way that their combined disruption leads to liver failure and death.
We used microarrays to detail the global programme of gene expression in Delta MET + EGFRi mice liver  vs control mice liver

overall_design: Systemic disruption of MET-EGFR signaling pathway in mice was carried out by using a tamoxifen inducible system to systemically delete exon 16 of MET; EGFR was inhibited by using Canertinib added to diet begining 4-day after tamoxifen clearence. Animals were sacrificed at 7 and 10 days after start of Canertinib diet. Controls were administered corn oil (control vehicle, no Tamoxifen). To remain consistent, we also allowed these animals a 4-day resting period, and then harvested their livers 7 and 10 days later.

first: Anastasia

last: Tsagianni


title: Comparison of gene expression pattern between wild-type and RhoE knockout embryo hearts

status: Public on Jul 04 2018

city: Houston

first: Jiang

last: Chang

state: TX

address: 2121 W. Holcombe Blvd.

department: Center for Translational Cancer Research

institute: Texas A&M University Institute of Biosciences and Technology

summary:
RhoE is a small GTPase that regulates actin cytoskeleton organization and cell migration. This analysis aimed at exploring the physiological function of RhoE in heart by means of knockout mouse model.
We used microarrays to compare differentital gene expression profiles in wild-type and RhoE knockout embryo hearts.

overall_design: Genetrap strategy was introduced to generate global RhoE knockout mouse. RhoE knockout mice died between E10.5 and E12.5. Three littermate pairs of wild-type and global RhoE knockout mouse embryos were obtained at E10.5. Total RNA was isolated from the embryo heart tissue and used for cDNA preparation. Microarray was performed with the Affymetrix GeneChip Mouse Genome 430 2.0 Array.

first: Xiangsheng

last: Yang

first: Lixia

last: Diao

first: Jing

last: Wang

first: Yuan

last: Dai


title: Transcriptome of normal mammary glands of Sprague-Dawley rats at six stages of development: pre-pubertal, peri-pubertal, pubertal, lactation, adult parous and age-matched nulliparous

city: New York

first: Kalpana

last: Gopalakrishnan

state: NY

address: 1428 Madison Avenue, Atran Building 03-02

institute: Icahn School of Medicine at Mount Sinai

summary: There is a lack of systematic investigations of large-scale transcriptome patterns associated with normal breast development. Herein, we profiled whole-transcriptome (by microarrays) of normal mammary glands in female Sprague-Dawley rats, an animal model widely used in breast cancer research, across six distinctive developmental stages – pre-pubertal, peri-pubertal, pubertal, lactation, and adult parous and age-matched nulliparous.

overall_design: Female Sprague-Dawley rats examined in this study are part of controls for a study on effects of environmental chemicals on developing mammary glands. These rats were regularly gavaged with olive oil by gastric intubation, the vehicle for chemical treatment in the parent study. Animals were sacrificed at six developmental time-points reflective of distinct stages of mammary gland development – pre-pubertal (n=10), peri-pubertal (n=5), pubertal (n=5), lactation (n=3), adult parous (n=5) and age-matched nulliparous (n=5). Pre-pubertal animals were sacrificed at postnatal day (PND) 21, peri-pubertal group at PND 42 and pubertal group at PND 63. Animals in the lactation group were sacrificed at the end of lactation at lactating day 28 (PND 146). Parous and age-matched nulliparous animals were sacrificed at PND 181.

first: Susan

last: Teitelbaum

first: James

last: Wetmur

first: Fabiana

last: Manservisi

first: Laura

last: Falcioni

first: Simona

last: Panzacchi

first: Federica

last: Gnudi

first: Fiorella

last: Belpoggi

first: Jia

last: Chen


title: Cardiac fibroblasts behave differently to isoproterenol-induced injury based on their genetic variability

status: Public on Jul 02 2018

city: Los Angeles

first: Fides

last: Lay

address: 615 Charles E Young Drive South, BSRB 457

department: MCDB

institute: UCLA

summary:
The goal of this study is to characterize molecular mechanisms that regulate cardiac fibrosis
This study compare the fibrotic response of ISO-treated hearts in 3 strains of mice (B6, C3H and KK)

overall_design: Expression profiles of Thy1+ HE cells from saline and ISO-treated hearts (day 14 and 21) were generated using sequencing on the Illumina Hi-seq 3000 platform


title: Gene expression data from primary neuroblastoma tumors

city: Gent

first: Pieter

last: mestdagh

address: De Pintelaan 185

country: Belgium

institute: Center for Medical Genetics

summary: This dataset contains gene expression data from the NRC series (Neuroblastoma Research Consortium) for a total of 283 primary neuroblastoma tumors. All tumor samples are fully annotated including patient age at diagnosis, overall and progresison free survival and MYCN amplification status, enabling subgroup analysis, survival analysis and gene expression network analysis.

overall_design: 283 primary untreated neuroblastoma tumors were analyzed. No replicates were included.

first: Rogier

last: Versteeg

first: Jan

last: Koster

first: Alexander

last: Schramm

first: Johannes

last: Schulte

first: Angelika

last: Eggert

first: Luigi

last: Varesio

first: Angela

last: Sementa

first: Jo

last: Vandesompele

first: Frank

last: Speleman

first: Raymond

last: Stallings

first: Ingrid

last: Ora


title: RNA-seq analysis of Slc39a8(neo/neo) versus wild-type mice: yolk sac, placenta and fetal liver, kidney, lung, heart and cerebellum

status: Public on Jul 01 2018

city: Cincinnati

first: Jing

state: OH

address: 3333 Burnet Ave

institute: CCHMC

summary: Slc39a8 encodes ZIP8, a ubiquitous divalent cation/bicarbonate symporter expressed in pluripotent mouse embryonic stem cell; ZIP8 influxes Zn2+, Mn2+ and Fe2+. Slc39a8(neo/neo) knockdown mice globally exhibit 10-15% of wild-type ZIP8 mRNA and protein levels, and show a pleiotropic phenotype of stunted growth, neonatal lethality, multi-organ dysmorphogenesis, and dysregulated hematopoiesis manifested as severe anemia. Herein we performed transcriptomics of GD13.5 yolk sac and placenta, and GD16.5 liver, kidney, lung, heart and cerebellum, comparing Slc39a8(neo/neo) with wild-type. Meta-data analysis of differentially-expressed genes revealed 29 unique genes from all tissues –– having enriched GO categories associated with hematopoiesis and hypoxia and KEGG categories of complement, response to infection, and the coagulation cascade –– consistent with dysregulated hematopoietic stem cell fate. Based on transcription factor (TF) profiles in the JASPAR database, and searching for TF-binding sites enriched by Pscan, numerous genes encoding zinc-finger TFs and associated with hematopoietic stem cell functions were identified. We conclude that, in this mouse model, deficient ZIP8-mediated Zn2+ transport affects zinc-finger (e.g. GATA proteins) and other transcription-factors (e.g. TAL1) predominantly in yolk sac, strongly supporting the observed dysmorphogenesis and anemia phenotype.

overall_design: mRNA samples of Slc39a8(+/+) and Slc39a8(neo/neo) yolk sacs and placentas at GD13.5, fetal liver, kidney, lung, heart and cerebellum at GD16.5 were profiled in triplicate using Illumina HiSeq.

first: Marina

last: Gálvez-Peralta

first: Xiang

last: Zhang

first: Jingyuan

last: Deng

first: Zijuan

last: Liu

first: Daniel

middle: W

last: Nebert


title: Tesmall indentifies small RNAs associated with targeted inhibitor resistance in melanoma

status: Public on Jun 29 2018

city: Cold Spring Harbor

first: Molly

middle: Gale

last: Hammell

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are small 21-22nt RNAs that act to regulate the expression of mRNA target genes through direct binding to mRNA targets. While miRNAs typically dominate small RNA transcriptomes, many other classes are present including tRNAs, snoRNAs, snRNAs, Y-RNAs, piRNAs, and siRNAs. Interactions between processing machinery and targeting networks of these various small RNA classes remains unclear, largely because these small RNAs are typically analyzed separately. Here we present TEsmall, a tool that allows for the simultaneous processing and analysis of small RNAs from each annotated class in a single integrated workflow. The pipeline begins with raw fastq reads and proceeds all the way to producing count tables formatted for differential expression. Several interactive charts are also produced to look at overall distributions in length and annotation classes. We next applied the TEsmall pipeline to small RNA libraries generated from melanoma cells responding to targeted inhibitors of the MAPK pathway. Targeted oncogene inhibitors have emerged as way to tailor cancer therapies to the particular mutations present in a given tumor. While these targeted strategies are typically effective for short intervals, the emergence of resistance is extremely common, limiting the effectiveness of single-agent therapeutics and driving the need for a better understanding of resistance mechanisms. Using TEsmall, we identified several microRNAs and other small RNA classes that are enriched in inhibitor resistant melanoma cells in multiple melanoma cell lines and may be able to serve as markers of resistant populations more generally.

overall_design: Examination of  small RNAs in parental and derived BRAF inhibitor resistant cell lines

first: Kathryn

last: O'Neill

middle: G


title: Sorafenib resistance associated gene expression in renal cell carcinoma

status: Public on Jun 30 2018

first: Linhui

last: Wang

address: 415 Fengyang Road, 200003, Shanghai China

department: Department of Urology

institute: Changzheng Hospital, Second Military Medical University

summary: To identify deregulated lncRNAs responsible for sorafenib unresponsiveness,

overall_design: Samples (five sorafenib-responsive and five sorafenib-nonresponsive RCC tumor tissues) were performed by Affymetrix GeneChip® Whole Transcript Sense Target Labeling Assay. Quantile normalization and subsequent data processing were performed using Agilent Gene Spring Software 11.5. Heat maps representing differentially regulated genes were generated using Cluster 3.0 software

first: Zhipeng

last: Xu

first: Yi

last: Bao


title: The Replication-initiation determinant protein (RepID) modulates replication by recruiting CUL4 to chromatin

status: Public on Jun 27 2018

city: Bethesda

first: Christophe

middle: E

last: Redon

state: MD

address: 37 Convent Drive

institute: NIH

summary: Cell cycle progression in mammals is modulated by two ubiquitin ligase complexes, CRL4 and SCF, which facilitate degradation of chromatin substrates involved in the regulation of DNA replication. One member of the CRL4 complex, RepID (DCAF14/PHIP), is a WD40-containing protein that selectively binds and activates a group of replication origins. We found that RepID recruits the CRL4 complex to chromatin prior to DNA synthesis, thus playing a crucial architectural role in the proper licensing of chromosomes for replication. In the absence of RepID, cells rely on the alternative ubiquitin ligase, SKP2-containing SCF, to progress through the cell cycle. RepID depletion markedly increases cellular sensitivity to SKP2 inhibitors, which triggered massive genome re-replication. Both RepID and SKP2 interact with distinct, non-overlapping groups of replication origins, suggesting that selective interactions of replication origins with specific CRL components execute the DNA replication program and maintain genomic stability by preventing re-initiation of DNA replication.

overall_design: Nascent strands were purified with the lambda exonuclease methods from U2OS RepID WT or HCT116 RepID KO cells. Chromatin from unsynchronized untreated cultures of U2OS RepID WT cells was subjected to ChIP-Seq with antibody directed against CUL4A, H3K4me3 and H3K9me3. Chromatin from unsynchronized untreated cultures of U2OS FLAG-RepID-FL overexpressed stable cells was subjected to ChIP-Seq with antibody directed against CDT2. Chromatin from unsynchronized untreated cultures of HCT116 RepID WT or RepID KO cells was subjected to ChIP-Seq with antibody directed against SKP2.

first: M

middle: I

last: Aladjem


title: A Porcine Model to Study the Effect of Neurologic Death (ND) on Kidney Genomic Responses

city: Irvine

first: Shlomit

last: Radom-Aizik

address: 101 Academy

department: Pediatrics

institute: University of California, Irvine

summary:
We investigated the porcine kidney genomic response six hours after brainstem herniation.
This study begins to identify the kidney underlying molecular mechanisms associate with the inflammatory process following neurologic death (ND), a first step towards optimizing the organ for successful transplant.

overall_design: Twenty porcine were randomized into two groups:  a control group (burr hole, catheters, and anesthesia only) and a ND group (control intervention plus inflation of subdural balloon catheter and confirmation of ND).

first: Mitchell

last: Sally

first: Darren

last: Malinoski

last: Zaldivar


title: Molecular profiling of ovarian carcinoma platinum-sensitive and -resistant cell lines

status: Public on Jun 26 2018

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

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

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

overall_design: Refer to individual Series


title: Molecular profiling of ovarian carcinoma platinum-sensitive and -resistant cell lines (microRNAs)

summary: Resistance to platinum compounds represents a major obstacle to the cure of ovarian carcinoma. The molecular profiling of drug-sensitive and drug-resistant cells may be helpful to clarify if altered expression of miRNAs can contribute to the drug-resistant phenotype. The expression pattern of miRNAs of three ovarian carcinoma cell lines was examined. The analysis revealed the modulation of several miRNAs in the two platinum-resistant cell lines as compared to parental platinum-sensitive cells. The integration of the information obtained through miRNA expression analysis may be useful to clarify the specific molecular alterations of factors and pathway favouring survival of tumor cells.

overall_design: To examine the expression patterns of miRNAs in platinum-sensitive cells versus platinum-resistant cells, we used three ovarian carcinoma cell lines: the parental cisplatin-sensitive IGROV-1 cell line, the platinum-resistant variants IGROV-1/Pt1, generated by exposure of parental cells to cisplatin and IGROV-1/OHP, obtained by exposure of parental cells to oxaliplatin. Three independent samples for each cell line were prepared. Exponentially growing cells were harvested using trypsin and counted. Cells were centrifuged and pellets (10 million cells/sample) were immediately frozen in liquid nitrogen. miRNAs were isolated and microarrays were run. Overall, nine samples were analysed consisting of three biological replicates for each cell line.

first: Laura

last: Gatti

first: Noemi

last: Arrighetti

first: Giacomo

last: Cossa

first: Paola

last: Perego


title: Leukocytes in non-tumor-bearing and tumor-bearing mice

status: Public on Jun 22 2018

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary: To clarify the functional role of migratory liver-resident leukocytes (LRLs) in the pre-metastatic lung, we identify differentially expressed genes and address biological significance in the liver.

overall_design: We analyzed gene expression profile by comparison among leukocytes from control and tumor-bearing mice.

first: Sachie

last: Hiratsuka

first: Hiroyuki

last: Aburatani

first: Yoshiro

last: Maru


title: RNA Sequencing Facilitates Quantitative Analysis of Wild Type and MEIS2 deleted H1 drived cells at day4 of hematopoietic differentiation.

status: Public on Jun 20 2018

city: Tianjin

first: Jiaxi

last: Zhou

state: Tianjin

address: 288# Nanjing Road, He ping district

institute: PUMC

summary:
Purpose: The goals of this study are to investigate the molecular mechanism by which MEIS2 controls HEP specification and EHT through compareing the mRNA profiling of Wild Type and MEIS2 deleted H1 drived cells at day4 of hematopoietic differentiation.
Methods: mRNA profiles of Wild Type and MEIS2 deleted H1 drived cells at day4 of hematopoietic differentiation were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Conclusions:a large number of genes were down-regulated in MEIS2-deleted H1 hESCs when compared with the wild-type cells. Among those, a number of mammalian hematopoiesis-associated genes such as TAL1 ,GFI and GATA2 were significantly down-regulated.

first: Hongtao

last: Wang


title: Gene expression data from E14.5 Pogz-WT and Pogz-KO fetal livers.

status: Public on Jun 21 2018

city: Frederick

first: Kristbjorn

middle: Orri

last: Gudmundsson

address: 1050 Boyles St.

department: MCGP

institute: NCI

summary: Fetal and adult β-globin gene expression is tightly regulated during human development. Fetal globin genes are transcriptionally silenced during embryogenesis through the process of hemoglobin switching. Efforts to understand the transcriptional mechanism(s) behind fetal globin silencing have led to novel strategies to derepress fetal globin expression in the adult, which could alleviate symptoms in hereditary b-globin disorders including sickle cell disease (SCD) and β-thalassemia. We identified a novel zinc finger protein, pogo transposable element with zinc finger domain (Pogz), expressed in mouse and human hematopoietic stem and progenitor cells, which represses embryonic b-like globin gene expression in mice. Ablation of Pogz expression in adult hematopoietic cells in vivo results in persistence of embryonic b-like globin expression without significantly affecting erythroid development or mouse survival. Elevated embryonic β-like globin expression correlates with reduced expression of Bcl11a, a known repressor of embryonic β-like globin expression, in Pogz-/- fetal liver cells. Pogz binds to the Bcl11a promoter, and, to erythroid specific intragenic regulatory regions. Importantly, Pogz+/- mice develop normally, but show elevated embryonic b-like globin expression in peripheral blood cells, demonstrating that reducing Pogz levels results in persistence of embryonic b-like globin expression. Finally, knockdown of POGZ in primary human CD34+ hematopoietic stem and progenitor cell derived erythroblasts, reduces BCL11A expression and increases fetal hemoglobin expression. These findings are significant since new therapeutic targets and strategies are needed to treat the increasing global burden of b-globin disorders.

overall_design: Total RNA was isolated from E14.5 Pogz-WT and Pogz-KO fetal livers (N=3 each genotype) and analyzed for differential gene expression using Affymetrix GeneChip Mouse Genome 430 2.0 arrays.

middle: O

first: Bjorg

last: Gudmundsdottir

first: Jonathan

last: Keller


title: LRL in liver and lung from tumor-stimulating mice.

city: Tokyo

address: 8-1 Kawada-cho Shinjyuku-ku

institute: Tokyo Women's Medical University

summary: To  understand the molecular mechanisms mediating Liver Resident Leukocytes (LRL) relocalization from the liver to the lungs in response to tumor progression, isolated  LRLs from the liver and lungs of tumor-stimulating mice using a cell sorter. LRLs remaining in the liver displayed increased liver signature when compared to those that migrated into the lungs.

overall_design: The isolated  LRLs in the liver and lungs of tumor condotioned media-stimulating mice using a cell sorter.

first: Takeshi

last: Tomita

first: Taishi

last: Mishima


title: Identification of Exosome-Like Nanoparticle Derived MicroRNAs from Eleven Edible Plants

status: Public on Jun 25 2018

city: Chengdu

first: Juan

last: Xiao

state: Sichuan

address: Huimin road No.211, Wenjiang

department: Institute of Animal Genetics and Breeding, College of Animal Science and Technology

institute: Sichuan Agricultural University

summary: In this study, we found that the highly expressed miRNAs appear in EPDELNs (Edible plant-derived exosome-like nanoparticles) have the potential to regulate human mRNA in a cross-kingdom manner. Target prediction and functional analysis revealed that highly expressed miRNAs were closely associated with inflammatory responses and cancer-related pathways. Therefore, we hypothesized that miRNAs in EPDELNs may be a crucial factor behind the regulatory function of EPDELNs.

sample_organism:
Actinidia chinensis
Cucumis melo
Pyrus
Glycine max
Lathyrus oleraceus
Solanum lycopersicum
Vaccinium
Cocos nucifera
Citrus x paradisi
Citrus reticulata
Zingiber officinale

overall_design: We investigated miRNA expression profiles from 11 EPDELNs (Blueberry; Coconut; Ginger; Grapefruit; Hami melon; Kiwifruit; Pea; Orange; Pear; Soybean; Tomato) by using high-throughput sequencing technology.

first: Siyuan

last: Feng


title: Identification of tomato genes responsive to loliolide, a metabolite of carotenoid metabolic pathways

status: Public on Jun 19 2018

city: Tsukuba

first: Shigemi

last: Seo

state: Ibaraki

address: 2-1-2 Kannondai

department: Plant and Microbial Research Unit, Division of Plant and Microbial Sciences

institute: National Institute of Agrobiological Sciences

summary: Loliolide, a metabolite of carotenoid metabolic pathways in plants, was identified as an inducer of resistance to herbivores such as the two-spotted spider mite, Tetranychus urticae, and the common cutworm, Spodoptera litura. To identify host factors involved in loliolide-induced herbivore resistance, microarray analysis of tomato plants treated with loliolide was performed. We identified several cell wall-associated defense genes as loliolide-responsive genes.

overall_design: Genes that were preferentially expressed in tomato (Solanum lycopersicum cv. Micro-Tom)  12 hours after treatment with loliolide were explored. The microarray analysis was performed in triplicate.

first: Mika

last: Murata

first: Yusuke

last: Nakai


title: Expression data from 7-month-old mdx mouse hearts wild-type and deficient for cardiomyocyte-specific IKKβ

status: Public on Jun 14 2018

city: Toledo

first: Jennifer

middle: M

last: Peterson

address: 2801 W Bancroft St

department: SERS

institute: The University of Toledo

summary: We found genetic deletion of IKKβ in mdx cardiomyocytes improved cardiac function and normalized calcium transients. We used microarrays to profile gene expression in hearts of mdx mice with intact IKKβ signaling and hearts of mdx mice with IKKβ-deficient cardiomyocytes to identify genes differentially regulated by NF-[kappa]B. signaling in dystrophic hearts.

overall_design: mdx mice conditionally deleted for IKKβ specifically in cardiomyocytes were created crossing IKKβ floxed mdx mice with mdx mice positive for the alpha myosin heavy chain (Myh6) promoter driving cre recombinase. Myh6 cre positive mice were our experimental mice and denoted “mdx heart Myh6-cre;IKKβ[delta]. Age matched littermates without the cardiac-specific Myh6 cre were our controls and denoted “mdx heart IKKβf/f”. RNA was prepared from 7-month-old whole hearts. 7 total samples were analyzed, 4 experimental and 3 control.

first: Denis

middle: C

last: Guttridge


title: Mutations in the SWI/SNF chromatin remodeling complex induce metabolic rewiring and dependence on oxidative phosphorylation [Affymetrix]

status: Public on Jun 17 2018

address: 1515 Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary: Lung cancer is a devastating disease that remains the top cause of cancer mortality. While targeted therapies against EGFR and EML4-ALK fusion and recent advances in immunotherapy have shown substantial clinical benefit for some patients, the vast majority of patients with lung cancer still lack effective therapies underscoring the dire need for more context-specific therapeutics. Cancer genomic studies have identified frequent genetic alterations in chromatin and epigenetic regulators including inactivating mutations in components of the SWI/SNF chromatin remodeling complex. In lung adenocarcinoma, about 20% of tumors have inactivating mutations in components of the SWI/SNF chromatin remodeling complex including SMARCA4 and ARID1A. With the aim of understanding the mechanism of tumor development driven by mutations in this complex, we developed a genetically engineered mouse (GEM) model of lung adenocarcinoma by selectively ablating Smarca4 in the lung epithelium. We demonstrate that Smarca4 acts as a bona fide tumor suppressor and cooperates with p53 loss and Kras activation. Cross species integrative gene expression analyses revealed signature of enhanced oxidative phosphorylation (OXPHOS) in SMARCA4 mutant murine as well as human lung adenocarcinomas. We further show that SMARCA4 mutant cells have increased oxygen consumption and increased respiratory capacity primarily driven by increased expression of the mitochondrial master regulator, PGC1-α. Importantly, we show that SMARCA4 and other SWI/SNF mutant lung cancer cell lines and xenograft tumors have exquisite sensitivity to inhibition of OXPHOS by a novel small molecule, IACS-010759, that is under clinical development. Mechanistically, we show that SMARCA4 deficient cells have a blunted transcriptional response to energy stress creating a therapeutically attractive collateral vulnerability. These findings provide the mechanistic basis for further development of OXPHOS inhibitors as therapeutics against SWI/SNF mutant tumors.

overall_design: Examination of gene expression changes upon glucose deprivation or IACS-10759 treatment in H1299 cells stably transduced with an inducible SMARCA4 vector upon doxycycline adminstration to induce expression of SMARCA4.

first: Yonathan

last: Deribe

first: Andrew

last: Futreal

first: Chia-Chin

last: Wu


title: Differential ageing of growth plate cartilage determines skeletal proportions

first: Julian

middle: CK

last: Lui

address: 10 Center Drive

institute: NICHD, NIH

summary: Bones at different anatomical locations vary dramatically in size.  The mechanisms responsible for these size differences are poorly understood.  Bone elongation occurs at the growth plates and advances rapidly in early life but then progressively slows due to a developmental program termed growth plate senescence. This developmental program includes declines in cell proliferation and hypertrophy, depletion of cells in all growth plate zones, and extensive underlying changes in the expression of growth-regulating genes. Here we use RNA-Seq to compare changes of gene expression with age in the longer bone (tibia, 1- vs 4-wk) with the difference of gene expression between long and short bones (tibia vs phalanx) at 1wk. We found that the developmental program of growth plate senescence is more advanced in the shorter bone and this differential senescence (or aging) underlies the disparities in bone length.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: tibia, 1wk vs 4wk; 1wk, tibia vs phalanx; in both mice and rats, proliferative zone or hypertrophic zone of growth plate (separated by laser capture microdissection)

first: Jeffrey

last: Baron


title: Microarray expression data of naïve CD4 and CD8 T cells stimulated with IL27.

city: Boston

first: Asaf

last: Madi

state: MA

address: 60 Fenwood Road, BTM 10016F

department: Neurology

institute: BWH

summary: Expression of co-inhibitory receptors, such as CTLA-4 and PD-1, on effector T cells is a key mechanism for ensuring immune homeostasis. Dysregulated co-inhibitory receptor expression on CD4+ T cells promotes autoimmunity while sustained overexpression on CD8+ T cells promotes T cell dysfunction or exhaustion, leading to impaired ability to clear chronic viral infections and cancer.  Here, we used RNA and protein expression profiling at single-cell resolution to identify a module of co-inhibitory receptors that includes not only several known co-inhibitory receptors (PD-1, Tim-3, Lag-3, and TIGIT), but also a number of novel surface receptors. We functionally validated two novel co-inhibitory receptors, Activated protein C receptor (Procr) and Podoplanin (Pdpn). The module of co-inhibitory receptors is co-expressed in both CD4+ and CD8+ T cells and is part of a larger co-inhibitory gene program that is shared by non-responsive T cells in multiple physiological contexts and is driven by the immunoregulatory cytokine IL-27. Computational analysis identified the transcription factors Prdm1 and c-Maf as cooperative regulators of the co-inhibitory module, which we validated experimentally. This molecular circuit underlies the co-expression of co-inhibitory receptors in T cells and identifies novel regulators of T cell function with the potential to regulate autoimmunity and tumor immunity.

overall_design: Gene expression analysis of IL-27 induced T cell gene signature invitro.


title: T Cell Genes Regulated by Short Chain Fatty Acids

status: Public on Jun 13 2018

city: West Lafayette

first: Chang

last: Kim

state: IN

address: 725 Harrison St

department: Comparative Pathobiology

institute: Purdue

summary: This is to determine the regulation of gene expression in different T Cell population with short chain fatty acids. This will provide the roles of SCFAs in regulation of adaptive immunity and T-cell-mediated inflammation.

overall_design: 3 groups T-Cell Subsets (Th17, Treg and Th1) with and without Short Chain Fatty Acid (sodium acetate at 10 mM). 2 arrays were used for Th1 and Treg while 3 arrays were used for Th17. T cells isolated from mouse lymphoid tissues were activated in vitro for 6-7 days in the presence or absence of acetate.

first: Jeongho

last: Park

first: Benjamin

middle: J

last: Ulrich

first: Ann

last: Feil


title: RBM-5 modulates U2AF large subunit-dependent alternative splicing in C. elegans

city: Changsha

first: Chuanman

last: Zhou

state: Hunan

address: Xiangya road 110

department: School of Life Sciences

institute: Central South University, Changsha, Hunan, China

summary: A key step in pre-mRNA splicing is the recognition of 3’ splicing sites by the U2AF large and small subunits, a process regulated by numerous trans-acting splicing factors. How these trans-acting factors interact with U2AF in vivo is unclear. From a screen for suppressors of the temperature-sensitive (ts) lethality of the C. elegans U2AF large subunit gene uaf-1(n4588) mutants, we identified mutations in the RNA binding motif gene rbm-5, a homolog of the tumor suppressor RBM5. rbm-5 mutations can suppress uaf-1(n4588) ts-lethality by loss of function and neuronal expression of rbm-5 was sufficient to rescue the suppression. Transcriptome analyses indicate that uaf-1(n4588) affected the expression of numerous genes and rbm-5 mutations can partially reverse the abnormal gene expression to levels similar to that of wild type. Though rbm-5 mutations did not obviously affect alternative splicing per se, they can suppress or enhance, in a gene-specific manner, the altered splicing of genes in uaf-1(n4588) mutants. Specifically, the recognition of a weak 3’ splice site was more susceptible to the effect of rbm-5. Our findings provide novel in vivo evidence that RBM-5 can modulate UAF-1-dependent RNA splicing and suggest that RBM5 might interact with U2AF large subunit to affect tumor formation.

overall_design: Detect expression differences between different strains during embryo development

first: Xiaoyan

last: Gao


title: Comparison of global gene expression in homeostatic and regenerating endothelium of the adult mouse aorta

status: Public on Jun 12 2018

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: We report the global transcript levels in an endothelial-enriched cell fraction from homeostatic and regenerating mouse aorta. These data provide insight into the molecular regulation of endothelial lining regenerating inside a large artery.

overall_design: Total RNA-seq comparing global gene expression in 4 conditions: 1) uninjured aorta segment 48 hours post-wound 2) endothelial fraction regenerating aorta 3 hours post-wound 3) endothelial fraction regenerating aorta 48 hours post-wound 4) tissue fraction of regenerating aorta 48 hours post-wound

first: Austin

last: McDonald

first: M

last: Iruela-Arispe


title: Utp14 interaction with the Small Subunit Processome.

city: Austin

first: Arlen

last: Johnson

state: Texas

address: 2506 Speedway

department: Molecular Biosciences

institute: The University of Texas

summary: The SSU Processome (sometimes referred to as 90S) is an early stable intermediate in the small ribosomal subunit biogenesis pathway of eukaryotes. Progression of the SSU Processome to a pre-40S particle requires a large-scale compaction of the RNA and release of many biogenesis factors. The U3 snoRNA is a primary component of the SSU Processome and hybridizes to the rRNA at multiple locations to organize the structure of the SSU Processome. Thus, release of U3 is prerequisite for the transition to pre-40S. Our lab proposed that the RNA helicase Dhr1 plays a crucial role in the transition by unwinding U3 and that this activity is controlled by the SSU Processome protein Utp14. How Utp14 times the activation of Dhr1 is an open question. Despite being highly conserved, Utp14 contains no recognizable domains, and how Utp14 interacts with the SSU Processome is not well characterized. Here, we used UV crosslinking and analysis of cDNA (CRAC) and yeast two-hybrid interaction to characterize how Utp14 interacts with the pre-ribosome. Moreover, proteomic analysis of SSU particles lacking Utp14 revealed that the presence of Utp14 is needed for efficient recruitment of the RNA exosome. Our analysis positions Utp14 to be uniquely poised to communicate the status of assembly of the SSU Processome to Dhr1 and possibly to the exosome as well.

overall_design: Data is available for two biological replicates for both Utp14-HTP (AJY4051) and an untagged control (BY4741).

first: Joshua

last: Black

first: Zhaohui

last: Wang

first: Lisa

last: Goering


title: RNA-Seq analysis of hearts from NBCe1 Na-HCO3 cotransporter cardiac conditional knockout (K) vs wild-type (W) mice

city: Cincinnati

first: Mario

last: Medvedovic

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: The purpose of this study was to investigate the hypothesis that cardiomyocyte-specific loss of the electrogenic NBCe1 Na+-HCO3- cotransporter is cardioprotective during in vivo ischemia-reperfusion (IR) injury. An NBCe1 (Slc4a4 gene) cardiac conditional knockout mouse (KO) model was prepared by gene targeting. Cardiovascular performance of wild-type (WT) and cardiac-specific NBCe1 KO mice was analyzed by intraventricular pressure measurements, and changes in cardiac gene expression were determined by RNA Seq analysis. Response to in vivo I/R injury was analyzed after 30 minutes occlusion of the left anterior descending artery followed by 3 hours of reperfusion. Loss of NBCe1 in cardiac myocytes did not impair cardiac contractility or relaxation and caused only limited changes in gene expression patterns, such as those for electrical excitability. However, following ischemia and reperfusion, KO heart sections exhibited significantly fewer apoptotic nuclei than WT sections. These studies indicate that cardiac-specific loss of NBCe1 does not impair cardiovascular performance, causes only minimal changes in gene expression patterns, and protects against I/R injury in vivo.

overall_design: An NBCe1 (Slc4a4 gene) conditional knockout mouse model was prepared. For cardiac myocyte-specific deletion of Slc4a4 exon 12, the mice were bred with a C57Bl6 mouse carrying the Cre recombinase gene driven by the β-myosin promoter, which is active in cardiac myocytes. Total RNA was isolated from whole hearts of 4-month-old male Slc4a4flx/flx and Slc4a4flx/flx(Cre) mice (n = 6 of each genotype). RNA Seq analysis was performed using the Illumina HiSeq 1000 platform, and sequence reads were aligned to the reference mouse genome using TopHat aligner. Statistical analysis was performed using the negative-binomial model of read counts. mRNA expression data are presented as Reads Per Kilobase per Million mapped reads.

first: K

last: Vairamani

first: V

last: Prasad

first: Y

first: W

last: Huang

last: Chen

first: J

middle: N

last: Lorenz

first: G

last: Shull


title: Gene expression induced by progesterone in mouse T cells

first: Chang

last: Kim

summary: To identify the genes that are induced by progesterone in T cells, naive mouse CD4+ T cells were treated with progesterone and TGFb1 or just TGFb1 alone. Then, Affymetrix gene chips were used to determine the T cell gene expression change with progesterone treatment.

overall_design: We compared the gene expression patterns of T cells treated with TGFb1 alone and TGFb1 and progesterone together.

middle: H

first: Seung

last: Kang

first: Ann

last: Feil

first: Benjamin

last: Ulrich

first: Jee

last: Lee


title: The role of Twist1 in mutant huntingtin-induced transcriptional alterations

status: Public on Jun 09 2018

city: St. Louis

first: Hiroko

last: Yano

address: 660 South Euclid Avenue

department: Neurological Surgery

institute: Washington University School of Medicine

overall_design: RNA-seq of wildtype and mutant Htt with control or Twist1 RNAi


title: Identification of chloroquine diphosphate as an autophagy inhibitor to treat PANC-1 cells [mRNA, circRNA, lncRNA]

city: Nanning

first: Qiao

last: Yu

address: Shuangyong road, qingxiu district，nanning

institute: First Affiliated Hospital of Guangxi Medical University

summary: Autophagy has been reported to be involved in the occurrence and development of pancreatic cancer. However, the mechanism of autophagy-related non-coding RNAs in pancreatic cancer remains largely unknown. In this study, we used microarrays to detect differential expression of mRNAs, miRNAs, lncRNAs and circRNAs post autophagy suppression by chloroquine diphosphate in PANC-1 cells.

overall_design: The autophagy-inhibited model was constructed with PANC-1 cells treated by chloroquine diphosphate. It was indicated that 100µM chloroquine diphosphate was the best choice to inhibit the autophagy of PANC-1 in humans.

first: Dan-ming

last: Wei

first: Meng-tong

last: Jiang

first: Peng

last: Lin

first: Hong

last: Yang

first: Yi-wu

last: Dang

first: Dan-yu

last: Liao

first: Dian-zhong

last: Luo

first: Gang


title: Identification of chloroquine diphosphate as an autophagy inhibitor to treat PANC-1 cells [miRNA]

overall_design: The autophagy-inhibited model was constructed with PANC-1 cells treated by chloroquine diphosphate. It was indicated that 100 uM chloroquine diphosphate was the best choice to inhibit the autophagy of PANC-1 in humans.

last: Chen


title: Identification of chloroquine diphosphate as an autophagy inhibitor to treat PANC-1 cells

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

overall_design: Refer to individual Series


title: Comparative analysis of cartilage tissue from ANP32A knockout mice and wildtype C57/Bl6 mice

status: Public on Jun 07 2018

city: Leuven

first: Rik

last: Lories

address: O&N1 Herestraat 49

department: Skeletal Biology and Engineering Research Center

institute: KU Leuven

summary: A genetic association between the ANP32A gene and osteoarthritis has been suggested. We compared transcriptome profiles of the articular cartilage and subchondral bone from mice deficient in ANP32A with wild-type mice to get insights into the role of ANP32A in the pathogenesis of ostearthritis.

overall_design: The articular cartilage and subchondral bone from the tibial plateau of the mouse knee joint was carefully dissected in one piece from 8-week-old ANP32 knockout mice and wild-type controls

first: Frederique

last: Cornelis

first: Silvia

last: Monteagudo


title: Isolation of A Unique Hepatic Stellate Cell Population Expressing Integrin a8 from Embryonic Mouse Livers

status: Public on Jun 06 2018

first: Kinji

last: Asahina

address: 1333 San Pablo Street

department: Pathology

institute: University of Southern California

summary:
There are a few markers for embryonic hepatic stellate cells in mouse embryonic livers
To identify genes expressed in embryonic hepatic stellate cells, we separated ALCAM+, ALCAM+ PDPN+, and ALCAM+ PDPN- cells from E12.5 mouse livers and analyzed these cells by microarray analysis. After finding expression of Itga8 in ALCAM+ PDPN- cells, we further separated ALCAM+ ITGA8- and ALCAM+ ITGA8+ cells and analyzed by microarray.

overall_design: Total RNA was extracted with RNAqueous Micro (Ambion) and the probes for the microarray were synthesized using the Ovation RNA amplification system V2 and FL-Ovation cDNA Biotin module V2 (Nugen). The labeled probes were hybridized with GeneChip Mouse Genome 430 2.0 arrays (Affymetrix) and signals were analyzed with Genomic Suite software (Partek).


title: Comparison of gene expressions between young and aged mice in the intestine, liver and spleen tissues

status: Public on Jun 02 2018

first: Yuki

last: Usui

state: Tokyo

address: 4-6-1 Shirokanedai, Mintato-ku, Tokyo, Japan

department: Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences

institute: The University of Tokyo

summary: We compared the gene expressions of the intestine, liver and spleen tissues between mice at 4 months of age and mice at 28 months of age. We used microarrays to examine the age-related changes of gene expressions of the jejunum, ileum, distal colon, liver and spleen in mice.   Abbreviations used: C, 28-month-old mice; Y, 4-month-old mice.

overall_design: We isolated the jejunum, ileum, distal colon, liver and spleen tissues from the ICR male mice at 4 months of age (n=6) and 28 months of age (n=9). Equal amounts of total RNA, previously extracted from the tissues of each mouse, were pooled and mixed for each group. The RNA mixtures (100 ng) were individually amplified using the GeneChip 3’IVT Express kit and then hybridized to an Affymetrix Mouse Genome 430 2.0 chip (GPL1261; 45,101 probes).

first: Yasumasa

last: Kimura

first: Takeshi

last: Satoh

first: Naoki

last: Takemura

first: Yasuo

last: Ouchi

last: Ohmiya

first: Kyosuke

last: Kobayashi

first: Hiromi

last: Suzuki

first: Satomi

last: Koyama

first: Satoko

last: Hagiwara

first: Hirotoshi

last: Tanaka

first: Seiya

last: Imoto

first: Gérard

last: Eberl

first: Yukio

last: Asami

first: Kosuke

last: Fujimoto

first: Satoshi

last: Uematsu


title: Effects of long-term intake of a yogurt fermented with Lactobacillus delbrueckii subsp. bulgaricus 2038 and Streptococcus thermophilus 1131 on mice