title: DNA 5-methylcytosine in Paramecium

status: Public on Apr 01 2018

city: Foster City

first: Daniel

last: Hogan

state: California

address: private address

type: Methylation profiling by high throughput sequencing

summary: 5-methyl-cytosine DNA methylation regulates gene expression and developmental programming in a broad range of eukaryotes. However, its presence and potential roles in ciliates, complex single-celled eukaryotes with germline-somatic genome specialization via nuclear dimorphism, are largely uncharted. While canonical cytosine methyltransferases have not been discovered in published ciliate genomes, recent studies performed in the stichotrichous ciliate Oxytricha trifallax suggest de novo cytosine methylation during macronuclear development. In this study, we applied bisfulfite genome sequencing, DNA mass spectrometry and antibody-based fluorescence detection to investigate the presence of DNA methylation in Paramecium tetraurelia. While the antibody-based methods suggest cytosine methylation, DNA mass spectrometry and bisulfite sequencing reveal that levels are actually below the limit of detection. Our results suggest that Paramecium does not utilize 5-methyl-cytosine DNA methylation as an integral part of its epigenetic arsenal.

overall_design: We performed bisulfite conversion and Illumina DNA sequencing on 3 samples: one from vegetative cells, one from starved vegetative cells, and one from cells undergoing macronuclear development.

first: Aditi

last: Sigh

first: Adreinne

last: Vancura

first: Alan

last: Hendrick

first: Rafal

last: Woycicki

first: Mariusz

last: Nowacki


title: Transcriptome of Brassica juncea nectaries and leaves

status: Public on Apr 04 2018

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

country: USA

institute: University of Minnesota Duluth

type: Expression profiling by high throughput sequencing

summary: Comparative RNA-Seq study of expression in B.juncea nectaries from different lines.

overall_design: Brassica juncea plants were grown on Sun Gro LC8 soil under a 16 hr day/8 hr night cycle, photosynthetic photon flux of 200 μmol m-2 s-1 at leaf level, and a temperature of 21°C. Three types of RNA samples were separately prepared from both the median and lateral nectaries of flowers, including: ‘pre-secretory’ (24 hours prior to anthesis/nectar secretion), ‘secretory’ (full anthesis, ~4-8 hours after dawn), and ‘post-secretory’ (12 hours after the ‘secretory’ stage). RNA was also isolated from leaf tissue collected at the same time as the nectary ‘secretory’ stage. All nectary tissues were separately dissected by hand from the flowers of primary inflorescences of ca. 40 day-old plants. Due to the small size of nectaries, dissections took place over several days from 4–8 hours after dawn (h.a.d.). Isolated nectaries were pooled in RNAlater™ solution (Ambion, Austin, TX) on ice, and stored at 4°C prior to RNA extraction. Up to four nectaries were collected per flower, with approximately 100 nectaries being processed as a single RNA sample. Each biological replicate was represented by nectaries pooled from different sets of plants. RNA was extracted from nectaries by mechanical disruption, with a microcentrifuge pestle, and using the RNAqueous®-Micro micro scale RNA isolation kit (Ambion, Austin, TX) with Plant RNA Isolation Aid (Ambion, Austin, TX). Agarose gel electrophoresis and UV spectrophotometry were used to assess RNA quality for all samples prior to submission to the University of Minnesota Genomics Center for barcoded library creation and Illumina HiSeq 2500 sequencing. Twenty-one TruSeq RNA v2 libraries were created (triplicate samples for both median and lateral nectaries at ‘pre-secretory’, ‘secretory’, and ‘post-secretory’ stages, as well as in triplicate for leaf) and sequenced via 50 bp, paired-end runs on the HiSeq 2500 using Rapid chemistry. All libraries were pooled and sequenced across two lanes to achieve the equivalent of 1 lane of output. This generated ≥162 M reads and the average quality scores were above Q30.

first: Clay

middle: J

last: Carter


title: Transcriptomes of Pleurotus ostreatus in four different development stages (mycelium, primordium, young fruit body, mature fruit body)

status: Public on Apr 12 2018

city: Wuhan

first: Danyun

last: Xu

address: No. 1, Shizishan Street

country: China

institute: Huazhong Agricultural University

summary: To elucidate the mechanisms of fruit body development in Pleurotus ostreatus, the transcriptomes of four different development stages including mycelium, primordium, young fruit body, and mature fruit body were obtained by RNA-seq.

overall_design: Total mRNA of Pleurotus ostreatus in four different development stages (mycelium, primordium, young fruit body, mature fruit body) were generated by deep sequencing, using Illumina HiSeq 2000.

first: Aimin

last: Ma


title: C. elegans: total mRNA vs. AWA-specifc mRNA

status: Public on Apr 03 2018

city: Hong Kong

first: king

middle: L.

last: Chow

state: Hong Kong

address: clear water bay

department: Life Science

country: Hong Kong

institute: HKUST

summary:
Transcriptional profiling of AWA neurons comparing total mRNA of C. elegans
The aforementioned results provided us a clear indication that a GPCR expressed in AWA would likely be used for pheromone perception. To get a male AWA-specific expression profile, we adopted a poly-A-binding protein (PABP) mRNA pull-down approach to isolate cell-specific genes (Kunitomo et al., 2005) and co-transformed into the worms a sex determination gene, fem-3, to masculinize its nervous system. Ectopic expression of fem-3 in all neurons can change the entire nervous system to adopt a male identity (Ahringer & Kimble, 1991; Rosenquist & Kimble, 1988). We established the male AWA single-cell transcriptional profile by pooling mRNA from AWA with ectopic expression of PABP there driven by an AWA-specific promoter from odr-7. This PABP fused with an epitope protein tag (FLAG tag) is then extracted using the corresponding antibody, while AWA enriched transcripts with poly-A tail, including the GPCRs, were pulled down together and subjected to microarray analysis. The results confirmed the existence of dyp-13 (hypodermal gene), myo-3 (muscle gene) and odr-10 (AWA-specific over-expression gene) in total RNA samples while odr-10 was found to be over-expressed in AWA enriched sample, where dpy-13 and myo-3 were depleted. The pull-down RNA sample was labeled with cyanine 5 (which is excited by a 532nm laser) and the total RNA sample was labeled with cyanine 3 (which is excited by a 633nm laser). Comparison between transcriptome profiles revealed key differences between whole worm and male AWA neurons, which allows identification of male AWA-enriched transcripts including those encoding GPCRs.

overall_design: Two-condition experiment, AWA-specific pull-down mRNA vs. total mRNA. Biological replicates: 4 control replicates, 4 AWA-specific pull-down replicates.

first: King

middle: L

first: Yuan

last: Zhou


title: Transcriptome of sunflower (Helianthus annuus) nectaries and leaf

summary: Comparative RNA-Seq study of expression in sunflower nectaries from different lines.

overall_design: Interspecific crosses of Helianthus annuus displaying differing nectar secretion phenotypes were grown on Sun Gro LC8 soil under a 16 hr day/8 hr night cycle (with supplemental lighting) and a temperature of 23°C in a greenhouse at the University of Minnesota Plant Growth Facility in March-April 2016. Floral nectaries were isolated from mature, secretory florets from each interspecific cross displaying ‘low’ (lines 412 and 441), ‘medium’ (lines 452 and 456) and ‘high’ (lines 434 and 467) levels of nectar production. Nectary and leaf tissue was also harvested from a maintainer line (ER). All nectary tissues were separately dissected by hand from the flowers of primary inflorescences of ca. 40 day-old plants. Due to the small size of nectaries, dissections took place over several days from 4–8 hours after dawn (h.a.d.). Isolated nectaries were pooled in RNAlater™ solution (Ambion, Austin, TX) on ice, and stored at 4°C prior to RNA extraction. Approximately 50 nectaries were processed as a single RNA sample. Each biological replicate was represented by nectaries pooled from different individual plants.

first: Jarrad

middle: R

last: Prasifka


title: Biosynthesis of the antifungal compound fragin is controlled by a novel quorum sensing signal

status: Public on Apr 05 2018

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

summary: Members of the diazeniumdiolate class of natural compounds show great potential for drug development. Yet, their biosynthesis has remained elusive to date. Here, we identify a gene cluster directing the biosynthesis of the diazeniumdiolate compound fragin in Burkholderia cenocepacia H111. We provide evidence that fragin is a metallophore and that metal chelation is the molecular basis of its antifungal activity. We also show that a subset of the fragin biosynthetic genes is involved in the synthesis of a novel cell-to-cell signaling molecule, valdiazen. RNA-Seq analyses revealed that valdiazen not only controls fragin biosynthesis but affects expression of more than 100 genes. Homologs of the valdiazen biosynthesis genes are found in various bacteria, suggesting that valdiazen is the first representative of a new signal molecule class. Using structural information, in silico prediction of enzymatic functions and biochemical data we propose a biosynthesis route for fragin and valdiazen.

overall_design: Triple RNA-seq datasets of B. cenocepacia H111 wild type compared with a mutant strain and the chemical complementation of the mutant strain.

first: Christian

last: Jenul

first: Simon

last: Sieber

first: Christophe

last: Daeppen

first: Anugraha

last: Mathew

first: Martina

last: Lardi

first: Dominic

last: Hoepfner

first: Markus

last: Neuburger

first: Anthony

last: Linden

first: Karl

last: Gademann

first: Leo

last: Eberl


title: Deciphering the dynamic transcriptional and post-transcriptional networks of macrophages in the healthy heart and after myocardial injury

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

country: Spain

institute: CNIC

summary: Macrophage plasticity has been studied in vitro, but transcriptional regulation upon injury is poorly understood.  In this study, we generated a data set for genome-wide transcriptome and miRNAome analysis of macrophages in the healthy heart and after myocardial injury.

overall_design: Cardiac macrophages GFP+ cells were isolated from Cx3cr1GFP/+ knock-in mouse hearts in steady-state and at different post-injury stages.

first: Mercedes

last: Ricote


title: Comparison of the responses of Mycobacterium tuberculosis and Mycobacterium bovis to nutrient starvation

status: Public on Apr 02 2018

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

summary: Transcriptional profiling of Mycobacterium tuberculosis H37Rv and Mycobacterium bovis Ravenel before (i.e., log-phase control) and at 24h and 96h after nutrient starvation. The transcriptional profile of the two strains were compared at log phase, and after 24h and 96h of starvation. In addition, the response of each strain to starvation was examined after 24h and 96h of starvation.

sample_organism: Mycobacterium tuberculosis variant bovis

overall_design:
For examination of the responses of each of the two strains to starvation 6 biological replicates were used and each log phase control (i.e., 6 for each strain) was compared to the starvation samples (i.e., at both 24h and 96h after starvation). This resulted in 24 comparisons (i.e., 12 for each strain).
For comparison of the two strains at each of the 3 time points (i.e., at log-phase, 24h and 96h after starvation) 4 biological replicates of one strain (M.tuberculosis H37Rv) were compared to 6 biological replicates of the other strain (M. bovis Ravenel). This involved a first experiment in which samples from 2 independent cultures of H37Rv were compared to 4 independent cultures of Ravenel (i.e., each H37Rv replicate was compared to each of 2 Ravenel replicates), followed by a 2nd experiment in which 2 independent cultures of H37Rv were compared to 2 independent cultures of Ravenel. This resulted in 18 total comparisons.

first: Morad

last: Hassani


title: Effect of topical treatment with either lung surfactant or selective MMP inhibitor on excisional wounds in mice

city: Hannover

first: Frank

last: Stahl

address: Callinstr. 3

department: Institut für Technische Chemie

country: Germany

institute: Universität Hannover

summary:
The aim of the study was to investigate the effect of bovine lung surfactant or selective MMP inhibition on skin wound healing. Excisional wounds were treated in one subpart of the study with Alveofact or control and in the other with a selective MMP-3 inhibitor UK 370106 in different concentrations.
Lung surfactant and selective MMP-3 inhibitor reduced expression of pro-inflammatory mediators. Lung surfactant treatment activated genes for cell migration and against fibrosis.

overall_design: Results from eight loops that map to eight different groups and two different observation points (day 8 and day 14) are compared in this study. The samples are excised wounds at day 8 or 14. Each sample includes 8-9 raw files which represent technical replicates.

first: Ursula

last: Mirastschijski

first: Patrick

last: Lindner

first: Marcel

last: von der Haar


title: Drought responsive transcriptome profiling in roots of contrasting rice genotypes IR20 and Nootripathu

city: Coimbatore

first: Raveendran

last: Muthurajan

state: Tamil Nadu

address: Tamil Nadu Agricultural University

department: Department of Plant Biotechnology

country: India

institute: Tamil Nadu Agricultural University

summary:
Drought avoidance mechanism is one of the component mechanisms contributing for drought tolerance in which roots serves as the master keys, but poorly understood. Comparative analysis of drought stress responsive root transcriptome between drought-tolerant Nootripathu and drought-susceptible IR20
In this study, we used microarrays to dissect out drought responsive changes in roots of two contrasting rice genotypes viz., IR 20 (a shallow rooted lowland indica genotype) and Nootripathu (a deep rooted upland indica genotype) at molecular level.

overall_design: Plants of two contrasting genotypes i.e. IR20 and Nootripathu were grown in 1m long PVC pipes and subjected to gradual drought stress. Root samples were collected from control and drought stressed plants for RNA extraction and used for hybridization on 52K Affymetrix rice genome expression arrays.

first: Muthukumar

last: Manoharan

first: Valarmathi

last: Ramanathan

first: Hifzur

last: Rahman

first: Jagadeeshselvam

last: Nallathambi


title: Expression analysis of Hepatocyte like-cells derived SHEDs (SHED-Hep cells)

city: Fukuoka

first: Junko

middle: K

last: Fujiyoshi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Pediatrics

country: Japan

institute: Graduate School of Medical Sciences, Kyushu University

summary:
Comparison of whole genome gene expression profiles of stem cells from exfoliated decidous teeth (SHEDs) ,Hepatocyte like-cells derived SHEDs (SHED-Hep cells), and human primary hepatocytes.
We showed that the profile of three different donors of MSC-Hep cells was close to that of human hepatocytes, but separate from that of three different donors of undifferentiated MSCs

overall_design: A fifteen chip study using total RNA recovered from SHEDs, SHED-Hep cells, and human primary hepatocytes, which were isolated from three or two different donors respectively.Total RNA was extracted and subjected to RNA microarray analysis.

first: Takayoshi

last: Yamaza

first: Haruyoshi

first: Soichiro

last: Sonoda

first: Ratih

last: Yuniartha

first: Erika

last: Tomoda

first: Tamotsu

last: Kiyoshima

first: Kenji

last: Ihara

first: Hidetoshi

last: Takada

first: Kazuaki

last: Nonaka

first: Songtao

last: Shi

first: Tomoaki

last: Taguchi

first: Shoichi

last: Ohga


title: Expression data from KOBU-induced Arabidopsis

city: Sendai

first: Satoshi

last: Naramoto

address: 2-1-1, Katahira

institute: Tohoku University

summary:
Plant viruses induce various disease symptoms, but their underlying mechanisms are poorly understood. Kobu-sho is a disease in gentian that show gall formation with ectopic development of lignified cells and vascular tissues such as xylem. Recently, we identified a novel unusual RNA virus, gentian Kobu-sho-associated virus (GKaV) from Kobu-sho-affected gentian. Here, we show that a gene fragment of GKaV, Kobu-sho-inducing factor (KOBU), induces gall formation accompanied with ectopic development of lignified cells and xylem-like tissue in Nicotiana benthamiana. We identify KOBU by screening using potato virus X vector in N. benthamiana, and confirm that transgenic gentian expressing KOBU causes tumorous symptom.
Transgenic Arabidopsis thaliana expressing KOBU activates signaling pathways regulating xylem development. KOBU protein forms granules and plate-like structures and co-localizes with mRNA splicing factors within nucleus. Our findings provide novel insights into not only virus disease development but also vascular development in plant.

overall_design: Arabidopsis that express KOBU by DEX dependent manner were selected at successive induced time for RNA extraction and hybridization on Affymetrix microarrays. We prepared samples afther the treatment with DEX for 4hr, 8hr, 12hr, 1day, 2day, 3day, 5day, and 7day.

first: Hakamada

last: Yukiko


title: Gene expression profile of AU019823-gene-trapped early mesodermal cells and their revertant cells

city: Kamakura

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Using our previously established homozygous mutant mouse ESC bank, we identified a previously uncharacterized novel gene AU019823, which we named “attenuated hematopoietic development (Ahed)”, whose null mutant ESCs exhibited attenuated production (70-fold fewer) of blood cells during the hematopoietic differentiation supported by coculture with OP9 stromal cells. Both mutant and revertant (almost identical to wild-type) ESCs normally differentiate into Flk-1-positive early mesodermal cells in vitro. In this study, to explore the function of this gene, we analyzed the gene expression profile of Flk-1-positive cells with these two genotypes.

overall_design: In this study presented here, a total of two samples were analyzed: Flk-1-positive cells differentiated from AU019823 gene-trapped (biallelically disrupted) ESCs and their revertant (almost identical to wild-type) ESCs were subjected to gene expression analyses.

first: Masahiro

last: Tokunaga

first: Junji

last: Takeda


title: Transcriptomic and hormonal control of Boron uptake, accumulation and toxicity tolerance in Poplar

city: tokat

first: Kubilay

last: Yıldırım

address: tasliciftlik kampusu

country: Turkey

institute: gaziosmanpasa university

summary: Boron (B) is an essential nutrient for normal growth of plants. Despite its low abundance in soils, B pollution and toxicity have been reported to increase in especially arid and semi-arid environments. Poplars are known to be tolerant species to B toxicity and accumulation. In the current study, physiological, transcriptomic and hormonal regulations behind B toxicity response were investigated comparatively in poplar species. Previously identified clones of Populus nigra (P.n) and Populus alba (P.a) having contrasting B accumulation and leaf B toxicity symptoms were treated with elevated soil B supply in a pot trial. The physiological results of treatment indicated better biomass growth, higher leaf chlorophyll content and more than three folds lower B accumulation in leaves of P.a compared to P.n. Microarray based transcriptomic analysis revealed 1902 and 1006 differentially regulated transcripts for the leaves and roots of P.a, respectively. Several transcripts responsible in salicylic acid (SA) production (salicylic acid binding protein 2) and SA dependent gene regulation (chitinases, proteases, lipases and protease inhibitors) were strongly upregulated specifically in P.a tissues under B toxicity. Furthermore, endogenous SA content in the roots and leaves of P.a increased with a soil B concentration-dependent manner while there was no significant alteration in the same hormone for P.n tissues under B toxicity. Therefore, increase in endogenous SA concentration was strongly attributed to lower B uptake and B toxicity tolerance in P.a. In addition to SA mediated gene regulation, genes responsible in external excretion process was also supposed to be functional in P.a for reduction of tissue B content under toxic conditions. On the other hand, transcriptome profiling of P.n under B toxicity revealed 1624 and 1419 altered transcripts for the leaves and roots, respectively.  Specific induction in transcripts annotated to ATP binding cassette B type transporters, glutathione S transferases and metallochaperones in P.n were linked to internal excretion of excess B in the species that could be related with much higher B uptake from the roots, directional transport to the leaves and detoxification under toxic B conditions.

sample_organism:
Populus nigra
Populus alba

overall_design: Total RNA used in microarray experiment was isolated from the leaves and roots of populus alba and populus nigra clones  which have contrasting B accumulation in their leaves. Total RNA used in the microarray experiment was isolated from leaves and roots of three black poplar saplings grown in ~ 1.5 ppm (control) and ~ 10 ppm (toxic) soil B contents. RNA isolation was made according to Lithium chloride precipitation method described in Chang et al. (1993). These three isolated RNAs (biological replicates) for each tissue loaded onto three Affymetrix poplar Gene Chips (technical replicates). Totally, 16 GeneChips (2 tissues × 2 different B treatment × 2 technical replicatesX 2 species) were used for transcriptional analysis.

last: YILDIRIM


title: Immunomodulation and effects on microbiota after in ovo administration of chicken cathelicidin-2

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

country: Netherlands

institute: Utrecht University

summary: Host Defense Peptides (HDPs) such as cathelicidins are multifunctional effectors of the innate immune system with both antimicrobial and pleiotropic immunomodulatory functions. Chicken cathelicidin-2 (CATH-2) has multiple immunomodulatory effects in vitro and the D-amino acid analog of this peptide has been shown to partially protect young chicks from a bacterial infection. However, the mechanisms responsible for CATH-2 mediated in vivo protection have not been investigated so far. In this study, D-CATH-2 was administered in ovo and the immune status and microbiota of the chicks were investigated at 7 days posthatch to elucidate the in vivo mechanisms of the peptide. In three consecutive studies, no effects on numbers and functions of immune cells were found and only small changes were seen in gene expression of PBMCs. Between studies, intestinal microbiota composition was highly variable, suggesting that it was strongly influenced by environmental factors. In both studies, in ovo D-CATH-2 treatment caused significant reduction of Ruminococcaceae and Butyricicoccus in the cecum and Escherichia/Shigella in both ileum and cecum. In conclusion, this study shows that, in the absence of an infectious stimulus, in ovo administration of a CATH-2 analog alters the microbiota composition, but does not affect the chicks immune system posthatch.

overall_design: Expression profiling of PBMCs from chicks treated in ovo with cathelicidin-2 or placebo

first: Tryntsje

last: Cuperus

first: Henk

last: Haagsman


title: Involvement of kallikrein-related peptidase 6 in epithelial to mesenchymal transition induced by ΔNp63 downregulation in oral squamous cell carcinoma through activation of protease activated receptors

first: Naoki

last: Kaneko

department: Division of Maxillofacial Diagnostic and Surgical Sciences

institute: Kyushu University Faculty of Dental Science

summary: Recent studies showed epithelial-mesenchymal transition (EMT) is involved in cancer progression.  Though we revealed that downregulation of ΔNp63 in oral squamous cell carcinoma (OSCC) induces EMT, the detailed molecular mechanisms remain to be elucidated.  DNA microarray analyses were thus performed by using OSCC cell line overexpressing ΔNp63 to examine the genes associated with EMT.  The results revealed that kallikrein related peptidase 6 (KLK6) was most upregulated in the OSCC cells overexpressing ΔNp63.

overall_design: We obtained two newly established clones: SQUU-BO with constitutive expression of DNp63b and SQUU-BC transfected with empty vector.  Then, Microarray was performed for comparison between gene expression of SQUU-BO and that of SQUU-BC.

first: Shintaro

last: Kawano

first: Ryota

last: Matsubara

first: Yuichi

last: Goto


title: Expression data from mouse bone marrow late pre-B cells

status: Public on Mar 31 2018

city: Cincinnati

first: Stephen

middle: Noel

last: Waggoner

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary:
B-cell development in the bone marrow proceeds through phenotypically defined stages. At the pre-B cell stage, cells stop cycling and rearrange the light chain of immunoglobulin. There are notable defects in the number of these cells and subsequent stages of B-cell development in mice with hematopoietic deficiency of the gene Ddx3x, when compared to wildtype control mice.
We used microarrays to determine differences in gene expression between bone marrow pre-B cells in wild-type mice and those deficient in Ddx3x in hematopoietic cells (Vav1-cre x Ddx3x-floxed, male, hemizygous)

overall_design: Bone marrow late pre-B cells (CD3-,Ly6C-,Ter119-,CD11b-,Gr1-,B220+,CD43-,IgM-,IgD-) were sorted from 4 male Ddx3x hemizygous (Vav1Cre+ Ddx3x-fl/Y) mice and 4 male littermates (Vav1Cre- Ddx3x-Fl/Y). Total cellular RNA was isolated from sorted cells and subjected to analysis on GeneChip Mouse Gene 2.0 arryas (Affymetrix).

middle: N

first: John

middle: B

last: Harley

first: Ke

last: Liu


title: Overexpression of 3 transcription factors uniquely induced by salt in Arabidopsis

city: GIFU

first: AYAN

last: SADHUKHAN

state: GIFU

address: 1-1 YANAGIDO

department: APPLIED BIOLOGICAL SCIENCES

institute: GIFU UNIVERSITY

summary: Overexpression of ERF019, BBX29 and CCA1 in Arabidopsis

overall_design:
Transcriptional profiling of transgenic Arabidopsis comparing wild type Col-0 seedlings with transgenic lines overexpressing ERF019(AT1G22810), BBX29(AT5G54470) and CCA1(AT2G46830).  Goal was to determine the effects of overexpression of these TFs on global gene expression in Arabidopsis to explain salt and drought tolerant phenotypes.
Two-condition experiment, WT vs. transgenic. Biological replicates: 2 wild type replicates, 2 transgenic replicates each for 3 gene overexpressors.

first: Ayan

last: Sadhukhan

first: Yuriko

last: Kobayashi

first: Hiroyuki

last: Koyama


title: Transcriptome analysis of Arid1a-deficient IPMN and Brg1-deficient IPMN

city: Kyoto

first: Yoshito

last: Kimura

state: Kyoto

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

department: Gastroenterology and Hepatology

institute: Kyoto University Graduate School of Medicine

summary: Mutations of subunit genes of the SWI/SNF chromatin remodeling complexes were found in 12-23% of human Pancreatic Ductal Adenocarcinoma (PDAC). We previously showed that Brg1, a catalytic ATPase subunit of the SWI/SNF chromatin remodeling complexes, inhibits the formation of intraductal pancreatic mucinous neoplasms (IPMN) and IPMN-derived PDAC from ductal cells. On the other hand, ARID1A is the most frequent target of mutations in the SWI/SNF chromatin remodeling complexes in human PDAC. We found that Arid1a loss in the context of mutant Kras resulted in formation of IPMN and PDAC. We also found that the incidence of PDAC formation in Ptf1a-Cre; KrasG12D; Arid1af/f mice was markedly lower than that in Ptf1a-Cre; KrasG12D; Brg1f/f mice despite the similarities between Arid1a-deficient and Brg1-deficient IPMNs. We extracted total RNA from intraductal papillary mucinous neoplasms (IPMNs) in Ptf1a-Cre; KrasG12D; Arid1af/f and Ptf1a-Cre; KrasG12D; Brg1f/f mice and perform microarray analysis.

overall_design: Analysis of mRNA from IPMNs in two Ptf1a-Cre; KrasG12D; Arid1af/f mice and three Ptf1a-Cre; KrasG12D; Brg1f/f mice.

first: Akihisa

last: Fukuda


title: Single-cell genetic analysis of clonal dynamics in colorectal adenomas indicates CDX2 gains as a predictor of recurrence

city: Bethesda

first: Yue

last: Hu

state: MD

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

institute: NCI

type: Genome variation profiling by genome tiling array

summary:
Colorectal adenomas are common precancerous lesions with the potential for malignant transformation to colorectal adenocarcinoma. Endoscopic polypectomy provides an opportunity for cancer prevention, however, recurrence rates are high. We collected formalin-fixed paraffin-embedded tissue of fourteen primary adenomas with recurrence, fourteen primary adenomas without recurrence, and fourteen matched pair samples (primary adenoma and the corresponding recurrent adenoma). These samples were analysed by array-based comparative genomic hybridisation (aCGH) to understand the dynamics of copy number alterations (CNAs) and to identify molecular markers to predict recurrence. ACGH analysis confirmed the genetic landscape specific for colorectal tumorigenesis, i.e., CNAs of chromosomes 7 (13.7%), 13q (13.7%), 18 (5.8%) and 20q (13.7%).
CNAs were detected in 41/51 (80.4%) of colorectal adenomas (2N). Focal aberrations (≤10 Mbp) were mapped to chromosome bands 6p22.1-p21.33 (33.3%), 7q22.1 (31.4%) and 16q21 (29.4%). Gains of CDX2 were exclusively seen in adenomas with recurrence compared to adenomas without recurrence. However, the average number of copy alterations failed to discriminate primary adenomas with recurrence from primary adenomas without recurrence.

overall_design: Array-based CGH experiment: DNA of 14 primary colorectal adenoma samples without recurrence, 27 primary colorectal adenoma samples with recurrence and 13 matched recurrent adenoma samples. Biological replicates: 41 colorectal adenomas (Cy3) versus control DNA (Cy5).

first: D

last: Fiedler

first: K

last: Heselmeyer-Haddad

last: Hirsch

first: L

last: Hernandez

first: I

last: Torres

last: Wangsa

first: J

last: Rueschoff

first: S

last: Belle

first: T

last: Ried

last: Gaiser


title: The effect of new probiotic mixture in DSS (dextran sulphate sodium) – induced colitis mouse model

status: Public on Mar 23 2018

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

summary:
The current study was designed to clarify signalling pathways and assess possible beneficial effect of new probiotic mixture in DSS (dextran sulphate sodium) – induced colitis mouse model. Manipulation of intestinal microbiota with probiotics represents a promising alternative or adjunct therapy in gastrointestinal disorders and inflammation.
RNA extracted from the middle part of colon tissue from ~11 weeks female C57BL/6JOlaHsd mouse strain was used for examination of the global gene expression using Affymetrix GeneChip Mouse Gene 2.0 ST microarrays.

overall_design: Two factor experimental design: two conditions (Healthy and DSS-induced colitis) and three treatments (None-saline, Probiotic, CsA-cyclosporine A), w/o CsA treatment of healthy animals. 4 biological replicates per condition, 20 mice altogether.

first: Rok

last: Košir

first: Diana

last: Paveljšek

first: Irena

last: Rogelj


title: MicroRNA expression in serum samples of sulfur mustard veterans as a diagnostic gateway to improve care

status: Public on Mar 01 2018

city: Kerman

first: Sedigheh

last: Gharbi

address: Mostafa Khomeyni St.

department: Department of Biology

country: Iran

institute: Shahid Bahonar University of Kerman

summary:
Sulfur mustard is a vesicant chemical warfare agent, which has been used during Iraq-Iran-war. Many veterans and civilians still suffer from long-term complications of sulfur mustard exposure, especially in their lung. Although the lung lesions of these patients are similar to Chronic Obstructive Pulmonary Disease (COPD), there are some differences due to different etiology and clinical care. Less is known on the molecular mechanism of sulfur mustard patients and specific treatment options. microRNAs are master regulators of many biological pathways and proofed to be stable surrogate markers in body fluids. Based on that microRNA expression for serum samples of sulfur mustard patients were examined, to establish specific microRNA patterns as a basis for diagnostic use and insight into affected molecular pathways. Patients were categorized based on their long-term complications into three groups and microRNA serum levels were measured. The differentially regulated microRNAs and their corresponding gene targets were identified. Cell cycle arrest, ageing and TGF-beta signaling pathways showed up to be the most deregulated pathways.
The candidate microRNA miR-143-3p could be validated on all individual patients. In a ROC analysis miR-143-3p turned out to be a suitable diagnostic biomarker in the mild and severe categories of patients. Further microRNAs which might own a link to the biology of the sulfur mustard patients are miR-365a-3p, miR-200a-3p, miR-663a. miR-148a-3p, which showed up only in a validation study, might be linked to the airway complications of the sulfur mustard patients. All the other candidate microRNAs do not directly link to COPD phenotype or lung complications. In summary the microRNA screening study characterizes several molecular difference in-between the clinical categories of the sulfur mustard exposure groups and established some useful microRNA biomarkers.

overall_design: 6 samples in three groups, two replicates each, are provided. n: denotes serum samples from healthy patients not affected by sulfur mustard. The i:mild and s:severe group comprises patients which show a weak or strong sulfur mustard disease phenotype maybe reflecting a true disease progression. The objectives of this study were to find out if the microRNA expression is differentially expressed in serum samples of SMV compared to normal ones, and which biological pathways are linked to the differentially expressed microRNAs. This can be exploited in defining therapeutic strategies for the clinical procedures or diagnostic applications. Here, microRNAs might offer an appropriate and reliable diagnostic alternative, which can be a substitute for more inaccurate diagnostic methods of SMV like high resolution CT scan and PFT. Finally, this study should help to reconfirm some preliminary aspects of previous research efforts.

first: Eberhard

last: Korsching

first: Seyed

last: Mowla


title: Microarray analysis of the eVSM population for the A2lox.empty cell line

status: Public on Mar 20 2018

city: Monterotondo

first: Christophe

last: Lancrin

state: RM

address: Via Ramarini 32

department: EMBL Rome

country: Italy

institute: EMBL

summary: The aim of the experiment was to study the transcriptome changes occuring after doxycycline treatment of the enriched vascular smooth muscles (eVSM) population.

overall_design: A total of 9 samples were analyzed. A2lox.empty ESCs were differentiated for 3 days. Flk1+ cells were isolated and were cultured in BL-CFC culture for 1 day. eVSM (CD41-/VE-cad-) cell population was FACS-sorted. We collected total RNA from eVSM before hemogenic endothelium (HE) culture (t0), eVSM–dox (24h post-HE culture) and eVSM+dox (24h post-HE culture). Each sample group was analyzed by microarray using 3 biological replicates.

first: Isabelle

last: Bergiers


title: Identification of cell-free DNA in gastric cancer patient

city: Daejeon

first: Jinjong

last: Bong

address: Daehak-ro

country: South Korea

institute: NEXBIO

summary: cfDNA (Cell-free DNA) was extracted from serum exosome of gastric cancer patient. We analyzed cfDNA by aCGH (array comparative genomic hybridization).

overall_design: T1 early carcinoma patients versus normal; T3 advanced carcinoma patients versus normal


title: Expression data from tomato root tissue inoculated or not with a plant growth promoting bacteria (PGPB) strain

status: Public on Jan 29 2018

city: Granada

first: Pablo

last: Ibort Pereda

state: Granada

address: Profesor Albareda 1

department: Microbiología del Suelo y Sistemas Simbióticos

institute: Spanish National Research Council (EEZ-CSIC)

summary:
Possitive effects of plant growth promoting bacteria (PGPB) inoculation on plant growth and development are dependent on interaction between bacterial strains and plant roots, which are usually the bacterial niche.  Furthermore, phytohormones are key regulators of plant physiology. Ethylene is essential in plant growth and development and in response to drought. Plant sensibility to ethylene is involved in plant response  to PGPB strain inoculation and plant growth promotion.
We used microarrays to detail the global programme of gene expression underlying plant interaction with two different PGPB strains (isolated from arid soils in southern Spain) regarding to plant sentitivity to ethylene by tomato ethylene receptor 3 (SlETR3).

overall_design: Ethylene-insensitive never ripe and its isogenic wild-type cv. Pearson lines were inoculated with either Bacillus megaterium or Enterobacter sp. C7 and grown until mature stage (eight weeks post-inoculation) under well-watered and drought conditions.  The present study pursued to assess the bacterial effects on gene expression in tomato (Solanum lycopersicum).  Root tissue samples inoculated or not with a bacterial strain were selected for RNA extraction and hybridization on Affymetrix microarrays.  To that end, we selected three samples per treatment according to plant sensitivity to ethylene, watering regime and inoculated bacteria: wild type cv Pearson (WT) and never ripe (NR) plants under well-watered and drought (D) conditions non-inoculated (NO, controls),  or inoculated either with Bacillus megaterium (BM), or Enterobacter C7 (C7).

last: Ibort

first: Sonia

last: Molina

first: Juan-Manuel

last: Ruiz-Lozano

first: Ricardo

last: Aroca


title: Genomic profiles of  unresectable localized peripheral neuroblastic tumours without MYCN amplificatioun of children over the age of 12 months

status: Public on Mar 22 2018

city: Paris

first: Nathalie

last: Clément

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary:
Background: The prognostic impact of segmental chromosome alterations (SCAs) in children older than 1 year, diagnosed with localised unresectable neuroblastoma (NB) without MYCN amplification enrolled in the European Unresectable Neuroblastoma (EUNB) protocol is still to be clarified, while, for other group of patients, the presence of SCAs is associated with poor prognosis.

Methods: To understand the role of SCAs we performed multilocus/pangenomic analysis of 98 tumour samples from patients enrolled in the EUNB protocol.

Results: Age at diagnosis was categorised into two groups using 18 months as the age cutoff. Significant difference in thepresence of SCAs was seen in tumours of patients between 12 and 18 months and over 18 months of age at diagnosis, respectively (P<0.04). A significant correlation (P<0.03) was observed between number of SCAs per tumour and age. Event-free (EFS) andoverall survival (OS) were calculated in both age groups, according to both the presence and number of SCAs. In older patients, a poorer survival was associated with the presence of SCAs (EFS<46% vs 75%, P<0.023; OS<66.8% vs 100%, P<0.003). Moreover, OS of older patients inversely correlated with number of SCAs (P<0.002). Finally, SCAs provided additional prognostic information beyond histoprognosis, as their presence was associated with poorer OS in patients over 18 months with unfavourable International Neuroblastoma Pathology Classification (INPC) histopathology (P<0.018).

Conclusions: The presence of SCAs is a negative prognostic marker that impairs outcome of patients over the age of 18 months with localised unresectable NB without MYCN amplification, especially when more than one SCA is present. Moreover, in older patients with unfavourable INPC tumour histoprognosis, the presence of SCAs significantly affects OS.

overall_design: multilocus/pangenomic analysis of 26 tumour samples from patients enrolled in the EUNB protocol

first: Gudrun

last: Schleiermacher


title: Microarray analysis of the Endo and eVSM populations for the A2lox.i8TFs cell line

summary: The aim of the experiment was to study the transcriptome changes occuring after overexpression of Erg, Fli1, Tal1, Lyl1, Lmo2, Runx1, Cbfb and Gata2 in endothelial (Endo) and enriched vascular smooth muscles (eVSM) populations.

overall_design: A total of 18 samples were analyzed. A2lox.i8TFs ESCs were differentiated for 3 days. Flk1+ cells were isolated and were cultured in BL-CFC culture for 1 day. Endo (CD41-/VE-cad+) and eVSM (CD41-/VE-cad-) cell populations were FACS-sorted. We collected total RNA from eVSM before hemogenic endothelium (HE) culture (t0), eVSM–dox (24h post-HE culture), eVSM+dox (24h post-HE culture), Endo before HE culture (t0), Endo–dox (24h post-HE culture) and Endo+dox (24h post-HE culture). Each sample group was analyzed by microarray using 3 biological replicates.


title: Iron starvation in Bifidobacterium breve UCC2003 increases bile resistance through enhanced expression of a bile salt hydrolase

city: Cork

first: Noreen

last: Lanigan

state: Cork

address: Biosciences Institute, University college Cork, cork, ireland.

department: Microbiology

country: Ireland

institute: University college cork

summary: Bifidobacterium are considered to be beneficial for human health and are classified as probiotic bacterium.  They must resist many environmental stress factors in order to survive in the gastrointestinal environment including; pH, oxygen availability, bile and nutrient starvation (eg: iron or carbon).  This study investigates Bifidobacterium breve UCC2003 global genome response to growth under ferrous and/or ferric iron limiting conditions. Revealing that growth under iron limitation effects many processes in the cell including carbon and nitrogen metabolism and induces/reduces the expression of numerous genes; including multiple iron uptake systems, DPS proteins (which are predicted to be involved in iron storage/DNA protection), Fe-S cluster associated proteins and a bile salt hydrolase (bshB). Insertional mutagenesis and survival assays were employed and demonstrated that iron starvation imposed on B. breve UCC2003 results in an increased resistance to bile stress due to in part the iron-inducible transcription of the bshB gene.  Furthermore, this study links BSH activity in B. breve UCC2003 to its ability to survive the deleterious effects of bile salt and suggest that B. breve UCC2003 may be use iron as a signal to adapt to the constantly changing environment within the small intestine.

overall_design: DNA-microarrays containing oligonucleotide primers representing each of the 1864 annotated genes on the genome of B. breve UCC2003 (O'Connell Motherway et al., 2011) were designed by and obtained from Agilent Technologies (Palo Alto, Ca., USA). Methods for cell disruption, RNA isolation, RNA quality control, complementary DNA synthesis and labeling were performed as described previously (Pokusaeva et al., 2009). Labeled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A). Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). DNA-microarray data were processed as previously described (Garcia De La Nava et al., 2003). Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long et al., 2001). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.

first: Douwe

last: van Sinderen


title: A translational repression complex in developing mammalian neural stem cells that regulates neuronal specification

status: Public on Jan 26 2018

city: Toronto

first: Freda

last: Miller

state: ON

address: 686 Bay Street

country: Canada

institute: Hospital For Sick Children

summary: The mechanisms instructing genesis of neuronal subtypes from mammalian neural precursors are not well-understood.  To address this issue, we have characterized the transcriptional landscape of radial glial precursors (RPs) in the embryonic murine cortex.  We show that individual RPs express mRNA but not protein for transcriptional specifiers of both deep and superficial layer cortical neurons.  Some of these mRNAs, including the superficial versus deep layer neuron transcriptional regulators Brn1 and Tle4, are translationally repressed by their association with the RNA-binding protein Pumilio2 and the 4E-T protein.  When these repressive complexes are disrupted in RPs mid-neurogenesis by knocking down 4E-T or Pum2, this causes aberrant co-expression of deep layer neuron specification proteins in newborn superficial neurons.  Thus, cortical RPs are transcriptionally primed to generate diverse types of neurons, and a 4E-T-Pum2 complex represses translation of some of these neuronal identity mRNAs to ensure appropriate temporal specification of daughter neurons.

overall_design: We obtained 3 biological replicates of IgG-bound RNA, Pum2-bound RNA, and corresponding total RNA input from E12/E13 mouse cortices. RNA samples were analyzed on Mouse Gene 2.0 ST Arrays (Thermo Fisher)

first: Siraj

last: Zahr

first: Guang

last: Yang

first: Hilal

last: Kazan

first: Michael

last: Borrett

first: Scott

middle: A

last: Yuzwa

first: Anastassia

last: Voronova

first: David

last: Kaplan

middle: D


title: The composition of the bacteria found in liver, spleen, oral cavity and fecal samples of mice subjected to an experimental periodontitis model

city: Tokyo

first: Masayuki

last: Tsukasaki

address: 7-3-1 Hongo Bukyo-ku

department: Department of Immunology  Graduate School of Medicine and Faculty of Medicine

institute: The University of Tokyo

summary: Periodontitis patients often develop bacteremia, but there has been little evidence showing that oral bacteria translocate into other organs. We found that bacterial colony formation occurs in a culture of liver and spleen cells of periodontitis-induced mice, and the bacterial species detected in the liver and spleen were found in the oral cavity as well, but not in fecal samples, indicating systemic dissemination of oral bacteria during the breakdown of the oral barrier.

overall_design: We performed this experiment to check if the bacteria found in liver and spleen originated from oral cavity or the gut during periodontitis. Bacterial DNA was extracted from the periodontitis-inducing ligature, fecal sample and tissue cultures with a NucleoSpin® Tissue Kit (Takara). The V4 region of 16S rRNA genes was PCR amplified (25 cycles, primer pair F515/R806), followed by barcoding (8 cycles) using a Nextera XT Index Kit v2 (Illumina) in triplicate. Barcoded amplicons were sequenced (150-bp paired-end sequencing) on an Illumina MiSeq (Illumina).

first: Noriko

last: Komatsu

first: Kazuki

last: Nagashima

first: Takeshi

last: Nitta

first: Warunee

last: Pluemsakunthai

first: Chisa

last: Shukunami

first: Yoichiro

last: Iwakura

first: Tomoki

last: Nakashima

first: Kazuo

last: Okamoto

first: Hiroshi

last: Takayanagi


city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

summary:
Genomic  characterization of mesothelioma patients by CGH arrays.
Genomic  characterization of mesothelioma patients by CGH arrays.

overall_design: The goal of this study was to determine the main genomic aberrations related to mesothelioma in a French cohorte.

first: Marie

last: Brevet


title: Transcriptomic responses of Clostridium (Ruminiclostridium) thermocellum ATCC27405 and ethanol tolerant strains to ethanol stress

city: Oak Ridge

first: Jason

last: Whitham

address: 1 Bethel Valley Rd Bld 1505 Rm 366 MS 6038

country: USA

institute: Oak Ridge National Labs

summary: Transcriptome profiles for Clostridium thermocellum ATCC 27405 wild type strain and two ethanol-adapted strains, E50A and E50C were generated to gain insights into ethanol tolerance. Details of the strains have been described, Shao X., et al. Appl Microbiol Biotechnol (2011) 92:641–652.

overall_design: Duplicate fermentations using MTC medium were conducted for Clostridium thermocellum strains, ATCC 27405 wild-type; ethanol adapted strain E50A (adapted to grow in presence of up to 50 g/L ethanol on Avicel); and ethanol adapted strain E50C (adapted to grow in presence of up to 50 g/L ethanol on cellobiose). These strains have been described previously by Shao X., et al Appl Microbiol Biotechnol (2011) 92:641–652. A fifty two array study using total RNA processed from fermenation cultures of Clostridium thermocellum ATCC 27405 and ethanol adapted strains E50C and E50A, which were shocked with either 10 or 40 g/L ethanol. Cells were harvested immediately after, 15 minutes, 1 hour, 2 hours, and 4 hours after ethanol shock.

first: Xiongjun

last: Shao

first: Babu

last: Raman

first: Courtney

middle: M

last: Johnson

first: Miguel

last: Rodriguez

first: Jonathan

last: Mielenz

first: Lee

last: Lynd

first: Steven

last: Brown


title: Tumor-stroma IL-1β-IRAK4 Feedforward Circuitry Drives Tumor Fibrosis, Chemo-resistance and Poor Prognosis in Pancreatic Cancer

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: Targeting the desmoplastic stroma of pancreatic ductal adenocarcinoma (PDAC) holds promise to augment the effect of chemotherapy, but so far success remains limited in the clinic. Furthermore, preclinical mouse models suggest that near-depletion of cancer-associated fibroblasts (CAFs) carries a risk of accelerating PDAC progression. These concerns underscore the need to concurrently target the key signaling mechanisms that drive the malignant attributes of both CAFs and PDAC cells. We previously reported that inhibition of Interleukin-1 Receptor Associated Kinase 4 (IRAK4) suppresses NF-kB activity and promotes chemotherapy response in PDAC cells. In this study, we show that CAFs in PDAC tumors robustly express activated IRAK4 and NF-kb. The role of IRAK4 and NF-kB in PDAC CAFs has not been reported, and should be clarified before advancing IRAK4 inhibitors to the clinic. Using shRNAs and small molecular inhibitors, we found that IRAK4 is a key driver of NF-kB activity in CAFs. We showed that CAFs utilizes IRAK4 to drive tumor fibrosis, support PDAC cells proliferation, survival and chemoresistance in vitro and in vivo. From cytokine array analysis of CAFs and microarray analysis of PDAC cells, we identified IL-1b as a key cytokine that activates IRAK4 in CAFs. Targeting IRAK4 or IL-1b renders PDAC tumors less fibrotic and more sensitive to gemcitabine in vivo. Moreover, high IL-1b expression by immunohistochemistry in PDAC stroma is strongly associated with poor overall survival. Together, our studies established a tumor-stroma IL-1b-IRAK4 feedforward circuitry that can be therapeutically disrupted to render chemotherapy more effective in PDAC.

overall_design: We use both pharmacological and shRNA approaches to explore the contribution of IRAK1/4 inhibition in pancreatic cancer cells. For pharmacological approach, we use PANC-1 and Capan-1 for study since these two cell lines express activated form of IRAK1 and IRAK4. For shRNA approach, we use PANC-1 for analysis.

first: Kian-Huat

last: Lim

first: Daoxiang

last: Zhang


title: Transcriptome analysis of  Streptomyces natalensis HW-2 to fungal elicitor using RNA-sequencing

city: Luoyang

first: wei

middle: lan

last: lan

address: Kaiyuan avenue

country: China

institute: Henan University of Science and Technology

summary: To characterize the differentially expressed genes between adding fungal elicitor and without  fungal elicitor on Streptomyces natalensis HW-2

overall_design: The elicitor was added to the fermentation medium of S. natalensis HW-2 after fermentation for 24 h at 28oC with the shaking of 180r/min.using RNA-sequencing,we determine the difference of gene expression in different time of fungal elicitor on Streptomyces natalensis

first: Lan

last: Wei


title: Long non-coding RNA profiling in 6 cell types

status: Public on Mar 30 2018

first: Philip

last: Marsden

address: 209 Victoria Street, Room 522

department: Medicine

institute: University of Toronto

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

summary: To identify endothelial cell (EC)-enriched long noncoding RNAs (lncRNAs), gene expression analysis was conducted on two EC cell types and 4 non-EC cell types. Specifically, the EC cell types were human umbilical vein endothelial cells (HUVEC) and human dermal microvascular endothelial cells (HMVEC). The 4 non-EC cell types were human aortic smooth muscle cells (HASMC), Fibroblasts, Hepatocytes, and keratinocytes. Of the 23 155 putative lncRNAs represented in the custom lncRNA microarrays, 18 524 lncRNAs were found to be expressed above the 20% percentile in at least one cell type. Importantly, 28 EC-enriched lncRNAs were identified in common between HUVEC and HMVEC with 28 and 59 enriched uniquely in either HUVEC or HMVEC, respectively. Of interest, STEEL, an EC-enriched lncRNA was identified and its role in EC biology was further characterized.

overall_design: RNA samples of HUVEC, HMVEC, HASMC, fibroblasts, hepatocytes and keratinocytes were extracted and subjected to gene expression analysis using a custom nimblegen microarray that recognizes 23 155 putative lncRNAs and 19 484 protein-coding genes.

first: H

middle: S

last: Man


title: Expression profiling of Cellvibrio japonicus using either glucose or xyloglucan

status: Public on Jan 25 2018

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

summary: Background: Xyloglucan (XyG) is a ubiquitous and fundamental polysaccharide of plant cell walls. Due to its structural complexity, XyG requires a combination of backbone-cleaving and sidechain-debranching enzymes for complete deconstruction into its component monosaccharides. The soil saprophyte Cellvibrio japonicus has emerged as a genetically tractable model system to study biomass saccharification, in part due to an innate capacity to utilize a wide range of plant polysaccharides for growth. Whereas the downstream debranching enzymes of the xyloglucan utilization system of C. japonicus have been functionally characterized, the requisite backbone-cleaving endo-xyloglucanases were unresolved. Results: Combined bioinformatic and transcriptomic analyses implicated three Glycoside Hydrolase Family 5 Subfamily 4 (GH5_4) members, with distinct modular organization, as potential keystone endo-xyloglucanases in C. japonicus.  Detailed biochemical and enzymatic characterization of the GH5_4 modules of all three recombinant proteins confirmed particularly high specificities for the XyG polysaccharide versus a panel of other cell wall glycans, including mixed-linkage beta-glucan and cellulose.  Moreover, product analysis demonstrated that all three enzymes generated XyG oligosaccharides required for subsequent saccharification by known exo-glycosidases.  Crystallographic analysis of GH5D, which was the only GH5_4 member specifically and highly upregulated during growth on XyG, in free, product-complex, and active-site affinity-labelled forms revealed the molecular basis for the exquisite XyG specificity among these GH5_4 enzymes.  Strikingly, exhaustive reverse-genetic analysis of all three GH5_4 members and a previously biochemically characterized GH74 member failed to reveal a growth defect, thereby indicating functional compensation in vivo, both among members of this cohort and by other, yet unidentified, xyloglucanases in C. japonicus.  Our systems-based analysis indicates distinct substrate-sensing (GH74, GH5E, GH5F) and attack-mounting (GH5D) functions for the endo-xyloglucanases characterized here. Conclusions: Through a multi-faceted, molecular systems-based approach, this study provides a new insight into the saccharification pathway of xyloglucan utilization system of C. japonicus. The detailed structural-functional characterization of three distinct GH5_4 endo-xyloglucanases will inform future bioinformatics predictions across species, and provides new CAZymes with defined specificity that may be harnessed in industrial and other biotechnological applications.

overall_design: One carbon condition (xyloglucan); Two sample points (exponential phase, stationary phase); Data collected in biological triplicate; Total of 6 samples

middle: G


title: Expression data from rice 10DAF developing seeds from wildtype and strains with high lysine levels

status: Public on Jan 24 2018

city: Yangzhou

first: Dongsheng

last: Zhao

address: Wenhui east road

institute: Yangzhou university

summary: We used microarrays to detail the global programme of gene expression underlying seed developing and lysine metabolism.

overall_design: Rice developing seeds were selected at 15DAF for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the relationship between seed developing and lysine metabolism. To that end, we selected 15DAF developing seeds of wild type and related transgenic plants to analyze the differentially expressed genes.

first: Qingqing

last: Yang

first: Qiaoquan

last: Liu


title: In cell Mutational Interference Mapping Experiment (in cell MIME) identifies the 5’ PolyA signal as a dual regulator of HIV-1 genomic RNA production and packaging

status: Public on Jan 19 2018

city: Strasbourg

first: Redmond

middle: P

last: Smyth

state: Alsace

address: 15 rue Rene Descartes

department: Architecture et Réactivité de L'ARN

institute: IBMC CNRS

summary: Non-coding RNA regulatory elements are important for viral replication, making them promising targets for therapeutic intervention. However, regulatory RNA is challenging to detect and characterise using classical structure-function assays. Here, we present in cell Mutational Interference Mapping Experiment (in cell MIME) as a way to define RNA regulatory landscapes at single nucleotide resolution under native conditions. In cell MIME is based on (i) random mutation of an RNA target, (ii) expression of mutated RNA in cells, (iii) physical separation of RNA into functional and non-functional populations, and (iv) high-throughput sequencing to identify mutations affecting function. We use in cell MIME to define RNA elements within the 5’ region of the HIV-1 genomic RNA (gRNA) that are important for viral replication in cells. We identify three distinct RNA motifs controlling intracellular gRNA production, and two distinct motifs required for gRNA packaging into virions. Our analysis identifies the 73AAUAAA78 canonical polyadenylation motif within the 5’ PolyA domain as a dual regulator of gRNA production and gRNA packaging, and demonstrates that a functional polyadenylation signal is required for viral packaging even though it negatively affects gRNA production.

overall_design: In cell Mutational Interference Mapping Experiment (in cell MIME) for identifying regulatory RNA controlling HIV-1 replication. Sequencing of input DNA, cellular RNA and viral RNA from two mutant libraries and a WT control (9 samples in total)

first: R


title: Clostridium difficile response to iron limitation

status: Public on Jan 20 2018

city: Silver Spring

first: Paul

last: Carlson

address: 10903 New Hampshire Ave

department: DBPAP

institute: Food and Drug Administration

summary: C. difficile was grown in BHIS broth or BHIS broth with 75uM dipridyl and gene expression was compared.

overall_design: Two conditions were tested at three timepoints with three replicates each (18 samples total).

middle: E

last: Carlson Jr


title: Modulation of the diet and gastrointestinal microbiota normalizes systemic inflammation and β-cell chemokine expression associated with autoimmune diabetes susceptibility

status: Public on Jan 23 2018

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary:
The incidence of Type 1 diabetes (T1D), a T-cell mediated autoimmunity that targets the insulin secreting β-cells, has significantly increased, suggesting greater environmental pressure.  In studies of T1D families and the BioBreeding rat model, we have identified a peripheral innate inflammatory state that is associated with diabetes susceptibility, consistent with pattern recognition receptor (PRR) ligation, but independent of disease progression.  Here, compared to control strains, islets of spontaneously diabetic BB DRlyp/lyp and nondiatetic BB DR+/+ weanlings provided a standard cereal diet were found to temporally express a proinflammatory transcriptional program consistent with microbial antigen exposure that included numerous cytokines/chemokines.  Dependence of this proinflammatory phenotype on the diet and gastrointestinal microbiota was investigated by transitioning DR+/+ weanlings to a hydrolyzed casein diet (HCD) or treating them with antibiotics to respectively alter or reduce PRR ligand exposure.
Sequencing of the bacterial 16S rRNA gene revealed that these treatments significantly altered the ileal and cecal microbiota, resulting in increases in the Firmicutes:Bacteriodetes ratio, and abundances of lactobacilli and butyrate producing genera.  Both treatments partially normalized the peripheral inflammatory state, reducing plasma cytokine, chemokine and TLR-4 activity levels.  The proinflammatory islet transcriptome was more extensively normalized by HCD and immune-fluorescent staining revealed reductions in β-cell chemokine expression.  HCD and antibiotic treatment did not normalize BB rat PBMC hyper-responsiveness to ex vivo mitogen stimulation.  Combined, these studies link islet-level T1D susceptibility in BB rats to a genetically controlled innate inflammatory state that is influenced by environmental determinants encompassing the diet and the intestinal microbiota.

overall_design: Pancreatic islet gene expression in DR (ND, HCD, and B/S) and F+/+ (ND) rat at day40 (+/-5 days) which is prior to insulitis. Islet transcriptomes of 40 day old F+/+ ND (CEL files labeled RT1uu,1 RNA pool, 6-8 equal contibutors per pool, 2 technical replicates per pool)  rats, DR+/+ HCD (1 RNA pool, 6-8 equal contibutors per pool, 2 technical replicates per pool) rats, and DR+/+ B/S  (1 RNA pool, 6-8 equal contibutors per pool, 2 technical replicates per pool) rats were compared to those of age matched DR+/+ ND (2 RNA pools, 6-8 equal contibutors per pool, 2 technical replicates per pool) rats.

first: Angela

last: Henschel

first: Susanne

last: Cabrera

first: Mary

last: Kaldunski

first: Shuang

last: Jia

first: Rhonda

last: Geoffrey

first: Mark

middle: F

last: Roethle

first: Vy

last: Lam

first: Xujing

last: Wang

first: Nita

middle: H

last: Salzman

middle: J


title: Pan-AcH4 ChIP-chip with High Resolution Tiling Arrays on HUVECs and HuAoVSMCs

first: Philip

last: Marsden

type: Genome binding/occupancy profiling by genome tiling array

summary: Differential EC enrichment of pan-AcH4 was assessed at 34 select genes, including 19 EC-enriched genes, 6 broadly expressed genes, and 9 EC-excluded genes, by pan-AcH4 (AcH4K5, AcH4K8, AcH4K12, and AcH4K16) ChIP-chip analysis on human umbilical vein endothelial cells (HUVECs) and human aortic vascular smooth muscle cells (HuAoVSMCs) with a high resolution tiling DNA microarray. Specifically, the tiling array analyzes the 50 kb genomic region upstream of transcription initiation, the intragenic regions , and 50 kb genomic region downstream of the last exon.

overall_design: Pan-AcH4 ChIP was conducted on HUVECs and HuAoVSMCs. These ChIP samples were hybridized to a custom 1 M agilent microarray for ChIP-chip analysis.

first: Matthew

last: Yan


title: Pan-AcH3 ChIP-chip with Custom High Resolution Tiling Arrays on HUVECs and HuAoVSMCs

summary: Differential EC enrichment of pan-AcH3 was assessed at 34 select genes, including 19 EC-enriched genes, 6 broadly expressed genes, and 9 EC-excluded genes, by pan-AcH3 (AcH3K9 and AcH3K14) ChIP-chip analysis on human umbilical vein endothelial cells (HUVECs) and human aortic vascular smooth muscle cells (HuAoVSMCs) with a high resolution tiling DNA microarray. Specifically, the tiling array analyzes the 50 kb genomic region upstream of transcription initiation, the intragenic regions, and 50 kb genomic region downstream of the last exon.

overall_design: Pan-AcH3 ChIP was conducted on HUVECs and HuAoVSMCs. These ChIP samples were hybridized to a custom 1 M agilent microarray for ChIP-chip analysis.


title: Comparison of HBO1 siRNA-treated Human Umbilical Vein Endothelial Cells (HUVECs) and control siRNA-treated HUVECs

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

summary: To determine the role of HBO1 in EC physiology, gene expression analysis was conducted on control and HBO1 siRNA-treated HUVECs. A total of 263 differentially regulated protein-coding transcripts were detected, many of which are key for growth and angiogenesis. Additionally, many genes involved in cell cycle, cell division, and DNA replication were dysregulated. HBO1-regulated genes were verified by qRT-PCR, including those with roles in vessel tone regulation (e.g. ACE1), vessel formation (e.g. CXCL16), EC activation (e.g. E-selectin), and cholesterol efflux (e.g. ABCG1).

overall_design: HUVECs were treated with control siRNA or HBO1 siRNA for 72 hours. Subsequently, these samples were subjected to gene expression analysis using a custom agilent microarray that recognizes 26109 protein-coding transcripts and 30586 lncRNAs.


title: miRNA expression data from human PBMC derived form acute infectious mononucleosis patients

status: Public on Jan 17 2018

city: Stanford

first: Vandana

last: Kaul

state: CA

address: 1201 Welch Rd., MSLS P328

department: Surgery

institute: Stanford University

summary:
Epstein Barr virus (EBV) is the etiological agent of acute infectious mononucleosis (IM). Since acute IM is a self-resolving disease with most patients regaining health in one to three weeks there have been few studies examining molecular signatures in early acute stages of the disease. microRNAs have been shown, however, to influence immune cell function and consequently the generation of antibody responses in IM. In this study, we performed a comprehensive analysis of differentially expressed microRNAs in early stage uncomplicated acute IM.
We used microarrays to profile microRNAs from patient peripheral blood obtained at the time of IM diagnosis and at subsequent time points, and identified differentially regulated microRNAs in this process.

overall_design: Peripheral blood samples were derived from symptomatic patients at diagnosis, 1 , 2 and 7 months and processed to obtain PBMCs which were frozen and then maintained in liquid nitrogen until use. PBMCs were also isolated from blood derived from healthy age-matched individuals. Patient (n = 16) and healthy control (n = 3) PBMCs were suspended and lysed in TRIzol Reagent  and cleaned-up with RNeasy spin columns using a modified protocol for isolation of total RNA and hybridized on Affymetrix GeneChip miRNA 4.0 arrays.

first: Sheri

last: Krams

first: Olivia

last: Martinez


title: Comprehensive gene expression pattern of developing lens of Foxp1 lens specific knockout mice

city: Minato-ku, Tokyo

first: Sumiko

last: Watanabe

address: 4-6-1 Shirokane-dai

department: Institute of Medical Science

institute: University of Tokyo

summary: Foxp1 was strongly expressed in developing lens, and its knockout in lens resulted in failure of appropriate lens development. By microarray analysis, we examined effects of loss-of Foxp1 for gene expression pattern of lens at P0 developmental stage.

overall_design: By using Foxp1 lens specific knockout mice and litter mates at P0, total RNA was purified from lens and subjected to microarray analysis

first: Haruna

last: Suzuki-Kerr


title: The transcription factor Gli3 promotes differentiation from double positive to CD4 single positive thymocyte by repression of Shh

city: London

first: Tessa

last: Crompton

address: 30 Guilford Street

department: Immunobiology

country: United Kingdom

institute: UCL

summary: We used Affymetrix microarrays to understand the genome wide differences in Wildtype and Gli3 mutant (Gli3+/- and Gli3-/-) (n=2) embryonic day 18.5 DP CD69-, DP CD69+ and SP4 thymocytes.

overall_design: Wildtype and Gli3 mutant (Gli3+/- and Gli3-/-) (n=2) embryonic day 18.5 fetal thymus were sorted for DP69- (CD4+CD8+CD69-), DP69+ (CD4+CD8+CD69+) and SP4 (CD4+CD8-) cells. RNA extracted from these cells was sequenced to help understand the transcriptional changes governing DP to SP thymocyte differentiation and selection in the Gli3 mutant.

first: Anisha

last: Solanki


title: Microarray analysis of gene expression profiles with or without manipulations of neuronal activity

status: Public on Jan 16 2018

first: Takahito

last: Higashi

address: 7-3-1 Hongo Bunkyo-ku

department: Department of Cellular Neurobiology

institute: Graduate School of Medicine and Faculty of Medicine, The University of Tokyo

summary: The process of synapse turnover is regulated by specific signaling mechanisms. Various molecules that promote formation and differentiation of synapses have been identified. Some of these molecules were classified as “synapse organizers,” as they were shown to initiate differentiation of hemi-synapses when they were expressed in non-neuronal cells and co-cultured with neurons.On the other hand, little is known about the mechanisms underlying destabilization and elimination of unnecessary synapses. We used microarray profiling of dissociated hippocampal culture to identify genes in response to the down-regulation of neuronal activity in hippocampal neurons.

overall_design: Cultured hippocampal neurons were prepared from embryonic day 16.5 ICR  mouse embryos. Hippocampi were dissected, trypsinized, and dissociated. Cells were plated onto  35 mm-diameter culture dishes (BD Falcon) . Cells were cultured in Minimum Essential Medium with B18 supplement and 5.5% Fetal Bovine Serum (Equitech-Bio). RNA from primary cultured neurons at 12 DIV with or without pharmacological treatments (2 μM TTX for 2days ) was purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions. After confirming the absence of RNA degradation, RNA samples were hybridized to Agilent 8X60K Whole Mouse Genome microarrays. Array data were analyzed by quantile normalization, determination of differential gene expression, and classification of different gene expression by ontology-based methods.

first: Shinji

last: Tanaka

first: Tadatsune

last: Iida

first: Shigeo

last: Okabe


title: Clostridium difficile response to oxygen

status: Public on Jan 14 2018

first: Paul

last: Carlson

overall_design: C. difficile was grown in either anaerobic conditions or 2% oxygen and gene expression was compared. Two conditions were tested with three replicates each (6 samples total)

last: Carlson Jr


title: Gene expression during adipocytic differentiation of human bone marrow stromal stem cells

status: Public on Jan 15 2018

city: Riyadh

first: Nehad

last: Alajez

address: 1st floor College of Medicne

department: Anatomy

country: Saudi Arabia

institute: King Saud University College of Medicine

summary: We have employed whole genome microarray  to identify changes in gene expression in human bone marrow MSCs (hMSC-TERT) upon differentiation into adipocytes (day 7)

overall_design: Human MSC line (hMSC-TERT) were differentiated into adipocytes for 7 days. Subsequently, RNA was extracted using Norgen total RNA isolation kit. Extracted RNA was labeled and then hybridized to the one-color Agilent Human GE 8x60K Microarray chip.


title: Bone marrow lympho-myeloid malfunction in obesity requires precursor cell-autonomous TLR4

city: Pittsburgh

first: Lisa

middle: Ann

last: Borghesi

state: PA

address: 200 Lothrop ST

department: Immunology

institute: University of Pittsburgh

summary: Obesity, a prevalent condition in adults and children, impairs bone marrow (BM) function. However, the underlying mechanisms are unclear. Here we show that obese mice exhibit poor emergency immune responses in a toll-like receptor 4 (TLR4)-dependent manner. Canonical myeloid genes (Csf1r, Spi1, Runx1) are enhanced, and lymphoid genes (Flt3, Tcf3, Ebf1) are reduced. Using adoptive transfer and mixed BM chimera approaches we demonstrate that myeloid>lymphoid bias arises after six weeks of high fat diet and depends on precursor cell-autonomous TLR4. Further, lean mice exposed to the TLR4 ligand lipopolysaccharide (LPS) at doses similar to that detectable in obese serum recapitulates BM lympho-myeloid alterations. Together, these results establish a mechanistic contribution of BM cell-intrinsic TLR4 to obesity-driven BM malfunction and demonstrate the importance of LPS. Our findings raises important questions about the impact of maternal obesity and endotoxemia to fetal hematopoiesis, as fetal immune precursors are also sensitive to TLR4 signals.

overall_design: Bone marrow  lymphoid progenitors (CLP) as well as myeloid progenitors (LKSneg) sorted from mice fed high fat or control diet for 20 weeks were analyzed by transcriptional profiling.

first: Ailing

last: Liu

first: Minhui

last: Chen

first: Rashmi

last: Kumar

first: Maja

last: Stefanovic-Racic

first: Robert

last: O'Doherty

first: Ying

last: Ding

first: Willi

last: Jahnen-Dechent


title: Transcriptomic comparison of FVB mouse strain lung Cells one week upon injecting mice intraperitoneally with urethane and with the mouse lung adenocarcinoma cell line FULA 1

status: Public on Jan 10 2018

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

institute: Helmholz Zentrum Munich

summary:
Transcriptomic comparison of FVB mouse strain lung Cells one week upon injecting mice intraperitoneally with either saline or Urethane. Mouse lung cell were also compared at the transcriptomic level with the mouse lung adenocarcinoma cell line FULA 1, which was established in our lab
We injected 6 (3 males, 3 females) FVB mice 8 weeks old, with either saline or urethane. One week later we sacrificed  and harvested their lungs. The dissected lungs were assayed to RNA extraction (via trizol) in order to identify their transcriptomic signature. Moreover we compared the gene expression of the mouse lung cells to the mouse lung adenocarcinoma cell line FULA 1.

overall_design: Samples from FVB mice lung cells and FULA 1 cells were analyzed using Genespring 12.5 GX to obtain the  data.

first: Nikolaos

middle: I

last: Kanellakis


title: Community composition of nitrous oxide related genes and their relationship to nitrogen cycling rates in salt marsh sediments

status: Public on Jan 13 2018

city: Nahant

first: Jennifer

last: Bowen

state: Massachusetts

address: 430 Nahant Rd.

department: Marine and Environmental Sciences

institute: Northeastern University

summary: Salt marshes provide many key ecosystem services that have tremendous ecological and economic value. One critical service is the removal of fixed nitrogen from coastal waters, which limits the negative effects of eutrophication resulting from increased nutrient supply. Nutrient enrichment of salt marsh sediments results in higher rates of nitrogen cycling and, commonly, a concurrent increase in the flux of nitrous oxide, an important greenhouse gas. Little is known, however, regarding controls on the microbial communities that contribute to nitrous oxide fluxes in marsh sediments. To address this disconnect, we generated microbial community profiles as well as directly assayed nitrogen cycling genes that encode the enzymes responsible for overall nitrous oxide flux from salt marsh sediments. We hypothesized that communities of microbes responsible for nitrogen transformations will be structured by nitrogen availability. Taxa that respond positively to high nitrogen inputs may be responsible for the elevated rates of nitrogen cycling processes measured in fertilized sediments.  Our data show that, with the exception of ammonia-oxidizing archaea, the community composition of organisms responsible for production and consumption of nitrous oxide was altered under nutrient enrichment. These results suggest that elevated rates of nitrous oxide production and consumption are the result of changes in community structure, not simply changes in microbial activity.

sample_organism:
synthetic construct
sediment metagenome

overall_design: Two color array (Cy3 and Cy5): the universal standard 20-mer oligo (custom-synthesized by IDT; 5'-\5Cy5\GTACTACTAGCCTAGGCTAG-3') is printed to the slide with a 70-mer oligo (an archetype).  Environmental DNA sequences (fluoresced with Cy3) within 15% identity of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array.  Signal is the ratio of Cy3 to Cy5. Two replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.

first: Bess

last: Ward

first: John

last: Angell

first: Xuefeng

last: Peng

first: Qixing

last: Ji

first: Ian

last: Craick

first: Amal

last: Jayakumar

first: Patarick

last: Kearns

middle: L


title: Comparison of wild type mouse cancer cell lines to transfected cell lines with IKKA, IKKB, Kras sh RNA and treated with Il-1b mouse protein

summary: We compared different mouse cancer cell lines to identify their unique cell signatures.

overall_design: Samples from different cancer cell lines were analyzed using Genespring 12.5 GX to obtain the data.


title: Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis

status: Public on Jan 09 2018

city: Seattle

first: Samuel

last: Miller

state: Washington

address: 1959 Pacific Ave Box 357710

institute: University of Washington

summary: E. coli isolates from different CF patients demonstrate increased growth rate when grown with glycerol, a major component of fecal fat, as the sole carbon source compared to E. coli from healthy controls. CF and control E. coli isolates have differential gene expression when grown in minimal media with glycerol as the sole carbon source. While CF isolates display a growth promoting transcriptional profile, control isolates engage stress and stationary phase programs, which likely results in slower growth rates.

overall_design: RNA-seq analysis was performed to analyze the transcriptomes of CF and control E. coli when grown on glycerol (GlyMM) or glucose (GluMM) as the sole carbon source. Since the different isolates are not isogenic mutants, transcriptome analysis on GluMM served to establish baseline gene expression for each of these genetically distinct strains.

first: Susana

last: Matamouros


title: Identification of the molecular signature of distinctive breast cancer associated fibroblasts (CAFs)

status: Public on Jan 08 2018

city: Guangzhou

first: Jiang

last: Liu

address: 107 Yanjiang West Road

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary:
Cancer associated fibroblasts (CAFs) are highly heterogeneous and different subsets of CAFs may exhibit distinct functions, To identify the molecular signature of distinctive CAFs , we compared mRNA expression profiles of CAFs isolated from tumors in sensitive patients and resistant ones before neo-adjuvant chemotherapy.
Compared the CAFs from sensitive samples, those from refractory samples exhibited a distinctive signature.

overall_design: A fourteen chip study using total RNA recovered from CAFs of 7 sensitive breast cancer patients and 7 resistant ones before neo-adjuvant chemotherapy. Each chip measures the expression 45033 genes were collected from the authoritative data source including NCBI.

first: Shicheng

last: Su

first: Jianing

last: Chen


title: Transcriptomic fingerprints of C. elegans exposed to citrate coated superparamagnetic iron oxide nanoparticles (C-SPIONs) and to superparamagnetic iron oxide nanoparticles coated with a monolayer of bovine serum albumin (BSA-SPIONs)

status: Public on Jan 05 2018

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

institute: King's College London

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

overall_design: Refer to individual Series


title: Leaf adaptive responses to aluminum-toxicity revealed by RNA-Seq in two citrus species with contrasting aluminum tolerance

city: Fuzhou

first: Chen

last: Lisong

address: Shangdian street NO.15

institute: Fujian Agriculture and Forestry University

summary:
Background: Limited data are available on aluminum (Al)-toxicity-induced alterations of gene profiles in woody plants. Seedlings of Al-tolerant Citrus sinensis and Al-intolerant Citrus grandis were fertigated with nutrient solution containing 0 and 1.0 mM AlCl3•6H2O. Thereafter, we investigated the Al-toxicity-induced alterations of transcriptomics in leaves by RNA-Seq.
Results: Using RNA-seq, we isolated 1162 (181) up- and 496 (234) downregulated genes from Al-treated C. grandis (C. sinensis) leaves. Clearly, gene expression was less affected by Al-toxicity in C. sinensis leaves than in C. grandis ones. Several Al-toxicity-responsive genes homologous to known Al-tolerance genes: ALUMINUM SENSITIVE 3 (ALS3), multidrug and toxic compound extrusion (MATE), glutathione S-transferase (GST), L-galactose dehydrogenase（L-GalDH) and lipoxygenase (LOX) were identified in citrus leaves. Genes related to signal transduction, and sulfur transport and metabolism might also play a role in the higher Al-tolerance of C. sinensis.
Conclusions: This is the first comparative investigation of transcriptomic responses in Al-treated citrus leaves. There were common and unique mechanisms for citrus Al-tolerance. These results provide a platform for further investigating the roles of genes possibly responsible for citrus Al-tolerance.

sample_organism:
Citrus sinensis
Citrus maxima

platform_organism:
Citrus sinensis
Citrus maxima

overall_design: Examination of mRNA levels in control and Al-treatment leave of C. grandis and C. sinensis with two biological replicates were generated by deep sequencing, using Illumina HiSeq 2000 device.

first: Peng

last: Guo

first: Li-Song


title: Transcriptomic fingerprints of C. elegans exposed to citrate coated superparamagnetic iron oxide nanoparticles (C-SPIONs)

summary: Superparamagnetic Iron Oxide Nanoparticles (SPIONs) are currently being investigated for a range of biomedical applications. Their use have been related with different cytotoxic mechanisms including the generation of oxidative stress and the induction of metal detoxification pathways, among others. We have investigated the molecular mechanisms responsive to in-house fabricated citrate coated SPIONs (C-SPIONs) in the nematode C. elegans to compare in vivo findings with previous in vitro studies. C-SPIONs (500 µg/ml) affected the transcriptional response of signal transduction cascades (i.e. TFG-beta), protein processing in the endoplasmic reticulum, and RNA transport, among other biological processes. They also triggered a lysosomal response, indicating a relevant biological role of this cellular compartment in the response to this nanoparticle treatment in C. elegans. Interestingly, other pathways frequently linked to nanotoxicity like oxidative stress or apoptosis were not identified as significantly affected in this genome-wide in vivo study despite the high dose of exposure.

overall_design: The global transcriptome was compared in wild type N2 raised in the presence or absence of citrate-coated superparamagnetic iron oxide nanoparticles (C-SPIONs) at the concentration of 500 µg/mL for 24 hours at the L4 stage in 50% M9 buffer.

first: Laura

last: Gonzalez-Moragas

first: Si-Ming

last: Yu

middle: R

first: Anna

last: Laromaine

last: Roig


title: Comparison of gene expression profilings between Mock-WS480, NonV50-OKS-SW480 and 2ndV50-OKS-SW480

status: Public on Jan 11 2018

city: Kobe City

first: Michiyo

last: Koyanagi-Aoi

address: Chuo-ku, Kusunoki-cho 7-5-1

institute: Kobe University

summary: We have previously reported that colon cancer stem-like cells can be induced from human colon cancer cell lines by retrovirally introducing OCT3/4, SOX2 and KLF4, and we designated these cells as induced cancer stem cells (iCSCs). iCSCs showed significantly enhanced CSC properties in terms of the marker gene expression, sphere formation, chemoresistance and tumorigenicity. In the current study, we generated iCSCs using a polycistronic retroviral expression vector, and indicated that iCSCs-derived tissues in vitro are able to recapitulate human colon cancer tissues. To identify the molecular mechanisms that promote the properties of CSCs, we compared the global gene expression patterns of Mock-SW480 cells, non-V50 cells from 1st V50-OKS cells, and 2nd V50-OKS cells.

overall_design: We extracted total RNA from 3 Mock-SW480 cells, 3 NonV50-cells from 1st V50-OKS cells and 3 2ndV50-OKS cells and hybridized them to Agilent gene expression microarrays.

first: R

last: Ishida


title: Comparison of gene expression in the GAS M1T1 strain 5448, wild-type vs pepO mutant

city: St Lucia

first: Stephan

last: Brouwer

state: QLD

address: Cooper Road, Building 76, Rm 151

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University of Queensland

summary:
Manuscript title: The endopeptidase PepO regulates the SpeB cysteine protease and is essential for the virulence of invasive M1T1 Streptococcus pyogenes.
The study investigates the effect of pepO mutation on global gene expression in GAS M1T1 strain 5448.

overall_design: Two-condition experiment, GAS M1T1 strain 5448 WT vs. pepO mutant. Biological replicates: 3, independently grown and harvested. One replicate of each strain per array.

first: S

first: A

last: Cork

first: C

last: Ong

first: T

middle: C

last: Barnett

first: N

last: West

first: K

last: McIver

first: M

last: Walker


title: Expression data from TabZIP6-overexpressed Arabidopsis before/after cold treatment

status: Public on Jan 01 2018

city: Shijiazhuang

first: Caili

last: Bi

state: Hebei

address: No.20 Road East. 2nd Ring South, Yuhua District

department: College of life sciences

institute: Hebei Normal University

summary: TabZIP6 is a Subgroup C bZIP protein from wheat. Some evidences have shown that TabZIP6 is involved in cold stress response. To elucidate the regulatory mechanism of TabZIP6 in plant cold response, cold treated/untreated TabZIP6-overexpressing Arabidopsis seedlings were used to perform microarray analysis.

overall_design: The seedlings of Arabidopsis ecotype Col-1 and TabZIP6-overexpressed Arabidopsis line (L20) were grown normally at 22°C for 10 days, then they were treated at 4°C for 6 hours. Samples were collected before/after cold treatment. Two biological replicates were included.

first: Wangting

last: Cai


title: Understanding gene expression signatures with pigmentation changes in Melanocytes

status: Public on Jan 03 2018

city: Delhi

first: Rajender

last: Motiani

state: Delhi

address: CSIR-IGIB, SUKHDEV VIHAR, MATHURA ROAD DELHI, OPPOSITE SUKHDEV VIHAR BUS DEPOT, ADJACENT TO CRRI DELHI-110020

department: SKIN BIOLOGY

institute: CSIR-IGIB

summary: This microarray experiment was performed for identifying the signaling pathways that could be differentially regulated in response to changes in the pigmentation levels in human melanocytes. Melanocytes were either treated with pigmentation inducing agent or depigmenting compound targeting tyrosinase (key enzyme involved in the melanogenesis). The samples were then processed for analyzing the differentially regulated signaling pathway by performing microarray on agilent platform. The pathway enrichment analysis was executed on DAVID software. The plot has been generated using the average enrichment score for the pathways under similar category of function.   Interestingly, along with the expected melanogenic and cAMP pathways, we observed differential regulation of Ca2+ signaling during pigmentation.   We then performed several experiments for evaluating the contribution of cytoplasmic and endoplasmic reticulum (ER) Ca2+ homeostasis to pigmentation.  After extensive studies in in vitro and in vivo pigmentation models, we demonstrate a critical role for ER Ca2+ sensor, STIM1 protein in the process of pigmentation.  Taken together, we performed the microarray experiment for identifying potential pathways wherein Ca2+ homeostasis came out as one of the several hits. We then specifically studied cytoplasmic and endoplasmic reticulum (ER) Ca2+ homeostasis and identified a novel regulator of pigmentation based on several lines of evidences including in vivo model system

overall_design: Melanocytes were treated with differentially pigmenting agents Tyrosine (the substrate of pigmentation to increase pigmentation), Phenylhiourea( a inhibitor of tyrosinase enzyme involved during pigment synthesis to suppress pigment syntheis) for 48 hours in culture media. All treatments were given 24 hours post seeding the cells in T25 flasks.

first: Shivangi

last: Khanna


title: Genome-wide profiling of miRNA associated with BCR-FGFR1 fusion kinase driven stem cell leukemia and lymphoma II

city: Augusta

first: John

last: Cowell

state: GA

address: 1410 Laney-Walker Blvd

institute: Augusta University

summary: The BBC1 and BBC2 cell lines were isolated from pre-B-cell lymphoma models of a murine BCR-FGFR1 driven SCLL. miRNA profiles for BBC2 cells, were established using miRNA arrays. First, BBC2 cells were compared with FACS sorted, normal, murine splenic CD19+ B cells isolated from BALB/c mice, where upregulated and downregulated miRNAs in BBC2 cells were identified. We next investigated which of these miRNAs were affected by loss of FGFR1 function. Previously we showed that the FGFR inhibitor BGJ398 suppresses suppressed phosphoactivation of chimeric FGFR1 kinases. When BBC2 cells were treated with 50nM BGJ398 for 24 hours, up- and down-regulated miRNAs by FGFR1 signaling were identified. By comparasion of the two subsets of differentially expressed miRNAs, we were able to define core candidate miRNAs which appear to be regulated by BCR-FGFR1 in SCLL.

overall_design: The miRNA profiles of BBC2 cell sample treated with DMSO and BGJ398 were detected with miRNA microarray.

middle: K

first: Tianxiang

last: Hu


title: Transcriptomic fingerprints of C. elegans exposed to superparamagnetic iron oxide nanoparticles coated with a monolayer of bovine serum albumin (BSA-SPIONs)

first: Stephen

last: Sturzenbaum

summary: Superparamagnetic Iron Oxide Nanoparticles (SPIONs) are currently being investigated for a range of biomedical applications. Their use have been related with different cytotoxic mechanisms including the generation of oxidative stress and the induction of metal detoxification pathways, among others. Different NP coatings are being explored, among them albumin which has been applied in some drugs delivery systems. We have investigated the molecular mechanisms responsive to in-house fabricated SPIONs coated with bovine serum albumin (BSA-SPIONs) in the nematode C. elegans to compare in vivo findings with previous in vitro studies. BSA-SPIONs (500 µg/ml) affected the transcriptional response of glycan metabolic pathways related to innate immune response, xenobiotics degradation, and triggered a lysosomal response, indicating a relevant biological role of this cellular compartment in the response to this nanoparticle treatment in C. elegans. Remarkably, key biological functions such as apoptosis or protein processing were not affected with significance despite the high dose of exposure.

overall_design: The global transcriptome was compared in wild type N2 raised in the presence or absence of superparamagnetic iron oxide nanoparticles coated with a monolayer of bovine serum albumin (BSA-SPIONs) at the concentration of 500 µg/mL for 24 hours at the L4 stage in 50% M9 buffer.

first: Laura

last: Gonzalez-Moragas

first: Si-Ming

last: Yu

first: Anna

last: Laromaine


title: BCL6 expression in AITL could be transcriptionally regulated

city: Madrid

first: Rebeca

last: Manso

state: Madrid

address: Av. Reyes Católicos, 2

department: Pathology

country: Spain

institute: Fundación Jiménez Díaz

summary: Peripheral T cell lymphoma (PTCL) is a very aggressive disease which currently lacks efficient targeted therapy. New therapeutic strategies are needed to improve the very poor outcome of these patients. However, little is known about the molecular pathogenesis of this disease. In this study, we performed a miRNAs expression profiling analysis of a series of 26 PTCL cases in order to find deregulated pathways or genes that could become therapeutic agents for PTCL patients.

overall_design: 26 PTCL and 4 reactive lymph node were hybridized on a 8 x 15K human miRNA one-color platform (Agilent) containing probes for 471 human miRNAs.

first: Nerea

last: Martínez-Magunacelaya

first: Socorro

middle: M

last: Rodríguez-Pinilla


title: Expression data from primary keratinocytes obtained from WT and keratinocyte specific Glut1-deficient mice [MTA-1_0]

city: Dallas

first: Richard

last: Wang

state: TX

address: 5323 Harry Hines Blvd

department: Dermatology

institute: UT Southwestern

summary:
Glut1 is highly expressed in basal cells of keratinocytes, but the regulation of Glut1 and expression of additional glucose transporters in the skin has not been explored, here we specifically ablate Glut1 in epidermal keratinocytes to elucidate the role of glucose transport in the keratinocytes.
we performed microarray analysis in WT and Glut1 deficient primary keratinocytes to determine the pathways might contribute to the impaired proliferation in Glut1 deficient keratinocytes.

overall_design: We harvest primary keratinocytes from 1 week old WT (n=4) and keratinocyte specific Glut1-deficient (n=4) mice, keratinocytes from each mice were seeded at one 10 cm dishes in complete KSFM medium. After 3 days, digest the cells, reseed the cell in new dishes with same number. The cells were harvested the next day. Two plates of cells of the same genotype were randomly harvested together, thus each genotype have 2 samples for microarray analysis.

first: Zhuzhen

last: Zhang


title: Array-CGH data of aneuploid tumor populations of different urothelial cancer sites in one patient

city: Basel

first: David

middle: Christian

last: Müller

address: Schönbeinstrasse 40

department: Institute for Pathology

country: Switzerland

institute: University Hospital Basel

summary: Donor-derived, metastatic urothelial cancer after kidney transplantation associated with BK polyomavirus bearing a critical deletion in the viral NCCR

overall_design: Copy number profiling of different tumor population in order to delineate clonal evolution in one patient.

first: Maarit

last: Rämö

first: Christian

last: Wetterauer

first: Valeria

last: Perrina

first: Luca

last: Quagliata

first: Tatjana

last: Vlajnic

last: Ruiz

first: Beate

last: Balitzki

first: Rainer

last: Grobholz

last: Gosert

first: Elvis

last: Ajuh

first: Hans

last: Hirsch

first: Lukas

last: Bubendorf

first: Cyrill

middle: A

last: Rentsch