title: Tissue-Specific and Genetic Regulation of Insulin Sensitivity-Associated Transcripts in African Americans [skeletal muscle]

status: Public on Mar 04 2017

city: Winston-Salem

first: Jeff

last: Chou

state: NC

address: Medical Center Blvd

institute: Atrium Health Wake Forest Baptist

summary:
Context:
Compared with European Americans, African Americans (AAs) are more insulin resistant, have a higher insulin secretion response to glucose, and develop type 2 diabetes more often. Molecular processes and/or genetic variations contributing to altered glucose homeostasis in high-risk AAs remain uncharacterized.
Objective:
Adipose and muscle transcript expression profiling and genotyping were performed in 260 AAs to identify genetic regulatory mechanisms associated with insulin sensitivity (SI). We hypothesized that: 1) transcription profiles would reveal tissue-specific modulation of physiologic pathways with SI, and 2) a subset of SI-associated transcripts would be controlled by DNA sequence variants as expression quantitative traits, and these variants in turn would be associated with SI.
Design and Settings:
The cross-sectional research study was performed in a clinical research unit.
Participants:
Unrelated nondiabetic AAs were recruited for the study.
Main Outcome Measures:
SI was measured by frequently sampled iv glucose tolerance test.
Results:
The expression levels of 2212 transcripts in adipose and 145 transcripts in muscle were associated with SI. Genes involved in eIF2, eIF4-p70S6K, and mTOR signaling were modulated with SI in both tissues. Genes involved in leukocyte extravasation signaling showed adipose-specific regulation, and genes involved in oxidative phosphorylation had discordant regulation between tissues. Intersecting cis-expression quantitative trait loci results with data from transcript-SI association analysis identified cis-regulatory single nucleotide polymorphisms for 363 and 42 SI-associated transcripts in adipose and muscle, respectively. Cis-eSNPs for three SI-associated adipose transcripts, NINJ1, AGA, and CLEC10A were associated with SI. Abrogation of NINJ1 induction in THP1 macrophages modulated expression of genes in chemokine signaling, cell adhesion, and angiogenesis pathways.
Conclusion:
This study identified multiple pathways associated with SI; particularly discordant tissue-specific regulation of the oxidative phosphorylation pathway, and adipose-specific regulation of transcripts in the leukocyte extravasation signaling pathway that seem to be important in insulin resistance. Identification of single nucleotide polymorphisms associated with SI and with modulation of expression of SI-associated transcripts, including NINJ1, reveals novel genetic regulatory mechanisms of insulin resistance in AAs.

overall_design: We systematically analyzed genome-wide transcript expression profiles of subcutaneous adipose and skeletal muscle (insulin-responsive tissues) from a metabolically characterized cohort of unrelated and non-diabetic African Americans to idetify genes associated with gluco-metabolic phenotypes

first: Neeraj

middle: K

last: Sharma

first: Satria

middle: P

last: Sajuthi

middle: W

first: J

last: Calles-Escandon

first: Samantha

last: Rogers

first: Lijun

last: Ma

first: Nicholette

last: Palmer

first: David

last: McWilliams

first: John

last: Beal

first: Mary

middle: E

last: Comeau

first: Kristina

last: Cherry

first: Greg

last: Hawkins

first: Lata

last: Menon

first: Ethel

last: Kouba

first: Donna

last: Davis

first: Marcie

last: Burris

last: Byerly

first: L

last: Easter

first: Donald

last: Bowden

first: Barry

last: Freedman

first: Carl

last: Langefeld

first: Swapan

last: Das


title: Tissue-Specific and Genetic Regulation of Insulin Sensitivity-Associated Transcripts in African Americans

first: Jeff

last: Chou

country: USA

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

overall_design: Refer to individual Series


title: Expression data from the uterus of ovariectomized young adult rats treated for three days with E2, 3-MC, E2+3-MC

status: Public on Mar 07 2017

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary:
Examination of crosstalk between Aryl hydrocarbonreceptor (AHR) and Estrogen receptor (ER) in the rat uterus on the level of mRNA transcriptome
The study was designed to see the overall gene-expression change in the uterus induced by E2, the AHR ligand 3-MC alone and in combination with E2.

overall_design: Ovariectomized young adult rats were treated with vehicle control (DMSO), 4µg/kg/d 17β-Estradiol (E2), 15 mg/kg/d 3-Methylcholanthrene (3-MC) and E2 + 3-MC for three consecutive days. Uteri were obtained 24 h after the last treatment. Biological samples from three rats were analyzed for each treatment group.

first: Janina

last: Helle

first: Georg

last: Kretzschmar


title: Light and BcLTF3-dependent gene expression profiles in the phytopathogenic fungus Botrytis cinerea

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

country: France

institute: INRAE

summary: Full transcriptomes of the Botrytis cinerea wild-type strain B0510 and the null-mutant deltaBcLTF3, cultured in continuous darkness or submitted to a light stimulation, were compared to identify light- or/and BcLTF3-dependent genes.

overall_design: The Botrytis cinerea wild-type strain and the null-mutant deltaBcLTF3  were cultured for 54h in continuous darkness ; then, cultures were exposed for 60 min to light before harvest (L) or were harvested after additional 60 min darkness (D). 4 replicates were performed. The 12 total-RNA samples (4 conditions* 3 replicates) were used for hybridization on NimbleGen 4plex gene expression arrays (20,885 gene models from Botrytis cinerea with three 60-mer probes per gene).

first: Julia

last: Schumacher

first: Beate

last: Brandhoff

first: Anne

last: Dornieden

last: Simon


title: Using DNA microarray to screen intracellular signal pathways of hypoglycemic activity by electroacupuncture of Zusanli (ST36) acupoints in streptozotocin-induced rats with diabetes

status: Public on Mar 01 2017

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

country: Taiwan

institute: China Medical University

summary: The aim of this study is to screen the possible effective intracellular signaling pathways of EA on bilateral Zusanli acupoint (ST36) by DNA microarray in rats with diabetes.  Streptozotocin (STZ) rats with diabetes were randomly assigned to the experimental (EA) group or the control (non-EA) group. The exploratory methods for analysis in this study were the following points: (i) detecting plasma glucose levels (ii) pathway analysis by DNA microarray in rats' gastrocnemius muscle. The pathway analysis of DNA microarray showed that the insulin signaling pathway, PPAR signaling pathway, MAPK signaling pathway or Wnt signal pathway might be related to the hypoglycemic effect of STZ rats with diabetes induced by EA. Using DNA microarray would be helpful in screening the possible targets of signaling pathways. The hypoglycemic effect of EA was close relative to insulin and relative intracellular signal pathways. Further research will be required to determine the details of the intracellular signaling pathways of the hypoglycemic effect induced by EA.

overall_design: STZ-induced diabetic rats were punctured at ST36 acupoint with 1.27 cm, 32 gauge acupuncture needles. After a 5-min needling period, EA was performed for 60 minutes at a frequency of 15 Hz with amplitude of 10 mA. Total RNA was then extracted from skeletal muscle for microarray analysis.

first: Tin-Yun

last: Ho


title: The genes regulated by JAK2 and Lnc-BM in breast cancer brain metastasis cells (231-BM, derived from MDA-MB-231 cells) treated with Oncostatin M (OSM)

city: Houston

first: chunru

last: lin

state: TX

address: 1515 Holcombe Blvd

department: Molecular & Cellular Oncology

institute: MD Anderson Cancer Center

summary: A long noncoding RNA (Lnc-BM) mediates JAK2 activity in 231-BM cells treated with OSM. Emerging evidence has shown that the effect of JAK2 is mainly mediated by three downstream signaling pathways including the AKT, MAPK, and STAT1/3/5 pathways. To determine the signaling pathways that are regulated by Lnc-BM, we performed gene expression microarray analysis on cells with Lnc-BM depletion or JAK2 KO and compared them to their corresponding controls following OSM stimulation.

overall_design: We performed cDNA microarray analysis to compare Lnc-BM stably knockdown 231-BM cell or JAK2 knockout (KO) 231-BM cell with its respcective control cells treated with or without OSM.

first: Shouyu

last: Wang

first: Liuqing

last: Yang

first: Chunru

last: Lin


title: Expression data from budding yeast exposed to simulated asbestos mine drainage

status: Public on Feb 24 2017

city: Northfield

first: Heather

middle: Elizabeth

last: Driscoll

state: VT

address: 158 Harmon Drive

department: Biology

institute: Norwich University

summary: Investigation of global gene expression changes in Saccharomyces cerevisiae strain NRRL Y-12632 (ATCC® 18824) grown in media made with asbestos mine tailings-laden water compared to the control grown in media made with double distilled water

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Total RNA was recovered from four Saccharomyces cerevisiae strain NRRL Y-12632 (ATCC® 18824) replicates exposed to simulated mine drainage for a 24 hour period and three Saccharomyces cerevisiae strain NRRL Y-12632 (ATCC® 18824) control replicates. Samples were run on Affymetrix Yeast Genome 2.0 Arrays.

first: Janet

middle: M

last: Murray

first: Elizabeth

middle: D

last: Dolci

first: Erika

middle: L

last: English


title: Colonic Gene expression in mice colonized with human gut microbiota from healthy and IBS patients

status: Public on Mar 02 2017

city: Hamilton

first: Premysl

last: Bercik

address: 1280 Main Street West

department: Medicine

country: Canada

institute: McMaster University

summary: Irritable Bowel Syndrome (IBS) is a disorder of the gut-brain axis, characterized by altered gut function and frequent psychiatric co-morbidity. Although altered intestinal microbiome profiles have been documented, their relevance to the clinical expression of IBS is unknown. To evaluate a functional role of the microbiota, we colonized germ-free mice with fecal microbiota from healthy controls or IBS patients with accompanying anxiety, and monitored gut function and behavior.  Mouse microbiota profiles clustered according to their human donors. Despite having taxonomically similar composition as controls, mice with IBS microbiota had distinct serum metabolomic profiles related to neuro- and immunomodulation. Mice with IBS, but not control microbiota, exhibited faster gastrointestinal transit, intestinal barrier dysfunction, innate immune activation and anxiety-like behavior. These results support the notion that the microbiota contributes to both intestinal and behavioral manifestations of IBS and rationalize the use of microbiota-directed therapies in ameliorating IBS.

overall_design: We extracted total RNA of colonic tissues extracted from germ-free NIH swiss mice (10-12 weeks) colonized with healthy human gut microbiota (10 mice per fecal sample, 5 fecal samples, total=50 mice), and mice colonized with human microbiota of IBS patients (10 mice per sample, 6 fecal samples, total =60 mice). We then pooled together all the RNA samples of all the mice colonized with the same microbiota, to form a  representative sample for the colonization with that specific human fecal sample. We finally ran 11 samples in total through the NanoString nCounter® Gene Expression CodeSet for mouse inflammation genes.

first: Giada

last: De Palma


title: Cancer-associated adipocytes microRNA

status: Public on Mar 09 2017

city: Seoul

first: Hyeong-Gon

last: Moon

address: 101, Daehak-ro Jongno-gu

department: Surgery

country: South Korea

institute: Seoul National University Hospital

summary: The role of adipocytes in cancer microenvironment has gained focus during the recent years. However, the characteristics of the cancer-associated adipocytes (CAA) in human breast cancer tissues and the underlying regulatory mechanism are not clearly understood. We reviewed pathology specimens of breast cancer patients to understand the morphologic characteristics of CAA, and profiled the mRNA and miRNA expression of CAA by using indirect co-culture system in vitro.

overall_design: We analyzed transcriptional changes in adipocytes (3T3-L1) induced by the paracrine effect of breast cancer cell MCF7 and MDA-MB-231 by using indirect co-culture system. Differentiated adipocytes were cultured in the bottom chamber of the transwell co-culture system with or without the breast cancer cells seeded in the top inserts. After the co-culture for certain periods, the adipocytes at the bottom wells were collected and used for further analysis.

first: Jiwoo

last: Lee


title: The B-cell receptor confers super competitor status to lymphoma cells via GSK3β inhibition I

status: Public on Apr 11 2017

city: Milan

first: Federica

last: Zanardi

address: via Adamello 16

country: Italy

institute: IFOM, the FIRC Institute of Molecular Oncology

summary:
Similar to resting mature B cells, where the B-cell antigen receptor (BCR) is essential for cellular survival, surface BCR expression is conserved in most mature B cell lymphomas. The identification of activating BCR mutations and the growth disadvantage upon BCR knockdown of cells of certain lymphoma entities has led to the view that BCR signaling is required for tumour cell survival. Consequently, the BCR signaling machinery has become a new target in the therapy of B cell malignancies. Here, we studied the effects of BCR ablation on MYC-driven mouse B cell lymphomas and compared them to observations in human Burkitt lymphoma. Whereas BCR ablation did not, per se, significantly affect lymphoma growth, BCR-negative (BCR-) tumour cells rapidly disappeared in the presence of their BCR-expressing (BCR+) counterparts in vitro and in vivo. This required neither cellular contact, nor factors released by BCR+ tumour cells. Instead, BCR loss induced the rewiring of central carbon metabolism increasing the sensitivity of receptor-less lymphoma cells to nutrient restriction. The BCR attenuated GSK3β activity to support MYC-controlled gene expression. BCR- tumour cells exhibited increased GSK3β activity and were rescued from their competitive growth disadvantage by GSK3β. BCR-negative lymphoma variants that restored competitive fitness, normalized GSK3β following constitutive activation of the MAPK pathway, commonly through Ras mutations. Similarly, in Burkitt lymphoma, activating RAS mutations may propagate Ig-crippled tumour cells, which usually represent a minority of the tumour bulk. Thus, while BCR expression enhances lymphoma cell fitness, BCR-targeted therapies may profit from combinations with drugs targeting BCR-less tumour cells.
In this dataset, we included the expression data obtained from BCR-positive (BCR+) and BCR-negative (BCR-) lymphoma cells co-cultured for 4 days in presence or absence of GSK3b inhibitor, CHIR99021. These data were used to obtain genes that are regulated by the BCR through GSK3b inhibition.

overall_design: BCR-positive (BCR.POS) and BCR-negative (BCR.NEG) lymphoma cells from 3 independent lymphomas (#2564, #2646, #2676) were co-cultured for 4 days in presence or absence of CHIR99021 (CT). BCR-positive and BCR-negative cells were sorted when counterselection of latter population was observed (4 days). Total RNA was extracted and gene expression profiling was performed on Affymetrix Mouse Gene 1.1 ST Arrays

first: Gabriele

last: Varano

first: Simon

last: Raffel

first: Martina

last: Sormani

first: Silvia

last: Lonardi

first: Christin

last: Zasada

first: Laura

last: Perucho

first: Valentina

last: Petrocelli

first: Andrea

last: Haake

first: Albert

first: M

last: Bugatti

first: Ulrike

last: Paul

first: Eelco

last: Van Anken

last: Pasqualucci

first: Raul

last: Rabadan

first: Reiner

last: Siebert

first: Stefan

last: Kempa

first: Maurilio

last: Ponzoni

first: Fabio

last: Facchetti

first: Klaus

last: Rajewsky

first: Stefano

last: Casola


title: Enhancer Remodeling during Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacologic Targeting of the P-TEFb Complex

status: Public on Mar 31 2017

city: Chapel Hill

first: Charles

middle: M.

last: Perou

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Triple negative breast cancer (TNBC) is heterogeneous with patients exhibiting at least two molecular subtypes, basal-like (BL) and claudin-low (CL). MEK inhibitor (MEKi) treatment of BL and CL cell lines and mouse model tumors induced subtype-specific alterations in overall kinome activity referred to as protein kinase reprogramming. BL- and CL-specific reprogramming involving increases in receptor tyrosine kinases was also seen in TNBC patients comparing tumor samples before and after a one week treatment with the MEKi, trametinib. Combination of kinase inhibitors targeted to the BL and CL reprogrammed signatures would need to be individually selected due to the heterogeneous resiliency of BL and CL kinomes. To overcome this “reprogramming dilemma” we targeted the transcriptional co-activator BRD4 with BET bromodomain inhibitors, JQI and IBET151; both strongly inhibited kinome reprogramming and onset of MEKi resistance in BL and CL cells. Targeting chromatin modifiers may therapeutically block resistance due to kinome reprogramming.BL and CL TNBC are commonly treated as a single disease despite genomic studies showing they represent distinct molecular subtypes1.  Recent Cancer Genome Atlas data demonstrated that the 518 protein kinases in the human genome (the kinome) were infrequently mutated in BL breast cancer; however, EGFR, KRAS and BRAF were amplified in 22, 32 and 31% of BL tumors, respectively. These findings are consistent with frequent activation of the BRAF-MEK-ERK pathway in TNBC2,3 and inhibitors targeting kinases in this pathway are currently in clinical trials for TNBC. As single agents, targeted kinase inhibitors generally fail to sustain durable responses when used to treat a range of human cancers including TNBC4-6. Onset of kinase inhibitor resistance can be due to selection of mutations in the targeted kinase7,8, activating mutations or amplification of RAS or downstream kinases9,10 or kinome reprogramming, a process in which there are system-wide changes in kinase networks11-13. Each of these resistance mechanisms allows the cancer cell to circumvent the targeted inhibition of specific kinases14. We previously developed chemical, proteomic methods that assay the activation state of protein kinases en masse15,16. Our methods utilize ¬Multiplexed Inhibitor Beads (MIBs), mixtures of covalently immobilized, linker adapted, kinase inhibitors. The immobilized inhibitors are primarily type I kinase inhibitors that preferentially bind activated (versus inactive) kinase17. Kinase capture is highly reproducible and is a function of kinase affinity for different immobilized inhibitors as well as the kinase activation state. Activated kinases preferentially bind, inactive kinases do not. By coupling MIB capture with mass spectrometry (MIB/MS), the technique allows quantitative interrogation of hundreds of kinases in a single mass spectrometry run. This also interrogates kinases known by sequence but which have been understudied due to lack of reagents such as specific phospho-antibodies. We report here both in preclinical models and patients that BL and CL TNBC have different baseline kinome activation states and both respond differently to MEKi with subtype-specific tyrosine kinase reprogramming. To avoid treatment strategy that uses multiple kinase inhibitors in individual patients, we discovered a novel pharmacologic strategy to block the initial reprogramming response to MEKi involving inhibition of epigenetic processes.

overall_design: reference x sample

first: James

middle: S

last: Duncan

first: Gary

last: Johnson


title: Tissue-Specific and Genetic Regulation of Insulin Sensitivity-Associated Transcripts in African Americans [subcutaneous adipose]

first: Jeff

last: Chou

first: Neeraj

last: Sharma

first: Satria

last: Sajuthi

first: J

last: Calles-Escandon

first: Samantha

last: Rogers

first: Lijun

last: Ma

first: Nicholette

last: Palmer

first: David

middle: R

last: McWilliams

first: John

last: Beal

first: Mary

last: Comeau

first: Kristina

last: Cherry

first: Greg

middle: A

last: Hawkins

first: Lata

last: Menon

first: Ethel

last: Kouba

first: Donna

last: Davis

first: Marcie

last: Burris

first: Sara

middle: J

last: Byerly

first: L

last: Easter

first: Donald

last: Bowden

first: Barry

middle: I

last: Freedman

first: Carl

last: Langefeld

first: Swapan

last: Das


title: Gene expression analysis in AML cells lines, AML primary blasts and in CD34+ normal progenitors after 6-hour exposure to HDACi

city: Naples

first: Angela

last: Nebbioso

state: Italy

address: Vico Luigi De Crecchio 7

department: Biophysics, Biochemestry and General Patology

institute: Seconda Università degli Studi di Napoli


title: miRNA expression data from neonatal rat ventricular myocytes (NRVM) silenced for KChIP2

status: Public on Feb 20 2017

city: Columbus

first: Thomas

last: Hund

state: OH

address: 473 W 12th Ave

institute: Ohio State University

summary: Loss of KChIP2 during cardiac stress has been suggested to have a transcriptional impact on cardiac ion channels through altered miRNA activity, contributing to maladaptive electrical remodeling. Therefore, we tested the consequence of KChIP2 loss, in the absence of cardiac stress, by treating cultured neonatal rat ventricular myocytes with siRNA for KChIP2 and subsequently performed miRNA microarray analysis to identify up-regulation of potential miRNA targets.

overall_design: NRVMs were isolated from the hearts of neonatal (day 1-2) Sprague Dawley rats. They were subsequently plated and cultured for 24-36 hrs then treated with either a control or KChIP2 siRNA. Cells were left in culture for an additional 72 hrs following siRNA delivery, after which they were collected for total RNA.


title: Gene expression analysis in wild-type and OsHOX24 Arabidopsis overexpression line

status: Public on Feb 14 2017

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

summary:
Homeobox transcription factors are known to regulate plant growth and development. Recently, they have also been implicated in abiotic stress responses. To analyze the role of HD-ZIP I subfamily member, OsHOX24, we constitutively overexpressed it in Arabidopsis. The physiological analyses revealed that overexpression of OsHOX24 gene severely reduced abiotic stress tolerance in transgenic plants as compared to wild-type.
We used microarrays to study the global effect of OsHOX24 overexpression in Arabidopsis under control condition.

overall_design: Wild-type and transgenic Arabidopsis seedlings were grown on MS medium for 10-days in a culture room with a daily photoperiodic cycle of 14 h light and 10 h dark. The 500 ng of total RNA sample isolated from each tissue sample was processed for microarray analysis according to Affymetrix protocol. Three biological replicates for each sample of wild-type and OsHOX24 overexpression line were used for microarray analysis.

first: Annapurna

last: Bhattacharjee


title: Development of DNA demethylation technology in HEK293T cells

status: Public on Feb 09 2017

city: Sendai

first: Shinichi

last: Fukushige

address: 2-1 Seiryo-machi, Aoba-ku

department: Department of Diabetes, Metabolism and Endocrinology

country: Japan

institute: Tohoku University Graduate School of Medicine

summary: DNA demethylating agents are epigenetic drugs for the therapy of myeloid leukemias. They not only induce DNA demethylation but also have significant cytostatic and cytotoxic effects, however, the relationships between these characteristics have not been established yet due to the lack of method to induce only DNA demethylation. Here we show that a fusion protein comprising the methyl-CpG binding domain (MBD) and the catalytic domain of Ten-eleven translocation protein 1 (TET1-CD) globally demethylates and upregulates a number of methylated genes. Gene expression microarray analyses using human embryonic kidney cell line 293T indicate that cells expressing wild-type (wt) TET1 catalytic domain with MBD (MBD-TET1-CDwt) upregulated more genes than ones expressing TET1-CDwt without MBD or catalytically inactive TET1-CD mutant (mut) with MBD (MBD-TET1-CDmut) and their upregulated genes frequently contained CpG islands (CGIs) within ± 1,000 bp of the transcription start site (TSS). Interestingly, 88% of genes upregulated 5-fold or more by MBD-TET1-CDwt were also reactivated after treatment with DNA demethylating agent, 5-azacytidine, suggesting that gene reactivation by both methods is primarily based on DNA demethylation.

overall_design: HEK293T cells were transfected with pcDNA6/myc-His vector,  pcDNA6-TET1-CDwt, pcDNA-MBD-TET1-CDwt, or pcDNA6-MBD-TET1-CDmut and two independent stable transformants expressing vector, TET1-CDwt, MBD-TET1-CDwt, or MBD-TET1-CDmut were constructed respectively. RNAs from these eight stable cell lines were prepared and analyzed by Agilent Human Gene Expression 4x44K v2 Microarray.

first: Yasuhiko

last: Mizuguchi


title: Expression analysis of EDS1-NLS

city: Wuhan

first: Kenichi

last: Tsuda

address: No.1 Shizishan Road

country: China

institute: Huazhong Agricultural University

summary: TIR-type nucleotide-binding leucine-rich repeat domain proteins (TNLs) constitute one major group of immune receptors in dicotyledonous plants. Under normal conditions, TNLs can detect non-self or modified-self within the plant cytoplasm to activate immune signaling characterized by extensive transcriptional reprogramming and efficiently counteracting pathogen infection. At the same time, TNLs, in negative epistatic interaction with a second endogeneous locus or allele are causal for induction of autoimmunity or hybrid necrosis. Both native, pathogen-induced TNL responses and autoimmunity are fully dependent on the plant-specific lipase-like protein EDS1, which is a central integrator for all TNL-mediated responses. EDS1 signals within structurally similar, but spatially distinct complexes with PAD4 and SAG101. We here analyzed stable transgenic lines expressing an EDS1 fusion with enforced nuclear localization. Even in absence of SAG101, nuclear-localized EDS1-PAD4 complexes are fully sufficient to function in basal and effector-triggered immunity. Furthermore, we show that nuclear EDS1, when expressed to high levels, can induce autoimmuity in combination with an RPP1-like gene cluster from ecotype Ler. RPP1-like genes are also implicated in several cases of hybrid necrosis, and we can identify the RPP1 paralog R8 as causal for autoimmunity induction by nuclear EDS1 and a previously characterized, EMS-induced mutation. This highlights the important role of EDS1-family proteins in the nuclear compartment in different immune-like responses.

overall_design: A 6 DNA microarray study using total RNA from EDS1-NLS and the wild type with three biological replicates.

first: Nora

last: Peine

first: Jane

last: Parker


title: Transcriptional expression profiling of the two aneuploidies in Arabidopsis

status: Public on Feb 08 2017

city: Taipei

first: Wan-Sheng

last: Lo

state: Taiwan

address: 128 Academia Road, Section 2, Nankang

department: IPMB

institute: Academia Sinica

summary:
There are various levels of aneuploidies in nature and many of them are highly associated with human tumer cells and genetic diseases.
To understanding the transcriptional profiling of different levels of anuploidies, the wild type Col, trisomy 2, and tertiary trisomy 2 identified in Arabidopsis were studied by using Affymetrix ATH1 GeneChips.

overall_design: Three samples (the wild type Col-0, trisomy 2, and tertiary trisomy 2) were analyzed.

first: Kuan-Lin


title: Identification of genes responsible for DNA damage induced senescence

city: Kobe

first: Shinji

last: Kamada

address: 1-1 Rokkodai-cho, Nada-ku

institute: Kobe University

summary: Cellular senescence is defined as permanent growth arrest induced by various stresses.  Although the transcriptional activity of p53 is essential for senescence induction, the downstream genes that are crucial for senescence remain unsolved. We developed an experimental system in which either senescence or apoptosis is specifically induced in the same cell line (hepatocarcinoma HepG2 cells having the intact p53 gene) by altering concentrations of a DNA-damaging drug and compared gene expression profiles by using microarray analysis to distinguish genes specific for senescence from those universally respond to DNA damage. When we compared the expression profiles at low versus high doses of etoposide, 20 genes were found to be differentially upregulated by more than 2-fold at a low dose of etoposide, which are expected to function in senescence induction. Microarray results were further confirmed by qPCR.

overall_design: DNA damage induced gene expression in human HepG2 cells was measured at 30 hours after treatment with etoposide at 0, 10, and 100 uM.


title: Effects of Long-term Exercise on Age-related Hearing Loss in Mice

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

summary: Regular exercise significantly slowed age-related hearing loss (AHL) and cochlear degeneration in a well- established murine model.

overall_design: We examined the effects of long-term voluntary wheel running on age-related hearing loss in CBA/CaJ mice, a well-established model of AHL. The CBA/CaJ mouse strain displays late-onset age-related hearing loss by 18-20 months of age and is a widely used model of AHL

first: Chul

last: Han

first: Dalian

last: Ding

first: Maria-Cecilia

first: Senthilvelan

last: Manohar

first: Yanping

last: Zhang

first: Mi-Jung

last: Kim

first: Hyo-Jin

last: Park

first: Karessa

last: White

first: Yong

middle: H

first: Paul

last: Linser

first: Masaru

last: Tanokura

first: Christiaan

last: Leeuwenburgh

first: Henry

last: Baker

first: Richard

last: Salvi

last: Someya


title: A global transcriptome analysis of skin wounds of diabetic mice (db/db) treated with miR-132 or control mimics

status: Public on Feb 01 2017

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

country: Sweden

institute: Karolinska Institutet

summary:
MiR-132 is one of the most upregulated miRNAs in human skin wounds at the inflammatory phase of healing. MiR-132 inhibits inflammation but promotes growth of epidermal keratinocytes, indicating that it may facilitate the inflammatory-proliferative phase transition during wound repair.
Following this line of research, here we evaluated the therapeutic potential of miR-132 in chronic wound using mouse in vivo wound model.
We performed a global transcriptome analysis of skin wounds of leptin receptor-deficient (db/db) mice treated with miR-132 or control mimics. Db/db mouse has been used as a type 2 diabetic model with impaired wound healing capacity.

overall_design: Expression profiling of skin wounds of db/db mice locally treated with miR-132 or control mimics for 6 days (5 mice in each group) was performed using Affymetrix mouse Clariom™ D assay.

middle: X

last: Landén


title: Expression Data from Arabidopsis suspension T87 cells, protoplasts, and osmotic stress-treated cells

city: Ikoma

first: Arata

last: Yoneda

address: 8916-5 Takayama

department: Graduate school of Biological Science

institute: Nara Institute of Science and Technology

summary:
Primary cell wall (PCW) in plant mainly consists of three kinds of polysaccharides, cellulose, hemicellulose, and pectin. Although many genes encoding a variety of enzymes involved in synthesis, degradation, or modification of the PCW-related polysaccharides have been reported, regulation on expression of these PCW-related genes during PCW formation is still not fully understood. In this study, expression changes of PCW-related genes were analyzed during PCW regeneration in protoplasts.
We used microarrays to reveal the global gene expression response against primary cell wall integrity stress during the primary cell wall regeneration in protoplasts.

overall_design: 4-day-old Arabidopsis T87 suspension cells were collected as the intact samples. The 4-day-old T87 cells were treated with enzyme mixture containing 1% cellulase Onozuka RS and 0.5% pectolyase Y-23 in 0.35 M mannitol for 1.5 h on a shaker at 50 rpm at 22 °C to digest the primary cell wall completely. Then the cells were washed by 0.4M mannitol three times, and re-suspended into the medium containing 0.4M mannitol. After 3 hours incubation at 22 °C, the cell wall-digested cells were collected as the protoplast samples. Also, 4-day-old T87 cells were treated with the medium containing 0.4M mannitol for 3 hours, and were collected as the osmotic stress-treated samples. Three independent biological replicate samples were obtained for RNA extraction and Affymetrix ATH-1 microarray.

first: Ryosuke

last: Sano

first: Taku

last: Demura


title: Ionomycin Treatment Renders NK cells Hyporesponsive

status: Public on Jan 29 2017

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

summary: Natural killer cells are cytotoxic lymphocytes important in immune responses to cancer and multiple pathogens. However, chronic activation of NK cells can induce a hyporesponsive state. The molecular basis of the mechanisms underlying the generation and maintenance of this hyporesponsive state are unknown, thus an easy and reproducible mechanism able to induce hyporesponsiveness on human NK cells would be very useful to gain understanding of this process. Human NK cells treated with ionomycin lose their ability to degranulate and secrete IFN-γ in response to a variety of stimuli, but IL-2 stimulation can compensate these defects. Apart from reductions in the expression of CD11a/CD18, no great changes were observed in the activating and inhibitory receptors expressed by these NK cells, however their transcriptional signature is different to that described for other hyporesponsive lymphocytes.

overall_design: Four biological replicated per sample type were analyzed by two-color agilent microarrays (AGILENT human gene expression 4x44K v2). Dye swap were applied to minimize dye biases.

first: Gema

last: Romera-Cárdenas

first: L

last: Thomas

first: Sheila

last: Lopez-Cobo

first: Eva

last: García-Cuesta

first: Eric

middle: O

last: Long

first: Hugh

middle: T

last: Reyburn


title: TGF-beta/atRA induced Tregs express a selected set of microRNAs involved in the repression of transcripts related to Th17 differentiation [miRNA]

status: Public on Jan 20 2017

city: Ribeirao Preto

first: Rodrigo

middle: Alexandre

last: Panepucci

state: São Paulo

address: R. Tenente Catao Roxo, 2501

country: Brazil

institute: Regional Blood Center of Ribeirâo Preto (FUNDHERP, HC-FMRP-USP)

summary: Regulatory T cells (Tregs) are essential regulators of immune tolerance. In light of its potential therapeutic use, in conditions involving transplant rejection and autoimmune disorders, understanding the mechanisms involved in the polarization between inflammatory and regulatory cells is of great importance. Although several studies have shown that atRA and TGF-β can inhibit the polarization of naïve T cells into inflammatory Th17 cells, favoring the generation of stable FOXP3 expressing iTregs, the exact regulatory mechanisms involved are not fully understood. Increasing evidences have suggested several roles for microRNAs in the development and function of different types of T helper cells; however, the roles of individual microRNAs in Tregs function and development are largely unexplored. Here, we explored how atRA may post-transcriptionally regulate distinct signaling pathways, through the induction of specific microRNAs, controlling the balance between Th17 and T regulatory cells. For this, CD4+CD25-CD45RA+ naïve T cells were immunomagnetically isolated from umbilical cord blood and activated with anti-human CD2/CD3/CD28 beads in the presence of IL-2 alone (CD4Med) or with the addition of TGF-β and atRA (CD4TGF/atRA). Immunophenotyping by flow cytometry, whole genome mRNAs and microRNAs profiling and functional characterizations were performed. We report the generation of highly suppressive CD4+CD25hiCD127-FOXP3+ iTregs in the CD4TGF/atRA condition, that exclusively express a set of microRNAs predicted to target important signaling pathways, including PI3K/Akt, mTOR, Toll-Like Receptor, and IL-6/Jak/Stat. Accordingly, percentages of IL-17 and STAT3 expressing cells were strikingly reduced in CD4TGF/atRA condition. Microarray and qPCR results showed that the expression of IL6R, IL6ST, JAK1 and STAT3 (heavily targeted by identified miRs) are all downregulated in CD4TGF/atRA, as compared to CD4med and naïve T cells. Finally, we show that selected synthetic mimics (namely, miR-23a, -30a, -636 and -1299) are able to knockdown IL6R and IL6ST transcript levels, functionally inhibiting IL-17 expression and favoring the generation of FOXP3+ cells. Our work adds novel evidences supporting the central roles played by microRNAs in the post-transcriptional regulation of major pathways involved in the generation and function of regulatory T cells.

overall_design: In order to identify potential microRNA/mRNA regulatory mechanisms involved in the specific roles of TGF-β and atRA in the generation of iTregs, we evaluated and compared the microRNA and mRNA expression profiles of fleshly isolated umbilical cord blood (UCB) naïve T cells and of cells activated with anti-human CD2/CD3/CD28 beads in the presence of IL-2 alone (CD4Med) or with the addition of TGF-β and atRA (CD4TGF/atRA). Microarray profiling was performed for freshly isolated naïve T cells and the corresponding CD4TGF/atRA and CD4Med cells, derived in culture, from three UCB samples (totaling 9 microarray profiles).

first: Josiane

last: Schiavinato

last: Haddad

first: Felipe

last: Saldanha-Araujo

first: João

last: Baiochi

first: Amélia

middle: G

last: Araújo

first: Priscila

last: Scheucher

first: Dimas

last: Covas

first: Marco

last: Zago


title: Acetylation enhances TET2 function in protecting against abnormal DNA methylation during oxidative stress [gene expression]

status: Public on Dec 31 2016

city: Baltimore

first: Stephen

middle: B

last: Baylin

state: MD

address: 1650 Orleans Street

department: Oncology

institute: Johns Hopkins University SOM

summary: Transcriptional profiling of A2780 cells with genetic TET2 knockout, generated by CRISPR. The aim was to identify genes affected by TET2 KO. Three individual KO clones were profiled. Control cells were cells that infected with control sgRNA.

overall_design: A2780 cells were infected with either Control or LentiCRISPR virus against TET2 genes for 2 days, followed by puromycin selection. Single clones were selected and validated after ~8 weeks selection in puromycin. Expression profiles of three TET2 KO clones were compared against those of two control clones prepared in parallel.

first: Yang

last: Zhang


title: CircRNA expression profiles for 6 human samples derived from patients with gastric cancer

status: Public on Jan 01 2017

city: Ningbo

first: Junming

last: Guo

address: 818 Fenghua Road

department: Department of Biochemistry and Molecular Biology, and Zhejiang Provincial Key Laboratory of Pathophysiology

institute: Ningbo University

summary: Investigation of circRNA expression profile of gastric cancer

overall_design: A six chip study using total RNA extracted from three gastric cancer tissues and three paracancerous tissues


title: A comparison of gene expression between the skin and flesh tissue of grape berries (CLAsf_05)

status: Public on Feb 13 2017

city: Glen Osmond

first: Mark

middle: Raymond

last: Thomas

state: SA

address: PO Box 350

department: Plant Industry

country: Australia

institute: CSIRO

summary:
Differences in gene expression were compared for grape berry flesh and skin.
The aim of this analysis is to identify key genes that are differentially expressed in the skin or flesh during berry development.
Keywords: Tissue specific gene expression analysis

overall_design: Two biological replicates were collected for each treatment. Biotin labeled probes were prepared from the extracted RNA from each deseeded berry sample and hybridized to the Vitis vinifera GeneChip. The sample/GeneChip position on the Affymetrix hybridization station was randomized using the AlgDesign package from R.

first: Christopher

last: Davies

first: Pat

last: Iocco


title: Functional characterization of Taf4b in Arabidopsis thaliana

status: Public on Dec 01 2016

city: lucknow

first: Samir

middle: V

last: Sawant

address: Rana pratap marg

department: Plant molecular biology

institute: National Botanical research Institute

summary:
Expression analysis was performed with two TDNA insertion mutants of taf4b i.e; taf4bprm (TDNA insertion in promoter region) and taf4bint (TDNA insertion in intronic region), Taf4b overexpression lines, taf4bprmcpr5 double mutant lines (Double mutant was generated by crossing taf4bprm with cpr5) and Col-0 in normal condition as well as with taf4bprm mutant and Col-0 infected with fungi AB (Alternaria brassicicola) and bacteria ES4 (Pseudomonas syringae pv.maculicola ES4326 ) in different perspectives.
Affymatrix expression analysis was executed to provide mechanistic details of regulation of genes by Taf4b in plants.

overall_design: The RNA of taf4b mutants (taf4bprm and taf4bint), Taf4b overexpression lines, taf4bprmcpr5 double mutant and Col-0 were isolated in normal and infected condition.The ATH1 gene chips were used for expression analysis.

first: Meenal

last: Srivastava

first: Poonam

last: Pant

first: Rakesh

first: Bindu

last: Pandey


title: Distinct populations of CD11b+ IRF4+ dendritic cells drive Th2 responses in the small intestine and colon

status: Public on Dec 10 2016

city: Glasgow

first: Simon

last: Milling

address: 120 University Place

department: Institute of Infection, Immunity and Inflammation

country: United Kingdom

institute: University of Glasgow

summary: We have identified the dendritic cell (DC) populations that are sufficient for the induction of T helper 2 (Th2) cell responses in the intestine against both live Trichuris muris worms, and inert Schistosoma mansoni eggs. Antigen-specific Th2 responses did not develop after deletion of IRF4 in DCs, yet IRF4-deficient DCs were not functionally affected. Instead, IRF4flox/flox CD11c-cre mice had fewer CD11b+ migrating DCs, and fewer DCs carrying parasite antigen from the intestine. Adoptive transfer of purified DCs from infected animals directly into intestinal afferent lymphatics enabled us to identify that CD11b+CD103+ DCs were central to the induction of Th2 responses in the small intestine, whereas CD11b+CD103- DCs were more important in the colon. Similarly, after pulsing with Schistosome egg antigen (SEA) in vitro, adoptively-transferred small intestinal or colonic DCs acquired the ability to induce SEA-specific Th2 responses.  These data demonstrate a functional specialisation among intestinal DC populations in inducing Th2 responses, and elucidate the roles of IRF4 in this process.

overall_design: Thoracic duct lymph was collected from C57BL/6 mesenteric lymphadenectomized (MLNx) mice for 18 hours, which allowed the collection of lymph draining intestinal DCs. CD11b+ CD103- and CD11b+CD103+ DCs were purfied by FACS and 30,000 cells of each subset (three replicates) were incubated with or without soluble Schistosoma mansoni egg antigen (SEA) for 18 hours, after which RNA extracton and microarray analysis were performed.

first: Johannes

middle: U

last: Mayer

first: Mimoza

last: Demiri

first: William

middle: W

last: Agace

first: Andrew

last: MacDonald

first: Marcus

last: Svensson-Frej


title: Arabidopsis overexpressing DRB2 and DRB3 genes

status: Public on Nov 30 2016

first: Misato

last: Ohtani

address: 8916-5 Takayama-cho

department: Graduate School of Biological Sciences

institute: NAIST

summary: The model plant Arabidopsis thaliana has five double-stranded RNA-binding proteins (DRB1-DRB5), two of which, DRB1 and DRB4, are well characterized. In contrast, the functions of DRB2, DRB3 and DRB5 have yet to be elucidated. In this study, we tried to uncover their functions using drb mutants and DRB-over-expressed lines. In over-expressed lines of all five DRB genes, the over-expression of DRB2 or DRB3 (DRB2ox or DRB3ox) conferred a downward-curled leaf phenotype, but the expression profiles of 10 small RNAs were similar to that of the wild-type (WT) plant. Phenotypes were examined in response to abiotic stresses. Both DRB2ox and DRB3ox plants exhibited salt-tolerance. When these plants were exposed to cold stress, drb2 and drb3 over-accumulated anthocyanin but DRB2ox and DRB3ox did not. Therefore, the over-expression of DRB2 or DRB3 had pleiotropic effects on host plants. Microarray and deep-sequencing analyses indicated that several genes encoding key enzymes for anthocyanin biosynthesis, including chalcone synthase (CHS), dihydroflavonol reductase (DFR) and anthocyanidin synthase (ANS), were down-regulated in DRB3ox plants. When DRB3ox was crossed with the pap1-D line, which is an activation-tagged transgenic line that over-expresses the key transcription factor PAP1 (Production of anthocyanin pigmentation1) for anthocyanin biosynthesis, over-expression of DRB3 suppressed the expression of PAP1, CHS, DFR and ANS genes. DRB3 negatively regulates anthocyanin biosynthesis by modulating the level of PAP1 transcript. Since two different small RNAs regulate PAP1 gene expression, a possible function of DRB3 for small RNA biogenesis is discussed.

overall_design: Total RNAs of the transgenic plants expressing 35S:PtSnRK2.7 treated with or without 200 mM NaCl.  As a control experiment, the wild-type plants were treated similarly. The total RNAs were used for microarray analysis to reveal genes affected by the PtSnRK2.7 overexpression.

first: Toshiyuki

last: Fukuhara


title: Expression data from Arabidopsis thaliana Col-0 challenged with Ralstonia solanacearum race 4 (roots)

status: Public on Dec 21 2016

city: NEW DELHI

first: DEVENDRA

middle: KUMAR

last: CHOUDHARY

state: DELHI

address: PUSA CAMPUS

department: PLANT PATHOLOGY

institute: INDIAN AGRICULTURAL RESEARCH INSTITUTE

summary:
Bacterial wilt caused by Ralstonia solanacearum is a serious seed/soil borne disease that causes severe yield and quality losses in many plants. In order to understand the change in genome expression of inculated plants, microarray analysis were performed.
Twenty one days old roots of Arabidopsis Col-0 were inoculated with Ralstonia solanacearum race 4 @ 10^9 & 10^8 cfu/ml in different plants, distil water were mock inoculated, after five days plants were taken for RNA extraction and hybridization on  Affymetrix microarrays. Plants were incubated in growth chamber for  disease development, temperature and humidity were maintained as per plant requirement for both treated and control plants.

overall_design: We used microarrays to detail the global programme of gene expression underlying disease development and identified distinct classes of up- and down-regulated genes during this process.

first: Devendra

middle: K

last: Choudhary

first: Aundy

last: Kumar


title: R:FR and blue signaling during competition at high plant densities

status: Public on Nov 23 2016

city: Utrecht

first: Ronald

last: Pierik

address: Padualaan 8

department: Plant Ecophysiology

country: Netherlands

institute: Utrecht University

summary:
Growth in dense stands induces shade avoidance responses. Late stages of stand development lead to low red:far-red (R:FR) and low blue light conditions.
We studied gene expression in late stages of canopy development when both light signals were present, and studied gene expression in the single and combined light treatments.

overall_design: Plants were grown either single (all light treatments, and canopy control), or put in a high density of 2066 plants / m2. Gene expression measured in petioles.

first: Mieke

last: de Wit


title: Global gene expression profiles of Arabidopsis thaliana wild type Columbia-0 and mutant er-105 in responses to 40℃ treatment

city: Shanghai

first: Li

last: Qun

state: Shanghai

address: 300 Fenglin Road

department: National Key Laboratory of Plant Molecular Genetics

institute: Institute of plant physiology & ecology, SIBS, CAS

summary:
Global warming seriously threats world food supply.  However, very few approaches have succeeded in genetically enhancing crop heat tolerance without growth penalty.
To reveal the underlying molecular mechanism of Erecta action in response to thermal stress, we performed transcriptional profiling of Col-0 and mutant er-105 plants with or without 40℃ heat treatment on a global scale using the Affymetrix Arabidopsis ATH1 GeneChip.

overall_design: 15-20 rosette leaves of 2-week-old Arabidopsis thaliana wild type Columbia-0 (Col-0) and mutant er-105 plants grown at 21℃ (control) or treated at 40℃ for 6h were harvested immediately after heat treatment and stored in liquid nitrogen. Three biological repeats were performed on Columbia-0 (wild-type, Col-0) and er-105 (mutant) with or without 40℃ heat treatment, respectively.

first: Shen

last: Hui

first: He

last: Zuhua


title: Reduced mTORC1 activity is associated with responsiveness to MEK inhibition (PD0325901) in gastric cancer cells.

city: yufu

first: yuka

last: hirashita

institute: Oita University

summary: Since gastric cancer (GC) is characterized by amplifications of receptor tyrosine kinases (RTK) and KRAS, targeting the RTK/KRAS downstream pathways could contribute to broader applicability of molecular targeted therapy in GC. Here, we assembled a panel of 49 GC cell lines and screened predictors for responsiveness to RAF/MEK/ERK pathway inhibition by comparing their sensitivity to MEK inhibition with alteration status of RTK/KRAS and phosphorylation status of RTK/KRAS downstream molecules. We found that GC cells with MET amplification or KRAS mutation tend to be sensitive to MEK inhibition. Furthermore, lower phosphorylation levels of mTORC1 targets, p70S6K and 4EBP1, was also significantly associated with sensitivity to MEK inhibition. Interestingly, the sensitive cells showed reduced mTORC1 activity accompanied by decreased rate of protein synthesis after MEK inhibition, suggesting that antiproliferative effect of MEK inhibition may be exerted through inhibition of protein synthesis, which was caused by reduced mTORC1 activity. Mechanistically, expression of some mTORC1 negative regulators, such as DDIT4, FOXO3, SESN1 and TSC1, were induced by MEK inhibition in highly-sensitive cell lines and knockdown of these negative regulators partially alleviated the suppression of mTORC1 activity and antiproliferative effect of MEK inhibition. Our data suggest that a subset of GCs, which would be distinguishable according to the predictive markers we identified, may be sensitive to MEK inhibition and have implications for the strategy in clinical trial of MEK inhibitors for GC.

overall_design: To identify genes specifically induced in MEK inhibitor-sensitive cell lines after MEK inhibition, we treated MEK inhibitor (PD0325901)-sensitive (HSC57 and SNU719) and -resistant (SH-10-TC and TMK1) cell lines with 1µM PD0325901 for 3 h. Then, RNAs were extracted from these cells and susequently subjected to gene expression-microarray analysis. The expression levels were normalized by the median expression for the all 24 samples (each 4 cell lines n=3) and expressed as log2ratio.

first: Yuka

last: Hirashita

first: Yoshiyuki

last: Tsukamoto

first: Kazuyoshi

last: Yanagihara

first: Masatsugu

last: Moriyama


title: Safety and immunogenicity of the recombinant BCG vaccine VPM1002, in South African infants

status: Public on Jan 09 2017

city: Berlin

first: Jeroen

last: Maertzdorf

address: Chariteplatz 1

country: Germany

institute: MPIIB

summary: Differential gene expression in human whole blood before and at 5 different timepoints following vaccination with BCG or VPM1002

overall_design:
Gene expression analysis of whole blood RNA before and after vaccination
contributor: VPM Study Group

first: André

last: Loxton

first: Leander

last: Grode

first: Hans

last: Mollenkopf

first: Stefan

last: Kaufmann

first: Gerhard

last: Walzl


title: Modeling of WGBS data from normal and cancer tissues, young and old cells, passaged fibroblasts and stem cells V

status: Public on Mar 15 2017

first: Andrew

middle: P

last: Feinberg

address: 855 N. Wolfe St., Rangos 570

department: Center for Epigenetics

institute: Johns Hopkins

type: Methylation profiling by high throughput sequencing

summary: We develop a novel analysis method for WGBS data that allows us to measure diverse aspects of methylation information genome-wide.

overall_design: modeling of WGBS data for a diverse set of samples. BAM files for data generated in this study can be found in SRP072078 (PRJNA315696), SRP072071 (PRJNA315694), SRP072075 (PRJNA315695) and SRP072141 (PRJNA315903). The rest of the data was downloaded from other studies: GSE46644, GSE49629, GSE52972, GSE31742. For the latter, N/As have been used in BioSample and instrument model fields.

first: Garrett

last: Jenkinson

first: Elisabet

last: Pujadas

first: John

last: Goutsias


title: Root Transcriptome of WT, SDI1 Overexpression Lines and sdi1sdi2 Double Knockouts Grown under Sulfur Sufficient and Deficient Conditions

status: Public on Oct 07 2016

city: Fukuoka

first: Akiko

last: Maruyama-Nakashita

address: 6-10-1, Hakozaki, Higashi-ku

institute: Kyushu University

summary:
Sulfur-deficiency-induced repressor proteins optimize glucosinolate biosynthesis in plants
Glucosinolates (GSLs) in the plant order of the Brassicales are sulfur-rich secondary metabolites harboring anti-pathogenic and anti-herbivory plant-protective functions as well as possessing medicinal properties such as carcinopreventive and antibiotic activities. Plants repress GSL biosynthesis upon sulfur deficiency (–S), hence, field performance and medicinal quality are impaired by inadequate sulfate supply. The molecular mechanism linking –S to GSL biosynthesis has remained understudied. We report here the identification of the –S marker genes Sulfur deficiency induced1 and Sulfur deficiency induced2 (SDI1, SDI2) acting as major repressors controlling GSL biosynthesis in Arabidopsis under –S condition. SDI1 and SDI2 expression negatively correlated with GSL biosynthesis in both transcript and metabolite levels. Principal component analysis of transcriptome data indicated that SDI1 regulates aliphatic GSL biosynthesis as part of –S-response. SDI1 was localized to the nucleus and interacted with MYB28, a major transcription factor promoting aliphatic GSL biosynthesis, in both yeast and plant cells. SDI1 inhibited transcription of aliphatic GSL biosynthetic genes through maintaining the DNA-binding composition in a form of a SDI1-MYB28 complex, leading to down-regulate GSL biosynthesis and prioritize sulfate usage for primary metabolites under sulfur-deprived conditions.

overall_design: Root tissues from WT, 2 lines of sdi1sdi2 double knockout mutants (sdi1sdi2-1 and sdi1sdi2-4) and 2 lines of SDI1 overexpression plants (SDI1ox-6 and SDI1ox-12) grown for 10 days were used for the analysis. WT and sdi1sdi2 double knockouts were grown under +S (1500 µM sulfate) or –S (15 µM sulfate) conditions and SDI1ox plants were grown under +S conditions. Experiments were duplicated for each condition. Hybridization were performed using the ATH1-121501.1 Array (Affymetrix) according to the manufacturer’s protocol.

first: Hideki

last: Takahashi


title: Response of Arabidopsis roots to combinations of nitrogen and hormonal signals

status: Public on Oct 26 2016

city: Montpellier

first: Gabriel

last: Krouk

address: 2 Place Pierre Viala

department: Biology

institute: CNRS

summary: Living organisms have to cope with multiple and combined fluctuations in their environment. According to their sessile mode of life, plants are even more subjected to such fluctuations impacting their physiology and development. In particular, nutrient availability is known to tune plant development through modulating hormonal signaling, and conversely, hormonal signals are key to control nutrient related signaling pathways (Krouk et al., 2011a). However, very few is known about molecular mechanisms leading to plant adaptation to such combined signals. Here we deployed an unprecedented combinatorial treatment matrix to reveal plant adaptation in response to nitrate (NO3-), ammonium (NH4+), auxin (IAA), cytokinins (CK) and abscisic acid (ABA) and their exhaustive binary combinations.

overall_design:
In order to study the effect of 5 signaling molecules we developed a matrix of treatment including NO3- (1mM or 0.5mM), NH4+ (1mM, or 0.5mM), indol-acetic-acid (IAA: 500 nM), Kinetin (CK: 500 nM), abscisic acid (ABA: 1µM). When present, the overall nitrogen treatment has been maintained to 1mM. As such, when NO3- and NH4+ are present in the same media their concentration was divided by 2. Proper mock controls include KCl, and DMSO. Plants are grown on NH4+-succinate for 12 to 14 days (first visible true leaves). Transferred 24 hours on a refreshed N-free media (reset the background that may be exhausted in several elements), and then transferred toward fresh media containing combinations of signals. Plant roots are harvested after 4 hours of treatment for gene expression analysis.

Please note that the treatment details for each sample were provided in the sample 'characteristics' column in 'NO-NH-IA-CK-AB' format followed by the Presence/Absence code used for each hormone/nutrient.

first: Gloria

last: Coruzzi


title: Genetic dissection of nutrition-induced plasticity in insulin/insulin-like growth factor signaling in a Drosophila MPP

status: Public on Jan 05 2017

city: Columbia

first: Elizabeth

last: King

state: MO

address: 105 Tucker Hall

department: Biological Sciences

institute: University of Missouri

summary: The nutritional environments that organisms experience are inherently variable, requiring tight coordination of how resources are allocated to different functions relative to the total amount of resources available. A growing body of evidence supports the hypothesis that key endocrine pathways play a fundamental role in this coordination. In particular, the insulin/insulin-like growth factor signaling (IIS) and target of rapamycin (TOR) pathways have been implicated in nutrition-dependent changes in metabolism and nutrient allocation, however little is known about the genetic basis of standing variation in the pathways. To characterize natural genetic variation in the IIS/TOR pathway, we used over 250 recombinant inbred lines (RILs) derived from a multiparental mapping population, the Drosophila Synthetic Population Resource (DSPR), to map QTL for transcript levels of the genes encoding 52 of the core components of the IIS/TOR pathway in three different nutritional environments (dietary restriction, control, and high sugar). In addition, we assayed lifespan for 80 RILs in both dietary restriction and control diets.  We identified cis (i.e., local) QTL for six transcripts, all of which are significant in multiple nutrient environments. Further, we identified trans (i.e., distant) QTL for two transcripts, specific to a single nutrient environment, and one “plasticity” QTL that influences the change in gene expression between the control and high sugar diet. Nearly all transcripts, 85%, were significantly differentially expressed between diets. A discriminant function analysis for the control and dietary restriction treatments identified which transcripts best predict the diet treatment. The resulting composite discriminant function scores are correlated with median lifespan (r = 0.45) and mapping these scores revealed a significant QTL within the dietary restriction diet. Our results corroborate the association between the IIS/TOR pathway and the increase in lifespan under dietary restriction in a natural population and identify new locations in the genome involved in regulating the IIS/TOR pathway.

overall_design: We have 918 total samples stemming from 259 recombinant inbred lines placed on three different diets. There is one replicate per line per diet for most samples with 20-30 flies pooled for each. The diets include dietary restriction, control, and high sugar. All fold change measurements are given relative to the control diet.

first: Patrick

middle: D

last: Stanley

first: Enoch

last: Ng'oma

first: Siri

last: O'Day


title: Dynamic equilibrium of lung Trm dictates waning immunity after IAV infection

status: Public on Nov 18 2016

city: Iowa City

first: Thomas

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

summary: Lung resident memory (Trm) CD8 T cells induced by influenza A virus (IAV), are pivotal for providing heterosubtypic immunity, but are not maintained long term, causing gradual loss of protection.  This contrasts sharply with long-term maintenance of Trm induced by localized infections of the skin and other tissues. Here we show that the decline in lung Trm is determined by an imbalance between apoptosis and lung recruitment/conversion to Trm of circulating memory cells. At the cellular level, circulating effector memory (Tem) rather than central memory (Tcm) cells are the precursors for conversion to lung Trm. Time-dependent changes in expression of genes critical for Trm differentiation together with enrichment of Tcm diminish the capacity of circulating memory CD8 T cells to form Trm, explaining why IAV-induced Trm are not stably maintained over time. Importantly, systemic booster immunization, through increasing the number of circulating Tem cells, induces an increase in lung Trm pool, providing a new rational for future IAV vaccines.

overall_design: Two treatment groups + naive control group. Treatment groups: 5 samples, each one represents an RNA pooled from 5 individual mice. Naive control: 3 samples, each one preresents RNA from individual naive P14 transgenic mouse. This series contains data only for the two treatment groups.

first: Budimir

last: Natalija


title: Expression data from Arabidopsis thaliana Col-0 challenged with Ralstonia solanacearum race 4

first: DEVENDRA

last: CHOUDHARY

summary: Bacterial wilt caused by Ralstonia solanacearum is a serious seed/soil borne disease that causes severe yield and quality losses in many plants. In order to understand the change in genome expression of inculated plants, microarray analysis were performed.

overall_design:
Arabidopsis Col-0 seeds were inoculated with Ralstonia solanacearum race 4 @ 10^8 cfu/ml, distil water were mock inoculated and twenty one days plants were taken for RNA extraction and hybridization on Affymetrix microarrays. Seeds were incubated in growth chamber for development, temperature and humidity were maintained as per plant requirement for both treated and control plants.
We used microarrays to detail the global programme of gene expression underlying disease development and identified distinct classes of up- and down-regulated genes during this process.

first: Aundy

last: Kumar

first: Devendra

last: Choudhary


title: Expression data from Arabidopsis Col and rglg1/2 mutant in response to Fe deficiency

status: Public on Oct 30 2016

city: Taichung

first: I-Chun

last: Pan

address: Kuo-Kuang

department: Horticulture

institute: Chung Hsing University

summary: Iron is an essential element for almost all organisms, catalyzing numerous essential redox reactions by virtue of its unique electrochemical properties. Iron levels in cells need to be carefully balanced. Rglg1/2 is an Arabidopsis mutant which display a pleiotropic phenotype partly resembling iron-deficient plants.To dissect global transcriptional regulation of gene expression in iron-deficient plants, we conducted genome-wide proteomic and transcriptomic surveys of leaves and roots from iron-sufficient and iron-deficient Col-0 wild-type plants and rglg1 rglg2 double mutants.

overall_design: Ten days old Col and rglg1/2 plants were treated with Fe-suficiency and Fe-deficiency for 3 days.  Leaves and roots sample were collected respectively.

first: Wolfgang

last: Schmidt


title: Expression data of HSFA6b-overexpression and HSFA6b dominant-negative mutant lines of Arabidopsis after NaCl or Heat shock treatment

status: Public on Dec 07 2016

city: Taipei

first: Ya-Chen

last: Huang

address: No. 1, Sec. 4, Roosevelt Road

department: Institute of Plant Biology and Department of Life Science

institute: National Taiwan University

summary:
In order to study the improtance of HSFA6b in salt and heat stresses of arabidopsis, we generated the HSFA6b-overexpression (HSFA6b-OE) and dominant-negative (HSFA6b-RD) mutant lines.
We used microarray to investigate how genes regulated by HSFA6b after NaCl or heat shock treatment.

overall_design: Seven-day-old seedlings of wild type (Col-0), HSFA6b-overexpression (HSFA6b-OE) and HSFA6b dominant-negative (HSFA6b-RD) mutant lines grown at 22℃ on 0.5X MS plates containing 1% sucrose were treated with 150mM NaCl for 6hr or 37℃ heat shock for 1hr, with 22℃ treatment as a control. Subsequently, samples were collected for RNA extraction by use of the RNeasy Kit (Qiagen). The results were representative of two independent biological replicates for analysis.

first: Tsung-Luo

last: Jinn


title: Transcriptomic signatures in follicular cells associated with failure of in vitro fertilization in humans

status: Public on Oct 03 2016

city: Quebec

first: Chloe

last: Fortin

state: Quebec

address: 2440 boulevard hochelaga

institute: Universite Laval

summary: IVF success rate remains low (usually around 30%) and many cycles are needed to achieve pregnancy, raising issues for patients and society. IVF success or failure mainly depends on quality of the oocytes retrieved and on the patient response to the ovarian stimulation. Hormonal stimulation prior to IVF influences the ovarian environment and therefore impacts oocytes and subsequent embryo quality. We believe that if more information was available to clinicians to analyze why a cycle has failed, they could adapt the next stimulation protocol accordingly and improve success rate. We believe that particular molecular signatures are associated with failure causes and that RNA analysis could be used as a diagnosis tool. The aim of this study was to compare gene expression between failed and successful IVF cycles and to determine how gene expression is affected in follicles from failed cycles. Gene expression in follicular cells obtained from IVF patients (n=32) was analyzed using microarray. Patients that did not become pregnant following the IVF cycle were compared to those that did. Quantitative RT-PCR was used to validate the microarray results and functional analysis was performed using ingenuity pathway analysis. 165 genes were differently expressed between the two groups, including many pro-inflammatory cytokines or other factors related to inflammation. For example, EGR1, IL1B, IL8, CXCL2, CCL3 and CCL4 were all up-regulated in the negative group compared to the positive group. Overexpression of several factors, some of which act upstream from VEGF, indicates increased permeability and vasodilation. Recruitment of immune cells to ovarian tissues also appears more pronounced in the negative group, and might reflect leukocytosis. Our results indicate an impaired balance between pro- and anti- inflammatory mediators in the failed IVF group and also suggest an intermediate state of OHSS that affects oocytes without leading to systemic problems. Some differentially expressed genes appear related to abnormal differentiation and increased apoptosis, which could also result from follicular aging. These findings provide potential biomarkers to identify failure causes, which should lead to improved stimulation protocols and more successful treatment of infertility.

overall_design:
8 samples were analysed, 4 samples of follicular cells associated to negative IVF outcome (no pregnancy) were compared to 4 control samples of follicular cells associated to positive IVF outcome (pregnancy). (total of 4 replicates).
Please note that the numeral identifiers (in the first column of the raw data files or of the normalized data matrix) are not Agilent feature extraction numbers (represented in the GPL10332 ID column)

first: Chloé

first: Arthur

last: Leader

first: Neil

last: Mahutte

first: Mathias

last: Gysler

first: Marc

last: Villeneuve

first: Marc-André

last: Sirard


title: Grape berry developmental series from a vineyard in Willunga, South Australia (WIL-04)

first: Mark

last: Thomas

institute: CSIRO

summary:
Changes in gene expression during berry development during a grape growing season were analysed.
Grape berries were collected and pooled on a weekly basis to obtain a developmental series comprising of 19 developmental stages from flowering until harvest across the grape growing season. Gene expression patterns during development were obtained.
Keywords: Time course, developmental series

overall_design: Nineteen consecutive developmental stages were analysed for gene expression changes using the Affymetrix one colour array platform. The developmental stages were numbered 1 to 19. Two biological replicates were collected for each developmental stage. Biotin labeled probes were prepared from the extracted RNA from each of the pooled berry samples and hybridised to the Vitis vinifera GeneChip. The sample/GeneChip position on the Affymetrix hybridisation station was randomised using the AlgDesign package from R.

middle: R

first: Christopher

last: Davies

first: Pat

last: Iocco


title: IL-4 signaling in human coronary artery endothelial cells

city: Zürich

first: TOM

last: SKARIA

address: Rämistr. 100

department: INTERNAL MEDICINE

country: Switzerland

institute: UNIVERSITY HOSPITAL ZURICH

summary:
IL-4 signalling is critically involved in Th2 driven allergic inflammatory responses. IL-4  generates a proinflammatory enviornment and may cause barrier dysfunction in vascular endothelial cells (VECs). However, the effectors responsible for IL-4 induced barrier dysfunction in adult human VECs still remain unclear.
Here we show that IL-4 upregulates the expression of Wnt5A which can mediate cytoskeleton remodeling in VECs. We further show that IL-4 induced cytoskeleton remodeling involving stress fiber formation can be decreased by antagonizing Wnt5A. Further we demonstrate that silencing Wnt5A significantly improves the barrier function of IL-4 treated endothelial monolayer. Additionally, we rule out the involvement of  IL-6 in IL-4 induced barrier dysfunction of VECs. These findings suggest a critical role for Wnt5A in mediating IL-4 induced endothelial barrier dysfunction and edem formation in Th2 driven  inflammatory diseases.

overall_design: A two color competitive hybridization design was chosen.  Samples from respective treatments are labelled with Cy5  and hybridized against a Cy3 labelled non-treated reference sample from the same experiment.

first: Tom

last: Skaria

first: Gabriele

last: Schoedon


title: Leaf margins of indeterminate Arabidopsis leaves

city: Rehovot

first: Idan

last: Efroni

address: POB 12

department: Plant Sciences

country: Israel

institute: Hebrew University

summary: Leaves are flat determinate organs derived from indeterminate shoot apical meristems. The presence of a specific leaf meristem is debated, as anatomical features typical of meristems are not present in leaves. Here we demonstrate that multiple NGATHA (NGA) and CINCINNATA-class-TCP (CIN-TCP) transcription factors act redundantly to suppress activity of a leaf margin meristem in Arabidopsis thaliana, and that their absence confers persistent marginal growth of leaves, cotyledons and floral organs. The marginal meristem is activated by the juxtaposition of adaxial and abaxial domains and maintained by WOX homeobox transcription factors, but other margin elaboration genes are dispensable for its maintenance. This genetic framework parallels the morphogenetic program of shoot apical meristems and may represent a relic from an ancestral shoot system from which seed plant leaves evolved.

overall_design: 2 Biological replicates were collected

first: John

last: Alvarez

first: Chihiro

last: Furumizu

first: Yuval

last: Eshed

last: Bowman


title: Liver-resident memory CD8+ T cells form a front-line defense against malaria liver-stage infection.

status: Public on Oct 02 2016

city: Parkville

first: Joel

middle: Zhi-Iong

last: Ma

state: Victoria

address: Grattan Street

institute: University of Melbourne

summary: In recent years, various intervention strategies have reduced malaria morbidity and mortality, but further improvements likely depend upon development of a broadly protective vaccine. To better understand immune requirement for protection, we examined liver-stage immunity after vaccination with irradiated sporozoites, an effective though logistically difficult vaccine. We identified a population of memory CD8+ T cells that expressed the gene signature of tissue-resident memory (Trm) T cells and remained permanently within the liver, where they patrolled the sinusoids. Exploring the requirements for liver Trm cell induction, we showed that by combining dendritic cell-targeted priming with liver inflammation and antigen recognition on hepatocytes, high frequencies of Trm cells could be induced and these cells were essential for protection against malaria sporozoite challenge. Our study highlights the immune potential of liver Trm cells and provides approaches for their selective transfer, expansion or depletion, which may be harnessed to control liver infections or autoimmunity.

overall_design: 9 samples were analyzed: 3 replicates of memory CD69+KLRG1low PbT-I CD8+ T cells and 3 replicates of memory CD69-KLRG1+ PbT-I CD8+ T cells isolated from the liver of C57/BL6 mice on day 30 p.i. with irradiated sporozoites; 3 replicates of memory KLRG1+CD69- PbT-I CD8+ T cells (Tem) isolated from the spleen of the same C57/BL6 mice on day 30 p.i. with irradiated sporozoites.

first: D

last: Fernandez-Ruiz

first: W

middle: Y

last: Ng

first: L

last: Holz

first: J

middle: Z

first: A

last: Zaid

first: Y

middle: C

last: Wong

middle: S

last: Lau

first: V

last: Mollard

last: Cozijnsen

first: N

last: Collins

last: Li

first: G

middle: M

last: Davey

last: Kato

first: S

last: Devi

first: R

last: Skandari

first: M

last: Pauley

middle: H

last: Manton

middle: I

last: Godfrey

last: Braun

last: Tay

first: P

last: Tan

last: Bowen

first: F

last: Koch-Nolte

first: B

last: Rissiek

last: Carbone

last: Crabb

last: Lahoud

first: I

last: Cockburn

middle: N

last: Mueller

last: Bertolino

last: McFadden

last: Caminschi

last: Heath


title: Expression data from Arabidopsis before and after bacterial RNA infiltration

status: Public on Oct 01 2016

city: Daejeon

first: Boyoung

last: Lee

address: 141 Gajeong-ro Yuseong-gu

institute: Korea Research Institute of Chemical Technology

summary: To analyze transcription in plants induced by total bacterial RNAs, we examined the transcriptomes of RNAs-treated plants at 0 and 6 h compared to those of control plants at the same time points.

overall_design: To compare two time point samples, we isolated total RNA from 5 plants 0h and 6h after infiltration of bacterial RNA and the synthesized cDNAs were hybridized on Affymetrix ATH1 microarrays.

first: Yong-Soon

last: Park

first: Soohyun

first: Choong-Min

last: Ryu


title: Expression data from cell aggregates before and after pre-differentiation

status: Public on Sep 22 2016

city: Columbus

first: Shuting

last: zhao

state: Ohio

address: Room 340H, 460 West 12th Ave., Biomedical research

country: USA

institute: The ohio state university

summary:
Cell aggregates were cultured with BMP4 and bFGF for 3 days as pre-differentaition process
We used microarrays to detect the expression of markers of pluripotency, three germ layers, and cardiac lineages

overall_design: Cell aggregates before pre-differentiation and after pre-differnetiation were collected for microarrays. Typical markers for pluripotency, three germ layers, and cardiac lineages were investigated.

first: Sarah

last: Warner

first: Huabao

last: Wang


title: Identification of HS memory-associated genes

status: Public on Sep 30 2016

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

institute: MPIMP

summary: To identify genes associated with the heat stress (HS) memory, transcript profiling using Affymetrix ATH1 microarrays was performed to compare Col-0 seedlings after the priming stimulus with control plants (unprimed).

overall_design: The experiment was designed to identify genes associated with HS memory. For the priming HS, seedlings were subjected to a heat regime of 1.5 h, 37°C; 1.5 h recovery at 22°C; and 45 min, 44°C. After the priming HS treatment, seedlings were returned to normal growth condition and harvested after 4, 8, 24 and 48 h, respectively.

first: Mastoureh

last: Sedaghatmehr

first: Bernd

last: Mueller-Roeber


title: Genomic data from pooled root and shoot tissue of Arabidopsis thaliana, Arabidopsis halleri and Arabidopsis lyrata

city: La Jolla

first: Vasantika

last: Suryawanshi

state: CALIFORNIA

address: 9420 Athena Circle

institute: La Jolla Institute of Immunology

summary:
Gene copy number variation (CNV) is a form of genetic polymorphism that contributes significantly to genome size and function but remains poorly characterized due to technological limitations. Inter-specific comparisons of CNVs in recently diverged plant species are crucial to uncover selection patterns underlying adaptation of a species to stressful environments. Especially given that gene amplifications have long been implicated in emergence of species-specific traits, we conducted a genome-wide survey to identify species-specific gene copy number expansions and deletions in the model extremophile species - Arabidopsis halleri that has diverged in evolutionarily recent time from Arabidopsis thaliana.
Cross-species cDNA array based comparative genomic hybridization was employed to compare and identify gene copy number variation in the two sister-species - the metallophyte Arabidopsis halleri and non-metallophyte Arabidopsis lyrata, both relative to Arabidopsis thaliana. We uncovered an unprecedented level of gene copy number polymorphism in Arabidopsis halleri, with a species-specific enrichment of metal homeostasis function in the genes found to be copy number expanded, thus indicating CNV as a mechanism that underlies the key physiological trait of metal hyperaccumulation and hypetolerance in A. halleri.

sample_organism:
Arabidopsis thaliana
Arabidopsis lyrata
Arabidopsis halleri

overall_design: A total of 6 gDNA samples were hybridized to Affymetrix cDNA microarrays, two biological replicates for each of the three Arabidopsis species.

first: Ina

last: Talke

first: Michael

last: Weber

first: Stephan

last: Clemens

first: Roland

last: Eils

first: Benedikt

last: Brors

last: Singh

first: Ute

last: Kraemer


title: Transcriptome analysis of diverse cell types infected with human cytomegalovirus [array]

status: Public on Sep 17 2016

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: Comprehensive RNA sequencing and splicing-sensitive microarray analysis of three diverse cell types infected with human cytomegalovirus (HCMV), including primary fibroblasts (HFFs), endothelial cells (ECs), and neural progenitors (NPCs) derived from embryonic stem cells. This global analysis includes both host and viral gene expression measurements, and an in-depth assessment of alternative RNA processing events. Extended comparisons were conducted through RNA sequencing analysis of human herpes simplex virus (HSV)-2 and human immunodeficiency virus type 1 (HIV-1) infections.

overall_design: Alternative host splicing analysis component of the study. This data subset was derived from triplicate sets of cell culture that were each subjected to splice-junction arrays.

first: T

middle: J

last: Stark

first: R

last: Batra

first: G


title: Comparison of infloresence transcriptome of bp er vs. bp er fil

status: Public on Sep 10 2016

city: Toronto

first: Dan

last: Riggs

state: ON

address: 1265 Military Trail

institute: University of Toronto

summary: BP and ER encode proteins that act synergistically to regulate Arabidopsis inflorescence architecture. To search for genes/proteins that influence the BP/ER signaling pathways, we conducted mutagenesis of the bp er double mutant and found that a mutation in FILAMENTOUS FLOWER (FIL) suppresses many of the morphological/developmental defects in bp er.  Given that FIL encodes a Zn-finger containing transcription factor, microarray analysis was conducted on bp er vs. the bp er fil line to identify genes that are misregulated and which might implicate specific genes/proteins/pathways that are involved in regulating inflorescence development.

overall_design: Plants of the  bp er parent line and the bp er fil suppressor line were grown in Conviron growth chambers.  Inflorescences that contained no more than 2 stage 13 flowers were harvested and triplicate samples were ultimately compared.

first: CD

last: Nyugen


title: Expression analysis of the genes induced by Ascophyllum nodosum extract in the presence of salinity stress

status: Public on Sep 07 2016

city: Truro

first: Balakrishnan

last: Prithiviraj

state: Nova Scotia

address: 50,Pictou Road

department: Plant, Food and Environmental Sciences

institute: Dalhousie University

summary:
Ascophyllum nodosum extract induced salinity tolerance in Arabidopsis thaliana
We used microarrays to detail the global programme of gene expression underlying ANE mediated salinity tolerance in the Arabidopsis thaliana

overall_design: Arabidopsis was initially exposed to 150 mM NaCl for 24 hours, after which plants were treated with either the methanol extract of A. nodosum (MEA) or the ethyl acetate sub-fraction of A. nodosum (EAA).

first: B


title: Stromal PTEN inhibits the expansion of mammary epithelial stem cells through Jagged-1

status: Public on Sep 09 2016

first: Gina

last: Sizemore

state: OH

address: 460 W. 12th Avenue

institute: Ohio State University

summary: Fibroblasts within the mammary tumor microenvironment are active participants in carcinogenesis mediating both tumor initiation and progression. Our group has previously demonstrated that genetic loss of PTEN in mammary fibroblasts induces an oncogenic secretome that remodels the extracellular milieu accelerating ErbB2-driven mammary tumor progression. While these prior studies highlighted a tumor suppressive role for stromal PTEN, how the adjacent normal epithelium transforms in response to PTEN loss was not previously addressed. To identify these early events, we have evaluated both phenotypic and genetic changes within the pre-neoplastic mammary epithelium of mice with and without stromal PTEN expression. We report that fibroblast-specific PTEN deletion greatly restricts mammary ductal elongation and induces aberrant alveolar side-branching. These mice concomitantly exhibit an expansion of the mammary epithelial stem cell (MaSC) enriched basal/myoepithelial population and further genome wide expression analysis followed by gene set enrichment analysis (GSEA) revealed that NOTCH signaling is diminished in these cells. NOTCH3 was confirmed to be downregulated in the MaSC-enriched pool by confirmatory qRT-PCR and immunofluorescence. Mechanistically, JAGGED-1, a transmembrane ligand for the NOTCH receptor, is downregulated in the PTEN-null fibroblasts leading to a loss in the paracrine activation of NOTCH signaling from the surrounding stroma.

overall_design: Each biological replicate of FACS sorted Lin-CD24+CD29Hi MaSC-enriched epithelial subpopulations was collected by pooling pre-neoplastic mammary tissue from 6-8 virgin ErbB2;Ptenfl/fl or ErbB2;Fsp-cre;Ptenfl/fl (8-9 weeks of age) mice. Microarray on three MaSC-enriched samples from both genetic groups was performed with GeneChip® Mouse Transcriptome Assay 1.0 (Affymetrix, Santa Clara, California, USA) at the OSUCCC Genomics Facility.

first: Subhasree

last: Balakrishnan

last: Ostrowski


title: Expression profiling of Col-0 and rps2 treated with Psm:AvrRpt2

status: Public on Sep 01 2016

city: Berkeley

first: Yangnan

last: Gu

address: 371 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

summary: Identification of differential gene expression during RPS2-mediated effector-triggered immunity in Arabidopsis

overall_design: Four-week-old leaves of Arabidopsis Col-0 wild type and rps2 mutant plant were infiltrated with Pseudomonas syringae pv. Maculicola carring effector AvrRpt2 at OD 0.01. Samples were collected at 0, 6 and 10 hours after infiltration for WT plants and at 0 and 10 hours after infiltration for rps2 plants. Three biological replicates were performed per genotype per time point.

first: Sophia

last: Zebell

first: Xinnian

last: Dong


title: Skewing in Arabidopsis roots involves disparate environmental signaling pathways

status: Public on Aug 31 2016

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

summary:
Background: Skewing root patterns provide key insights into root growth strategies and mechanism that produce root architectures Roots exhibit skewing and waving when grown on a tilted, impenetrable surface, and while the genetics guiding these morphologies have been examined, the underlying molecular mechanisms of skewing and waving remain unclear. In this study, transcriptome data were derived from two Arabidopsis ecotypes, WS and Col-0, under three tilted growth conditions in order to identify candidate genes involved in skewing. WS is a skewing ecotype. Col-0 is a non-skewing ecotype. Results: This work identifies a number of genes that are likely involved in skewing, using growth conditions that differentially affect skewing and waving. Comparing the gene expression profiles of WS and Col-0 in different tilted growth conditions identified 11 candidate genes as potentially involved in the control of skewing. These 11 genes are involved in several different cellular processes, including sugar transport, salt signaling, cell wall organization, and hormone signaling. Conclusions: Many of the 11 identified genes are involved in signaling and perception, rather than the physical restructuring of roots, leading to the conclusion that root skewing is enabled through diverse environmental signaling pathways. These findings revealed further insights into the molecular mechanisms behind root skewing.
This work investigated the transcriptional differences between skewing and non-skewing roots. Comparisons within WS revealed gees that that responded to the angle of growth (Agp) during the process of skewing. These genes were cross referenced with transcripts differing between the WS and Col-0 genotypes to refine the list of genes that are most probably be involved in root skewing. More of the highly probable skew gene candidates (HPSGC) are associated with environmental sensing (e.g. salt, sugar, hormones, darkness) than with physical growth differences (e.g. cell wall remodeling, cell division, cell elongation).  Thus, the root behavior of skewing appears to be primarily driven by pathways that respond to disparate signals from the root local environment. Future studies could investigate the HPSGC to find the specific pathways and molecular mechanisms contributing to root skewing.

overall_design: Arabidopsis thaliana plants (wild type cultivars Col-0 and WS) were grown on media plates made from 0.5x MS liquid media, autoclaved with 0.5% Phytagel and poured in square-gridded plates (Fisherbrand, Fisher Scientific, Pittsburgh, PA). Seeds were wet sterilized in 1.7 mL Eppendorf microfuge tubes (Eppendorf, Hamburg, Germany) using a 5-minute 70% ethanol wash, followed by a 5 minute 50% v/v sodium hypochlorate solution wash (8.3%; Clorox, Oakland, CA), followed by 6 washes with sterile ddH2O. Seeds were planted on plates and moved to 4°C for two days, followed by three days of vertical growth (Agp 90°) in 19°C +/- 2°C, and 24-hour fluorescent light at approximately 80 μmol m-2 s-1 PAR. Plates were photographed, moved to their respective experimental condition (Agp 45°, 90°, or 135°), and photographed again on day 8. Plants were harvested and fixed in RNAlater (Ambion, Grand Island, New York, USA).

first: Eric

last: Schultz

first: Agata

last: Zupanska

first: Anna-Lisa

last: Paul


title: Evolution of the herbivore associated elicitor induced early defence signalling networks in Nicotiana

status: Public on Aug 23 2016

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

summary: Identifying whether FAC-induced early defence signalling genes were regulated by JA

overall_design: Gene expression in leaves of Nicotiana attenuata wild type and ir-AOC plants was measured at 30 min after elicitation with FAC (C18:3-Glu) and water (control). Three biological replicates were performed with both wild type and  ir-AOC plants. In total 12 microarraies were hybridized.

first: Shuqing

last: Xu


title: Expression profiling of dexamethasone inducible expression of YFP-CPR5-C in Arabidopsis

summary: Identification of early transcriptional responses to CPR5 function loss in Arabidopsis

overall_design: Expression of CPR5 C terminal half efficiently interferes with native CPR5 protein function and causes a dominant negative effect. Four-week-old leaves of Col-0 WT and transgenic Dex:YFP-CPR5-C plant were sprayed with water or 50 uM dexamethasone to induce expression of CPR5-C. Samples were collected at 24 hours after treatment. Three biological replicates were performed per genotype per treatment.


title: Transcriptomic changes of Escherichia coli expressing BnTR1 at normal and heat stress conditions

status: Public on Aug 19 2016

city: Köln

first: Yulong

last: Niu

state: Nordrhein-Westfalen

address: Carl-von-Linne-Weg 10

department: Plant Microbe Interactions

institute: Max Planck Institute for Plant Breeding Research

summary: The heat shock response is critical for organisms to survive at a high temperature. Heterologous expression of eukaryotic molecular chaperons protects Escherichia coli against heat stress. Here we report that expression of the plant E3 ligase BnTR1 significantly increase the thermotolerance of Escherichia coli. Different from eukaryotic chaperones, BnTR1 post-transcriptionally regulates the heat shock factor σ32 though zinc fingers of the RING domain, which interacts with DnaK resulting in stabilizing σ32 and subsequently up-regulating heat shock proteins. Our findings indicate the expression of BnTR1 confers thermoprotective effects on E. coli cells, and it may provide useful clues to engineer thermophilic bacterial strains.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: E. coli cells transformed with pET-28a or pET-28a-BnTR1 (OD600nm = 0.6) were induced with 0.1 mM IPTG at 37°C for 1 hour. Then cells were transferred and incubated at 37°C and 42°C for 1 hour, respectively.

first: Yi

last: Yang


title: Gene Expression in whole roots of the Arabidopsis nlp7-1 mutant

status: Public on Jul 31 2016

city: West Lafayette

first: Anjali

last: Iyer-Pascuzzi

state: IN

address: 915 W. State Street

department: Botany and Plant Pathology

institute: Purdue University

summary:
The root cap surrounds the root meristem, protecting it from harsh environments and facilitating root movement through soil. In Arabidopsis, new root cap cells produced in the meristem displace older cells toward the root periphery, where they undergo programmed cell death and are released from the root. This rapid cell turnover is a unique feature of the root cap and is modulated in part by the combined action of four NAC transcription factors, as well as cell wall modification enzymes. Here we show that the transcription factor NIN-LIKE PROTEIN 7 (NLP7) regulates root cap maturation in Arabidopsis by modulating expression of each of the NAC TFs as well as several cell wall modifying enzymes. NLP7 is a homolog of NIN, a transcription factor required for nodulation in Lotus japonicas, and is highly expressed in the columella root cap. Mutants have altered columella root cap development and decreased levels of homogalacturonan, a major component of pectin. Reverse genetic analysis of genes differentially expressed in nlp7 roots showed that two cell wall modifying enzymes, CELLULASE5 and XTH5, modulate root cap maturation likely downstream of NLP7. Plant cell wall modification is critical for nodulation, and we propose that this characteristic is also present in NLPs.
We used microarrays to identify the differences in gene expression between whole roots of WT and nlp7-1 Arabidopsis plants

overall_design: Roots were cut at the root/hypocotyl junction and collected into RLT buffer in the RNeasy plant mini kit. Approximately 60 roots were collected per replicate, with two biological replicates.  RNA was extracted using the RNeasy Micro Kit. Probes for array analysis were preparedfrom 1μg total RNA with the one-cycle amplification protocol by Affymetrix according to the manufacturer's instructions. Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Arabidopsis Whole Genome ATH1 Affymetrix GeneChips.


title: Transcriptome profiling of HeLa-S3 cells treated with siRNAs targeting LATS1 and/or LATS2

status: Public on Jul 26 2016

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Chromatin modifying activities for construction of appropriate epigenetic landscapes by polycomb repressive complex 2 (PRC2) play an essential role in development and tumorigenesis. However, the spatiotemporal mechanisms by which PRC2 achieves diverse epigenomes for specific tissue or cellular contexts remain poorly understood. Here, we discovered that LATS2 knockout causes dysregulation of PRC2 and subsequent transcriptome changes for differentiation in both mouse and human cells. LATS2 depletion dependent dysregulation of PRC2 also effects H3K4me3 and forms negative feedback loop for maintenance of PRC2. Further analyses reveal that LATS2 on chromatin binds to EZH2 and LATS2 has ability to phosphorylate PRC2 in vitro. These LATS2 dependent H3K27me3 targets are highly induced during neurogenesis, and statistical analysis of glioblastoma multiforme reveals that LATS2-high cases show more dedifferentiated transcriptome and poor prognosis with silencing of H3K27me3 targets. These observations suggest that LATS2-mediated epigenome coordination is pivotal for development and disease, including cancer.

overall_design: Four conditions (mock, siLATS1, siLATS2 and siLATS1/LATS2) were analyzed by Agilent Whole Human Genome Microarray 4x44K v2 (eArray) one color experiments, resulting in four individual microarrays.

first: Kosuke

last: Torigata


title: Gene expression profiling of the MLL-AF9 induced AML cells (wild type and Dnmt3b-KO)

status: Public on Jul 01 2016

city: Tianjin

first: Yawei

last: Zheng

state: Tianjin

address: 288 Nanjing Road

department: Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary:
Acute myeloid leukemia (AML) is a heterogeneous hematopoietic disorder with a poor prognosis. Abnormal DNA methylation is involved in the initiation and development of AML. The de novo methyltransferases Dnmt3a and Dnmt3b are responsible for the generation of genomic methylation patterns. While DNMT3A is frequently mutated in hematologic malignancies, DNMT3B is rarely mutated. To investigate the role of Dnmt3b in AML, we genetically inactivated Dnmt3b in an MLL-AF9 induced AML mouse model.
Gene profiling using a microarray revealed the upregulation of the oncogenic gene set and the downregulation of the cell differentiation gene set. Our results indicate that Dnmt3b plays the role of a tumor suppressor in MLL-AF9 AML progression, which reveals new insights into the roles of DNA methylation in leukemic development.

overall_design: Microarray experiments were conducted for 6 samples, including three control leukemia cells and three Dnmt3b knockout (KO) leukemia cells sorted from the BM of leukemia recipient mice.

first: Tao

last: Cheng


title: Influence of human P53 on plant gene expression

status: Public on Jun 26 2016

city: Shanghai

first: Shui

last: Wang

address: 100 Guilin Rd

department: College of Life Sciences

institute: Shanghai Normal University

summary: We used microarrays to identify differentially expressed genes

overall_design: 10-day-old wild type (Col-0) and 35S:P53-transgenic plants. Replicates are derived from three independent biological experiments.