title: Involvement of B cells, immunoglobulins, and Syk in the pathogenesis of abdominal aortic aneurysm II

status: Public on Apr 25 2018

city: Kurume

first: Hiroki

last: Aoki

state: Fukuoka

address: 67 Asahimachi

department: Cardiovascular Research Institute

country: Japan

institute: Kurume University

summary: Background—Abdominal aortic aneurysm (AAA) is a potentially life-threatening disease that is common in older individuals. Currently, therapeutic options are limited to surgical interventions. Although it has long been known that AAA tissue is enriched in B cells and immunoglobulins, their involvement in AAA pathogenesis remains controversial.   Methods and Results— We investigated the role of B cells and immunoglobulins in a murine model of AAA, induced with a periaortic application of CaCl2, and in human AAA. Both human and mouse AAA tissue showed B cell infiltration. Mouse AAA tissue showed deposition of IgG and activation of Syk, a key molecule in B cell activation and immunoglobulin function, which were localized to infiltrating cells including B cells and macrophages. B cell-deficient muMT mice showed suppression of AAA development that was associated with reduced activation of Syk and less expression of Mmp9. Administration of exogenous immunoglobulins restored the blunted Syk activation and AAA development in muMT mice. Additionally, exogenous immunoglobulins induced IL-6 and MMP9 secretions in human AAA tissue cultures. Furthermore, administration of R788, a specific Syk inhibitor, suppressed AAA expansion, reduced inflammatory response, and reduced immunoglobulin deposition in AAA tissue.  Conclusions—From these results, we concluded that B cells and immunoglobulins participated in AAA pathogenesis by promoting inflammatory and tissue destructive activities. Finally, we identified Syk as a potential therapeutic target.

overall_design: We used wild type (WT) or B cell-deficient (uMT) mice to obtain this data set of mouse aortic transcriptome. Mice were without (pre) or with periaortic application of 0.5 M CaCl2 (Ca) to induce abdominal aortic aneurysm. Aortic samples were obtained 7 days (day7) or 42 days (day42) after the CaCl2 challenge. Sham operation was performed with periaortic application of physiological saline instead of CaCl2. Aortic tissues were homogenized in TRIzol (Invitrogen) and total RNA was isolated with RNeasy (Qiagen). Transcriptome analyses were performed using the SurePrint G3 Mouse Gene Expression 8x60K Microarray Kit (Agilent).

first: Aya

last: Furusho


title: Involvement of B cells, immunoglobulins, and Syk in the pathogenesis of abdominal aortic aneurysm

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

overall_design: Refer to individual Series


title: The evolutionary emergence of the rac3b/rfng/sgca regulatory cluster refined mechanisms for hindbrain boundaries formation

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Developmental programs often rely on parallel morphogenetic mechanisms that guarantee precise tissue architecture. While redundancy constitutes an obvious selective advantage, little is known on how novel morphogenetic mechanisms emerge during evolution. In zebrafish, rhombomeric boundaries behave as an elastic barrier, preventing cell intermingling between adjacent compartments. Here, we identify the fundamental role of the small-GTPase Rac3b in actomyosin cables assembly at hindbrain boundaries. We show the novel rac3b/rfng/sgca regulatory cluster, which is specifically expressed at the boundaries, emerged in the Ostariophysi superorder by chromosomal rearrangement that generated new cis-regulatory interactions. By combining 4C-seq, ATAC-seq, transgenesis and CRISPR-induced deletions, we characterized this regulatory domain, identifying hindbrain boundaries-specific cis-regulatory elements. Our results suggest that the capacity of boundaries to act as an elastic mesh for segregating rhombomeric cells evolved by cooption of critical genes to a novel regulatory block, refining the mechanisms for hindbrain segmentation.

overall_design: 4C-seq samples from rac3b gene promoter in whole 24hpf zebrafish embryos and ATAC-seq in 24hpf zebrafish hindbrain samples

first: J

last: Letelier

last: Terriente

first: I

last: Belzunce

first: A

last: Voltes

first: C

middle: A

last: Undurraga

first: R

last: Polvillo

first: L

last: Devos

middle: J

last: Maeso

first: S

last: Retaux

middle: L

last: Gomez-Skarmeta

middle: R

last: Martínez-Morales

last: Pujades


title: Role of TaVAP in stress tolerance in plants

city: Amritsar

first: Brinderjit

last: Singh

state: Punjab

address: Amritsar

department: Biotechnology

country: India

institute: Guru Nanak Dev University

summary:
Abiotic stresses like drought, salinity, high and low temperature, and submergence are major factors that limit the crop productivity. Hence, identification of genes associated with stress response in crops is a prerequisite for improving their tolerance to adverse environmental conditions. In this study, we have analyzed the expression profiles of three genotypes WT, TaVAP mutant and TaVAPOE plants in Arabidopsis thaliana in col-0 background using microarray technology to identify the genes differentially expressed under control conditions.
We used microarrays to detail the global programme of gene expression underlying differential expression and identified distinct classes of up-regulated  and downregulated genes during this process.

overall_design: Five-day-old light-grown Arabidopsis seedlings from three genotypes were grown under controlled conditions, which were further used for RNA extraction and hybridization on Affymetrix microarrays. Two biological replicates of each sample were used for microarray analysis.

first: P

last: Khurana

middle: P

first: Prabhjeet


title: Involvement of B cells, immunoglobulins, and Syk in the pathogenesis of abdominal aortic aneurysm I

last: Aoki

overall_design: We used B cell-deficient (uMT) mice to obtain this data set of mouse aortic transcriptome in the absence of B cells. Mice were treated with periaortic application of 0.5 M CaCl2 (uMT_Ca) to induce abdominal aortic aneurysm. Periaortic application of physiological saline instead of CaCl2 was performed as a sham operation (uMT_sham). To observe the effect of immunoglobulins, a group of mice with CaCl2 treatment received intraperitoneal injection of mouse polyclonal IgG (uMT_Ca+IgG). Aortic samples were obtained 7 days after the CaCl2 challenge. Mouse gamma globulin Aortic tissues were homogenized in TRIzol (Invitrogen) and total RNA was isolated with RNeasy (Qiagen). Transcriptome analyses were performed using the SurePrint G3 Mouse Gene Expression 8x60K Microarray Kit (Agilent).


title: Transcriptional profiling of Primary Human Hepatocytes (PHH) depleted for CAR and treated with CITCO or Phenobarbital in -/+EGF medium

status: Public on Apr 27 2018

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

summary: In primary human hepatocytes (PHH) the involvement of the Constitutive Androstane Receptor (CAR) in genes regulations has never been evaluated at the transcriptomic level. Here we investigated the impact of CAR depletion and epidermal growth factor on CAR dependent gene modulation in PHH. The xenosensor was activated by its direct (CITCO) or indirect (Phenobarbital/PB) agonists in presence or in absence of EGF.

overall_design: Primary Human Hepatocytes were isolated from 5 different human donors. Cells were cultured in presence or in absence of EGF for 6 days. Transfections with siRNA unspecific (siCT) or targeting CAR (siCAR) were performed at day 2 and 5. RNA was extracted at D6 after 24h treatment with DMSO, CITCO (1µM) or PB (0.5mM). Transcriptomic profiling was performed using Affymetrix HG-U133+PM arrays.

first: Hugues

last: de Boussac

first: Michael

last: Römer

first: Martine

last: Daujat-Chavanieu


title: Transcriptional profiling of Primary Human Hepatocytes (PHH) depleted for PXR and treated with CITCO or Phenobarbital in -/+EGF medium

summary: In primary human hepatocytes (PHH) the involvement of the Pregnane X Receptor (PXR) in genes regulations by Phenobarbital (PB) has never been evaluated at the transcriptomic level. Here we investigated the impact of PXR depletion and epidermal growth factor on PXR dependent gene modulation by PB in PHH. The potential crosstalk with CAR was investigated using Phenobarbital and the direct CAR activator (CITCO) in presence or in absence of EGF.

overall_design: Primary Human Hepatocytes were isolated from 5 different human donors. Cells were cultured in presence or in absence of EGF for 6 days. Transfections with siRNA unspecific (siCT) or targeting PXR (siPXR) were performed at day 2 and 5. RNA was extracted at D6 after 24h treatment with DMSO, CITCO (1µM) or PB (0.5mM). Transcriptomic profiling was performed using Affymetrix HG-U133+PM arrays.


title: Organic pollutants in salmon oil and health effect

status: Public on Apr 20 2018

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

summary:
Transcriptional profiling of rat adipose tissue and skeletal muscle submitted to high fat diets made with either crude (HFC) or refined salmon oil (HFR).

Keywords: transcriptomic analysis

overall_design: Two groups of rats were submitted to high fat diet containing either crude salmon oil (HFC) or refined salmon oil (HFR). After 28 days, adipose tissue or skeletal muscle were retrieved and RNA extracted. A pool of RNA from HFR group was used as the reference group. Each HFC was compared to reference group (pool of HFR). Five biological replicates were processed.

first: E

last: Meugnier

last: Pesenti

first: H

last: Vidal

last: Ruzzin


title: Function annotation and clinical implications of KIT mutation and overexpression associated microRNAs in gastrointestinal stromal tumours

city: Wuhan

first: Yu

last: Wang

state: Hubei

address: 1095 Jiefang Dadao

country: China

institute: Institute of Pathology

summary: Activating mutation of KIT is well known as a key molecular event for the development of gastrointestinal stromal tumors(GISTs). Dysregulation of microRNAs(miRNA) might elucidate KIT mutation, KIT overexpression and the resulting tumorigenesis in GIST. Herein we identified miRNA expression profiles that associated with KIT mutation and KIT overexpression in GIST by  miRNA microarrays and Real-time PCR in GISTs. The potentially target genes of selected miRNAs were analyzed by bioinformatic techniques with GO and KEGG pathway analysis. We showed that 6 miRNAs were differentially expressed in CD117IHC+/KITmutant GISTs compared to CD117IHC-/wild-type GISTs. Of these, 2 miRNAs including miR-483-3p and miR-589 were up-regulated, while the other 4 miRNAs including miR-140-5p, miR-148b-3p, miR-1587 and miR-4507 were down-regulated. GO and KEGG analysis demonstrated that miRNAs with significant change were involved in regulation of target genes related to the development of GIST. Among the candidate miRNAs studied, miR-148b-3p and miR-140-5p may be involved in GIST tumorigenesis via targeting mutant KIT or via intermediate molecules of PDGFRA, PI3K-AKT and MAPK pathway, such as AKT2, MAPK1, MAPK10, STAT5A, SMAD4, SMAD5 and PTEN. Furthermore, the reduced expression of miR-140-5p and miR-148b-3p were inversely correlated with high-risk grade, recurrence and metastasis of GIST. The current findings indicated that miR-148b-3p and miR-140-5p were not only involved in tumorigenesis of GIST, but might also participate in the progression of GIST and could be considered as novel biomarkers for potentially predicting the prognosis of GIST.

overall_design: We elected this study to investigate miRNAs expression signatures which respect to KIT mutation and KIT overexpression of GISTs by conducting miRNA expression profiles in 5 CD117IHC+/KITmutant GISTs and 5 CD117IHC-/wild-type GISTs. The selected candidate miRNAs were subsequently validated in a cohort of 59 GIST patients including of 45 CD117IHC+/KITmutant GISTs and 14 CD117IHC-/wild-type GISTs.

first: Dong

last: Kuang

first: Xiaoyan

first: Yuanli

last: Zhu

first: Sanpeng

last: Xu

first: Yaobin

last: Chen

first: Henghui

last: Cheng

first: Qiu

last: Zhao

first: Yaqi

last: Duan

first: Guoping


title: Whole transcriptome and miRNAome analysis of porcine muscle tissue in terms of muscle growth and development

status: Public on Apr 23 2018

city: Balice near Krakow

first: Klaudia

last: Pawlina-Tyszko

address: Krakowska 1

department: Deaprtment of Animal Genomics and Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: The aim of present research was to identify miRNAs potentially related with muscle growth in pig
Methods: miRNA-seq analysis was performed on longissimus lumborum samples collected from 13 pigs representing two sire-line breeds – Pietrain and Hampshire. Based on dissection data, pigs were selected from a larger population in terms of weight of loin muscle to obtain the most extreme groups in each breed The miRNA libraries were constructed form  total RNA with the use Neb Next Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to the protocol. The quantification of obtained libraries was performed on a Qubit 2.0 spectrophotometer (Invitrogen, Life Technologies) and a TapeStation 2200 instrument (D1000 ScreenTape; Agilent). The miRNA-seq was performed in 36 single-end cycles on HiScanSQ platform (Illumina) with the use of TruSeq SR Cluster Kit v3- CBOT-HS and TruSeq SBS Kit v 3 - HS (Illumina). Differentially expressed microRNAs were detected using the DESeq2 software while validation was performed by qPCR.
Results: miRNA-seq approach allowed to identify 196 known and 149 potentially novel miRNAs in both breeds. The comparison of miRNA profiles between pig groups with different loin weight showed differential expression of 57 microRNAs for Hampshire pigs and 34 miRNAs for Pietrain pigs. Furthermore, 18 common microRNAs with differential expression were identified for both breeds tested. The Gene Ontology analysis (DIANA mirPath v.3 tool) confirmed that detected genes were involved in regulation of cell cycle, fatty acid biosynthesis, regulation of actin cytoskeleton, lysine degradation and ubiquitin mediated proteolysis. According to the KEGG Database, these DE miRNAs enrich the following pathways, i.a.: the Hippo signaling pathway, TGF-beta signaling pathway and PI3K-Akt signaling pathway.
Conclusions: Obtained results allow to propose the panel of miRNAs, which can be related with porcine muscle growth and development. Such analysis can be the basis of future research in terms of identification of candidate miRNAs related with important production traits in pigs.

overall_design: The muscle (longissimus dorsi) microRNA sequencing was performed for 13 samples collected form pigs representing two breeds - Pietrain and Hampshire, using Illumina HiScan SQ and applying 36 single-end cycles.

first: Katarzyna

last: Ropka-Molik

first: Artur

last: Gurgul

last: Piórkowska


title: Effect of rosiglitazone treatment on insulin sensitivity in type 2 diabetic patients skeletal muscle

last: meugnier

summary:
The goal of this study was to analyse the effect of a 12 weeks treatment with rosiglitazone on insulin sensitivity in the muscle of type 2 diabetic patients.  Ten diabetic patients were submitted to a 3 hours euglycemic-hyperinsulinemic clamp. Skeletal muscle biopsies were taken before and after the clamp. Samples from the same patients (obtained before and after the clamp) were hybridized on the same microarray. Biopsie taken before the clamp was considered as the control. Then, the patients were treated with rosiglitazone, agonist of PPAR gamma, during 12 weeks. After the treatment, all the patients were submitted to a second 3 hours euglycemic-hyperinsulinemic clamp. Skeletal muscle biopsies for 7 patients were taken before and after the clamp. Samples from the same patients (obtained before and after the clamp) were hybridized on the same microarray. Biopsie taken before the clamp was considered as the control.
Set of arrays that are part of repeated experiments
Compound Based Treatment: patient biopsies taken before (no) and after (yes) rosiglitazone (TZD) treatment`

overall_design: Computed

first: Karine

last: Clement


title: Cell-free lncRNA expression signatures in urine serve as novel noninvasive biomarkers for diagnosis and recurrence prediction of bladder cancer

city: Jinan

first: Lutao

last: Du

state: Shandong

address: 247 Beiyuan Street, Jinan 250033, Shandong, China

institute: The Second Hospital of Shandong University

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

summary: To identify lncRNAs dysregulated in BC, we assessed the lncRNA expression profile in pooled urine samples of 10 BC patients and 10 controls by microarray. A total of 3093 lncRNAs determined differential expression (fold change>=2.0) between BC patients and controls. Among them, 1680 lncRNAs were up-regulated and 1413 lncRNAs were down-regulated in BC. Of all the differentially expressed lncRNAs indicated by lncRNA expression profiling, 26 lncRNAs (fold change>25) were firstly selected for further evaluation, in which 16 lncRNAs were up-regulated and 10 lncRNAs were down-regulated in BC.

overall_design: Recent studies have demonstrated that cell-free long non-coding RNAs (lncRNAs) were stably present in urine and could serve as novel noninvasive biomarkers for cancer detection. This study was designed to identify unique lncRNA expression signatures in urine for diagnosis and prognosis of bladder cancer (BC). Pooled urine samples from 10 patients with BC and 10 healthy controls were labled as normal group and cancer group, respectively.  Initial screening of lncRNAs by microarray analysis was respectively performed on urine sample of normal group and cancer group. Differential expression of candidate lncRNAs would be selected from the microarray results.


title: Transcriptional effects after the expression of MYB30, MYB55 or MYB110 gene

status: Public on Apr 22 2018

city: Tsukuba

first: Akira

last: Takahashi

address: 2-1-2, Kannnondai

institute: National Institute of Agrobiological Sciences

summary:
Transcriptional profiling of rice transgenic calli which were stably transformed with the vector containing the dexamethasone (DEX)-inducible promoter and each of three MYB gene (MYB30, MYB55 or MYB110) or control.
Calli were treated with DEX for 4 h to induce transgene expression. Ethanol was the solvent of DEX and used as control.

overall_design: Two-condition experiment, DEX-treated calli vs. ethanol-treated calli. No biological replicates.

first: Mitsuko

last: Kishi-Kaboshi


title: To investigate the alteration of gene expression profiles after NCSTN gene silencing in HaCaT cells employing Agilent whole genome microarray

status: Public on Apr 28 2018

city: Nanjing

first: Xuemin

last: Xiao

address: St. 12 Jiangwangmiao

department: Institute of Dermatology

institute: Chinese Academy of Medical Sciences

summary:
The present study was designed to use small interfering RNA (siRNA) approach to identify the effects of NCSTN silencing on human immortal keratinocyte cell line, HaCaT.
The alteration of gene expression profiles after NCSTN gene silencing in HaCaT cells was investigated employing Agilent whole genome microarray

overall_design: In 3 days after siRNA transfection, total RNA was extracted following administration of HaCaT cells cells with either a siRNA shown previously to efficiently and specifically knock down NCSTN expression, or with a control, mismatch siRNA(n=3).


title: Transcriptomic analyses reveal genes with sexual dimorphic expression in the Arapaima gigas gonads and brain

status: Public on Apr 30 2018

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

country: USA

institute: Xiphophorus Genetic Stock Center

type: Expression profiling by high throughput sequencing

summary: Pirarucu (Arapaima gigas, or A. gigas) is a native fish species to Amazon basin and, economically important in the Brazilian Amazonian for its great potential to aquaculture. In the natural environment the A. gigas is captured only in the sustainable development reserves of the State of Amazonas by applying a system of rotation in fishing in order to avoid overfishing of this important fishing resource. The reproductive biology of A. gigas has long been intriguing; however, very little is known about the molecular pathways underlying their sexual differentiation and determination.  Using the SOLiD sequencing platform, a total of 432,058,560 short sequencing reads were produced. An average of ~30% of sequencing reads could be mapped to Asian arowana reference cDNAs. 305 genes showed higher expression in female brain against 8 gene with higher expressing in male brain. In gonad, there are 120 genes higher expressed in female against 10 gene higher expressed in male.

overall_design: To identify genes representing the sex specific gene expression, a comprehensive transcript dataset for the gonads and brain of A. gigas was produced using SOLiD platform. The sequencing reads were mapped to the genome of a close species Scleropages formosus (Asian arowana). Differential gene expression between male and female were then identified using the quantified gene expression values.

first: Carlos

middle: H

last: Santos

first: Vera

middle: M

last: Almeida-Val

first: Adalberto

last: Val


title: Expression data from mouse colorectal cancer grown in non-adipose environment or white adipose environment

status: Public on Apr 24 2018

city: Shanghai

first: Yunlong

last: Yang

address: Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Dong'an road 130

institute: Fudan University

summary:
Cancers located adjacent to adipose tissues often show intrinsic and acquired resistance to antiangiogenic therapy. The resistance is developed potentially via tumor cell metabolic paradigm shift.
We use microarrays to detail the gene expression upon tumor grown in the adipose tissues or non-adipose tissues. Inflammatory profiling and fatty acid oxidation related genes have been detected.

overall_design: Mouse colorectal cancer are injected in the white adipose tissues or non-adipose tissues. Tumor tissues were collected for array when tumor size is 1-1.5 cm3 (n=3 mice/group)

first: Yihai

last: Cao


title: Microarray expression profile and functional analysis of circular RNAs in cervical cancer

first: Hanbo

last: Ma

state: Shanghai

address: 389 Xin cun Road

department: Department of Obstetrics and Gynecology

institute: Tongji hospital

summary: Five human cervical cancer cell lines (HeLa, CaSki, SiHa, C-33A, SW756) and one human normal cervical epithelial cell line HcerEpic were included in the study. Microarray based circRNA expression profiles were acquired using the Arraystar Human circRNA Array (8x15K, Arraystar). We identified circRNAs differentially expressed in human cervical cancer cell lines compared to human normal cervical epithelial HcerEpic cells (control).

overall_design: In the study presented here, the circRNA expression in human cervical cancer cell lines was compared to circRNA expression in human normal cervical epithelial cells (control).


title: Expressioin data from mouse colorectal cancer grown in healthy liver or fatty liver with or without antiangiogenic treatment

summary:
Cancers located adjacent to adipose tissues often show intrinsic and acquired resistance to antiangiogenic therapy. The resistance is developed potentially via tumor cell metabolic paradigm shift.
We use microarrays to detail the gene expression upon tumor grown in the healthy or fatty liver with or without antiangiogenic treatment. Inflammatory profile, fatty acid oxidation-related genes, FFA transporter-related genes, and energy metabolism-related genes have been examined.

overall_design: Mouse colorectal cancer are injected in the healthy or fatty livers with or without antiangiogenic treatment. Tumor tissues were collected for array (n=3 mice/group)


title: BMI1 drives metastasis of prostate cancer in Caucasian and African-American men and is a potential therapeutic target: hypothesis tested in race-specific models

status: Public on Apr 19 2018

city: Minneapolis

first: Mohammad

last: Saleem

state: Mn

address: 2231 6th St SE

department: Urology

institute: University of Minnesota

summary: MDA-PCa2b cells  were treated with PCT-209 or control (DMSO) for 24h and subjected to the qRT-PCR based microarray analysis (Qiagen, Germantown, MD).

overall_design: qPCR gene expression profiling. Metaststic African american prostate cancer cell line MDA-Pca2b cells were treated with BMI-1 inhibitor PTC-209  or control  as indicated in the summary. Equal amount total RNA from Treated and control was used for gene expression analysis.

first: Firdous

last: Beigh


title: Genes specific to cowpea: cowpea vs adzuki bean

city: Hangzhou

first: Pei

last: Xu

address: 198 Shiqiao Rd

department: Vegetable Institute

institute: Zhejiang Academy of Agricultural Sciences

summary:
Comparative hybridization analysis
Microarray-based genomic hybridization was used here as a high-throughput analog to traditional southern hybridization, which is the classical standard method for detecting specific DNA fragments in a genome.

sample_organism:
Vigna angularis
Vigna unguiculata

overall_design: Genomic DNA from cowpea and adzuki bean were labeled with fluorochromes Cy3 and Cy5, respectively, purified, combined, and mixed with SeqCap EZ Developer Reagent to hybridize with the Agilent SurePrint G3 Custom Microarray representing 29,728 unigenes from the cowpea unigene assembly P12.


title: IRF8 regulates transcription of Naips for NLRC4 inflammasome activation

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: Inflammasome activation is critical for host defense against various microbial infections. Activation of the NLRC4 inflammasome requires detection of flagellin or type III secretion system (T3SS) components by NLR family apoptosis inhibitory proteins (NAIPs); yet how this pathway is regulated is unknown. Here we found that interferon regulatory factor 8 (IRF8) is required for optimal activation of the NLRC4 inflammasome in bone marrow-derived macrophages infected with Salmonella Typhimurium, Burkholderia thailandensis, or Pseudomonas aeruginosa but is dispensable for activation of the canonical and non-canonical NLRP3, AIM2, and Pyrin inflammasomes. IRF8 governs the transcription of Naips to allow detection of flagellin or T3SS proteins to mediate NLRC4 inflammasome activation. Furthermore, we found that IRF8 confers protection against bacterial infection in vivo, owing to its role in inflammasome-dependent cytokine production and pyroptosis. Altogether, our findings suggest that IRF8 is a critical regulator of NAIPs and NLRC4 inflammasome activation for defense against bacterial infection.

overall_design: We used microarrays to explore the gene expression profiles differentially expressed in Salmonella-infected bone marrow derived macrophages (BMDM) isolated from IRF8-/- and wild-type mice.

first: Rajendra

last: Karki

first: Ein

last: Lee

first: Parimal

last: Samir

first: Subbarao

last: Malireddi

first: Thirumala-Devi

last: Kanneganti


title: microRNA expression data of paired esophageal NEC samples

city: Shantou

first: Qian

state: Guangdong

address: Xinling 22 Road

institute: Medical College of Shantou University

summary: We detected the expression of miRNA in an esophageal NEC sample and the corresponding normal esophagus tissue. Then, we identified the differentially expressed miRNAs in this rare disease.

overall_design: miRNA profiling of esophageal NEC tissue and matched normal esophagus tissue from the same individual using Agilent-41686 microarrays.

first: En-Min

last: Li

first: Li-Yan


title: HiSeq of small RNA in muscle of large yellow croaker

status: Public on Apr 26 2018

city: Ningbo

first: Mingyue

state: Zheijang

address: 818, Fenghua Rod, Jiangbei District

institute: Ningbo University

summary: We obtained the credible target sequences by filtrating high-throughput profiling of muscle tissue in large yellow croaker.The goal of this study is to measured almost all small RNA in muscle not only at the common feeding but also during the fasting period. We set the data of  microRNA as a mainspring of  study. By bioinformatics analysis, all possible target binding site were compared and predicted in both known and unknown.

overall_design: Examination of 2 different starvation periods of large yellow croaker, including one group with normal diet and the other group with  fasting by 21 days.

first: Liangyi

last: Xue

first: Yayun

last: Zhao


title: Salamander Temperature Exposure Experiment

city: Ploen

first: Till

last: Czypionka

address: August-Thienemann-Strasse 2

department: Evolutionary Genetics

country: Germany

institute: MPI for Evolutionary Biology

summary: Transcriptomes of organisms reveal differentiation associated with the use of different habitats. However, this leaves open how much of the observed differentiation can be attributed to genetic differences or to transcriptional plasticity. In this study, we disentangle causes of differential gene expression in larvae of the European fire salamander from the Kottenforst forest in Germany. Larvae inhabit permanent streams and ephemeral ponds and represent an example of a young evolutionary split associated with contrasting ecological conditions. We found ample evidence for differentiation among larvae occupying different habitats in nature with 2800 out of 11797 genes being differentially expressed based on transcriptome data from salamander sampled in their natural habitat (see GEO Series GSE100819). We then quantified transcriptional plasticity towards temperature and genetic differentiation based on controlled temperature laboratory experiments. Gene-by-environment interactions modelling revealed that 28 % of the gene expression divergence observed among samples in nature could be attributed to plasticity related to water temperature. Expression patterns of only a small number of 101 genes were affected by the genotype. Our analysis demonstrates that effects of environmental factors must be taken into account to explain variation of gene expression in salamanders in nature. Notwithstanding, it provides first evidence that genetic factors determined gene expression divergence between pond and stream ecotypes and could be involved in adaptive evolution.

overall_design: For the analysis of genetic and temperature effects on gene expression of larvae of the pond and stream ecotype the transcriptomes total of 32 larvae raised at two temperatures (9°C and 17°C) were analyzed. At each temperature, the transcriptomes of 6 larvae of a permanent stream (Vennerbach (KOGC) population), 6 larvae from a temporary pond (population TPKoE)and 4 larvae from another temporary pond (population TPKoV2) were assessed.

first: Daniel

last: Goedbloed

first: Steinfartz

last: Sebastian

first: Nolte

middle: W

last: Arne


title: Rosiglitazone effect on type 2 diabetic patients: adipose tissue

first: emmanuelle

last: meugnier

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

overall_design: Refer to individual Series


title: Diversity in gene expression profiles captured through highly resolved whole-transcriptome profiling of clinical and laboratory-adapted malaria parasite isolates

city: London

first: Sarah

last: Tarr

address: Keppel Street

country: United Kingdom

institute: LSHTM

summary:
We present highly replicated whole transcriptome gene expression profiles of schizont-stage malaria parasites using RNA-seq analysis of multiple clinical isolates and laboratory-adapted lines
Methods: Transcript profiles of schizont-stage laboratory-adapted and clinical malaria parasite isolates were generated by RNA sequencing.  Five to ten replicates were sequenced per sample. Illumina stranded TruSeq libraries were sequenced using an Illumina MiSeq. Paired-end fastQ files were aligned using hisat2 and converted to indexed bam files using samtools.  Bam files were filtered to exclude reads with MAPQ scores below 60.  Reads were counted using SummarizeOverlaps feature of the GenomicAlignments package in R. Differential expression analysis was conducted using DESeq2 in R. qRT–PCR validation of differentially expressed genes was performed using SYBR Green assays for eight genes.
Results: We show that increasing sample replication improves the true-positive discovery rate, and that when fewer replicates are available, focussing on the most highly expressed genes maintains the true-positive discovery rate.  We identify schizont-stage genes that appear to alter in expression through the process of culture adaptation, as well as genes that show variable expression between isolates.  We extend transcript quantitation for variably expressed genes to an even wider panel of ex vivo clinical isolate samples.
Conclusions: Our study represents the first detailed analysis of replicated P. falciparum schizont-stage transcriptomes. Our data show that high levels of replication are necessary to capture gene expression differences among parasite isolates. We identify schizont-stage expressed genes that may be differentially expressed as a mechanism of immune evasion.

overall_design: TruSeq stranded mRNA libraries of schizont-stage P. falciparum isolates, with five to ten replicates, were sequenced using an Illumina MiSeq

first: David

last: Conway


title: Effect of rosiglitazone treatment on insulin sensitivity in adipose tissue of type 2 diabetic patients

summary:
The goal of this study was to analyse the effect of a 12 weeks treatment with rosiglitazone on insulin sensitivity in the adipose tissue of type 2 diabetic patients.
Diabetic patients were submitted to a 3 hours hyperinsulinemic- euglycemic clamp. Adipose tissue biopsies were taken before and after the clamp, labelled A & B respectively.
Then, the patients were treated with rosiglitazone, agonist of PPAR gamma, during 12 weeks. After the treatment, all the patients were submitted to a second 3 hours hyperinsulinemic-euglycemic clamp. Adipose tissue biopsies were taken before and after the clamp, labelled C & D respectively.

overall_design: Adipose tissues Biopsies from 7 diabetic patients were used in this study. The samples from the same patients (obtained before and after the hyperinsulinemic-euglycemic clamp) were compared on the same microarray. Biopsie taken before the clamp was considered as the control. A dye switch protocol was applied.

first: Emmanuel

last: Disse

first: Emmanuelle

last: Meugnier

first: Sophie

last: Rome

first: Sandra

last: Pesenti

first: Martine

last: Laville

first: Hubert

last: Vidal


title: Differential metabolic effects of insulin detemir versus NPH in patients with type 2 diabetes

summary: We investigate whether lower weight gain with insulin detemir is due to a decrease in energy intake or an increase in energy output and whether any change in energy balance is accompanied by changes in hormones, lipid metabolism and muscle gene expression.

overall_design: Twenty subjects with type 2 diabetes were titrated for 8 weeks with NPH insulin, then randomized to detemir or NPH for 16 weeks. Body composition, energy expenditure (EE), energy intake, fasting and prandial metabolites and hormones were measured at 8 and 24 weeks. In a subset of subjects (n=10), gene expression profiling was performed in skeletal muscle biopsies taken at 8 weeks (pre-treatment) and 24 weeks (post-treatment).

first: Ben

last: Sheldon

first: Margot

last: Umpleby


title: Analysis of Rosiglitazone therapy on adipose tissue in type 2 diabetic patients

summary:
The goal of this study was to analyse the effect of a 12 weeks treatment with rosiglitazone on gene expression in adipose tissue of type 2 diabetic patients.

Diabetic patients were  treated with rosiglitazone, agonist of PPAR gamma, during 12 weeks. Adipose tissue biopsies were taken before and after the treatment.

overall_design: Adipose tissues Biopsies from 6 diabetic patients were used in this study. The samples from the same patients (obtained before and after the 12 weeks of treatment) were compared on the same microarray. Biopsie taken before the treatment was considered as the control. A dye switch protocol was applied.


title: C4 Photosynthesis: Gene expression in mesophyll and bundle sheath cells of bundle sheath defective2 mutant

city: Ithaca

first: Thomas

middle: P.

last: Brutnell

state: NY

address: Cornell University

institute: Boyce Thompson Institute for Plant Research

summary: Zea mays is a C4 plant that utilizes two distinct cell types, mesophyll (M) and bundle sheath (BS), to cooperatively fix carbon. Regulation of M and BS cell differentiation is poorly understood. Here, we explore the transcriptional networks of M and BS cells by microarray analysis. The maize mutant bundle sheath defective2 lacks the accumulation of Rubisco small and large subunits (Roth et al 1996; Brutnell et al 1999) and cannot perform the Calvin Cycle (Smith et al 1998). Therefore, this mutant provides an opportunity to study M and BS cell differentiation in a perturbed BS background, potentially revealing regulons important to cell identity. M and BS cells were independently isolated from mutant and wild-type siblings. Transcriptional profiling was then performed in a cell specific manner between mutant and wild-type.

overall_design: Both M and BS cell experiments were performed using the Maize Oligonucleotide Array (University of Arizona). For each experiment, six biological replicates were conducted in a dye swap arrangement using the 900MPX Expression Array Detection Kit and company protocol (Genisphere). After scanning, feature intensity values were log-transformed, corrected for local background, and filtered to include only those that were at least 2x background. The data was then LOWESS normalized and corrected for dye-effect. Differentially expressed genes were identified by moderated-t test and the false discovery rate (q) was determined.

last: Covshoff

first: Peng

last: Liu

first: Hong

last: Hua


title: VASCULAR PLANT ONE-ZINC FINGER1 (VOZ1) and VOZ2 interact with CONSTANS in photoperiodic control of flowering

status: Public on Apr 18 2018

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

summary: In plants, endogenous and environmental signals such as light control the timing of the transition to flowering . Two phytochrome B-interacting transcription factors, VASCULAR PLANT ONE–ZINC FINGER1 (VOZ1) and VOZ2 redundantly promote flowering in Arabidopsis thaliana. In the voz1 voz2 mutant the expression of FLOWERING LOCUS C (FLC) was up-regulated and expression of FLOWERING LOCUS T (FT) was down-regulated, which was proposed to be the cause of late flowering in voz1 voz2. However, the detailed mechanism by which the VOZ genes promote flowering is not well understood. Here, we show that neither the reduced FT-expression nor the late-flowering phenotype of voz1 voz2 is suppressed in the voz1 voz2  flc triple mutant . Genetic interaction experiments between voz1 voz2 and constans-2 (co-2) mutants reveal that the VOZs and CO work in the same genetic pathway. Using in vitro pull-down, electrophoretic mobility shift assays and bimolecular fluorescence complementation assays, we show that VOZ1 and VOZ2 interact with CO. The voz1 voz2 35S::CO:YFP plants show suppression of the early-flowering phenotype induced by CO-overexpression, showing that CO requires VOZ for induction of flowering.  Determination of the VOZ consensus binding site followed by genome-wide sequence analysis failed to identify any VOZ-binding sites near known flowering-time genes. Together, these results indicate that the VOZ genes regulate flowering primarily through the photoperiod pathway, independent of FLC, and suggest that VOZs modulate CO function to promote flowering.

overall_design: Agilent Microarray Gene Expression 8X60K-Arabidopsis thaliana  (AMADID: 37661) designed by Genotypic Technology Pvt.Ltd.

first: Sushil

last: Kumar

first: Utpal

last: Nath


title: Systems genomics study reveals expression quantitative trait loci, regulator genes and pathways associated with boar taint in pigs (SNP60v2 BeadChip data set)

city: Kongens Lyngby

first: Haja

middle: N

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

summary: Boar taint is an offensive odour and/or taste from a proportion of non-castrated male pigs caused by skatole and androstenone accumulation during sexual maturity. Castration is widely used to avoid boar taint but is currently under debate because of animal welfare concerns. This study aimed to identify expression quantitative trait loci (eQTLs) with potential effects on boar taint compounds to improve breeding possibilities for reduced boar taint. Danish Landrace male boars with low, medium and high genetic merit for skatole and human nose score (HNS) were slaughtered at ~100 kg. Gene expression profiles were obtained by RNA-Seq, and genotype data were obtained by an Illumina 60K Porcine SNP chip. Following quality control and filtering, 10,545 and 12,731 genes from liver and testis were included in the eQTL analysis, together with 20,827 SNP variants. A total of 205 and 109 single-tissue eQTLs associated with 102 and 58 unique genes were identified in liver and testis, respectively. By employing a multivariate Bayesian hierarchical model, 26 eQTLs were identified as significant multi-tissue eQTLs. The highest densities of eQTLs were found on pig chromosomes SSC12, SSC1, SSC13, SSC9 and SSC14. Functional characterisation of eQTLs revealed functions within regulation of androgen and the intracellular steroid hormone receptor signalling pathway and of xenobiotic metabolism by cytochrome P450 system and cellular response to oestradiol. A QTL enrichment test revealed 89 QTL traits curated by the Animal Genome PigQTL database to be significantly overlapped by the genomic coordinates of cis-acting eQTLs. Finally, a subset of 35 cis-acting eQTLs overlapped with known boar taint QTL traits. These eQTLs could be useful in the development of a DNA test for boar taint but careful monitoring of other overlapping QTL traits should be performed to avoid any negative consequences of selection.

overall_design: Genomic DNA was extracted from ham muscle of 48 Danish Landrace pigs with low- medium and high genetic merit of boar taint and genotyped with Illumina Porcine SNP60v2 BeadChip.

first: Markus

last: Drag

first: Mathias

middle: B

last: Hansen

first: Ruta

last: Skinkyté-Juskiené

first: Duy

last: Do

first: Lisette

last: Kogelman


title: Gene expression signatures for murine B cells from tumor-draining lymph nodes

first: Yan

last: Gu

address: 800 Xiangyin Road

department: Immunology

institute: Second Miilitary Medical University

summary: To determine the influence of primary tumors on pre-metastatic lymph nodes, we have employed whole genome microarray expression profiling as a discovery platform to identify gene signatures of B cells from tumor-draining lymph nodes, compared with normal lymph nodes. We subcutaneously inoculated C57BL/6 mice with the 4T1 mammary carcinoma. Two weeks later, tumor-draining lymph nodes were dissociated and B cells (CD19+) were sorted. Lymph nodes B cells from normal mice without tumor bearing were set as controls.

overall_design: Primary tumor induced gene expression in B cells from tumor-draining lymph nodes was measured at 2 weeks after tumor inoculation subcutaneously. Lymph node B cells from normal mice without tumor bearing were set as controls.

first: Xuetao

last: Cao


title: Angiogenin/ribonuclease 5 is an EGFR ligand and a serum biomarker for erlotinib sensitivity in pancreatic cancer

city: Houston

first: Mien-chie

last: Hung

state: Texas

address: 1515 Holcomb Blvd

department: Molecular and Cellular Oncology

institute: M.D. Anderson Cancer Center

summary: Pancreatic ribonuclease (RNase) is a secreted enzyme critical for host defense. We discover an intrinsic RNase function, serving as a ligand for epidermal growth factor receptor (EGFR), a member of receptor tyrosine kinase (RTK), in pancreatic ductal adenocarcinoma (PDAC). The closely related bovine RNase A and human RNase 5 (angiogenin/ANG) can trigger oncogenic transformation independently of their catalytic activities via direct association with EGFR. Notably, high plasma ANG level in PDAC patients is positively associated with response to EGFR inhibitor erlotinib treatment. These results identify a previously unrecognized role of ANG as a serum biomarker, which may be used to stratify patients for EGFR-targeted therapies, and offer insights into the ligand-receptor relationship between RNase and RTK families.

overall_design: Gene expression profiling of two pancreatic cancer cell lines before and after EGF and ANG/hRNase 5 treatments

first: Ying-Nai

last: Wang

first: Heng-Huan

last: Lee

first: Chao-Kai

last: Chou

first: Wen-Hao

last: Yang

first: Yongkun

last: Wei

first: Chun-Te

last: Chen

first: Jun

last: Yao

first: Jennifer

last: Hsu

first: Cihui

last: Zhu

first: Haoqiang

last: Ying

first: Yuanqing

last: Ye

first: Wei-Jan

first: Seung-Oe

last: Lim

first: Weiya

last: Xia

first: How-Wen

last: Ko

first: Xiuping

first: Chang-Gong

first: Xifeng

last: Wu

first: Huamin

first: Donghui

last: Li

first: Laura

last: Prakash

first: Matthew

last: Katz

first: Yann

last: Kang

first: Michael

last: Kim

first: Jason

last: Fleming

first: David

last: Fogelman

first: Milind

last: Javle

first: Anirban

last: Maitra

first: Mien-Chie


title: Key players of cisplatin resistance: towards a systems pharmacology approach

status: Public on Apr 17 2018

city: Bonn

first: Ganna

last: Kalayda

address: An der Immenburg 4

department: Clinical Pharmacy

institute: University of Bonn

summary: The cellular transcriptome of untreated and cisplatin-treated A549 non-small cell lung cancer cells and their cisplatin-resistant sub-line A549rCDDP2000 was screened with a whole genome array for gene candidates relevant for cisplatin resistance.

overall_design: Sensitive and resistant non-small cell lung cancer cells were treated with 11 or 34 µM cisplatin or with the drug-free medium. Total RNA was isolated and analysed.

first: Navin

last: Sarin

first: Florian

last: Engel

first: Holger

last: Fröhlich


title: Evolution of genome architecture in Archaea: spontaneous generation of a new chromosome in Haloferax volcanii by homologous recombination

city: Norwich

first: Conrad

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

summary:
Eukaryotic genomes typically consist of multiple (linear) chromosomes that are replicated from multiple origins. Several hypothetical scenarios have been proposed to account for the evolution of multi-origin/multi-chromosome genomes, which are encountered in modern eukaryotes and archaea.
Here we report an example of the generation of a new chromosome in the halophilic archaeon Haloferax volcanii through one of these scenarios: acquisition of new replication origins and splitting of an ancestral chromosome into two replication-competent chromosomes. The multi-origin main chromosome has split into two genome elements via homologous recombination. The newly generated elements possess all the features of bona fide chromosomes. To our knowledge, the spontaneous generation of a new chromosome in prokaryotes without horizontal gene transfer has not been reported previously.

overall_design: Measurement of genome replication time in Haloferax volcanii:  a replicating sample (from log phase) was obtained from H26 laboratory strain, H1689 orc5 and H2202 orc3 orc5 mutants. Replicating samples were normalyzed to a non-replicating sample of H26 laboratory strain (from stationary phase).

first: Darya

last: Ausiannikava

last: Mitchell

first: Hannah

last: Marriott

first: Michelle

last: Hawkins

first: Kira

middle: S

last: Makarova

first: Eugene

middle: V

last: Koonin

first: Thorsten

last: Allers


title: Gene expression signatures for murine stromal cells from tumor-draining lymph nodes

first: Yan

last: Gu

summary: To determine the influence of primary tumors on pre-metastatic lymph nodes, we have employed whole genome microarray expression profiling as a discovery platform to identify gene signatures of stromal cells from tumor-draining lymph nodes, compared with normal lymph nodes. We subcutaneously inoculated C57BL/6 mice with the 4T1 mammary carcinoma. Two weeks later, tumor-draining lymph nodes were dissociated and stromal cells (CD45-) were sorted. Lymph nodes stromal cells from normal mice without tumor bearing were set as controls.

overall_design: Primary tumor induced gene expression in stromal cells from tumor-draining lymph nodes was measured at 2 weeks after tumor inoculation subcutaneously. Lymph nodes stromal cells from normal mice without tumor bearing were set as controls.

first: Xuetao

last: Cao


title: Characterization of the trehalose utilization operon in Streptococcus mutans reveals that the TreR transcriptional regulator is involved in stress response pathways and toxin production

status: Public on Apr 16 2018

city: Rochester

first: Roberta

middle: C

last: Faustoferri

address: 601 Elmwood Ave. Box 611

department: Center for Oral Biology

institute: University of Rochester Medical Center

summary: Streptococcus mutans, the organism most frequently associated with the development of dental caries, is able to utilize a diverse array of carbohydrates for energy metabolism.  One such molecule is trehalose, a disaccharide common in human foods, which has recently been implicated in enhancing the virulence of epidemic strains of the pathogen, Clostridium difficile.  In this study, deletion mutants of all three genes in the putative S. mutans trehalose utilization operon were characterized and shown to be required for wild-type levels of growth when trehalose was the only carbohydrate source provided.  Interestingly, the TreR transcriptional regulator appeared to be critical for responding to oxidative stress, and for mounting a protective stress tolerance response following growth at moderately acidic pH.  RNAseq of a treR deletion mutant suggested that in S. mutans, TreR acts as a trehalose-sensing activator of transcription of the tre operon, rather than a repressor, as described in other species.  In addition, deletion of treR caused the down-regulation of a number of genes involved in genetic competence and bacteriocin production, supporting results of a recent study linking trehalose and the S. mutans competence pathways.  Finally, deletion of treR compromised the ability of S. mutans to inhibit the growth of the competing species, Streptococcus gordonii and Lactococcus lactis.  Taken together, this study solidifies the role of the S. mutans tre operon in trehalose utilization and suggests novel functions for the TreR regulator, including roles in stress response and competitive fitness.

overall_design: Transcriptional profiling was performed using RNA extracted from cultures of S. mutans parent strain UA159 and the ∆treR derivative grown in tryptone-yeast extract medium supplemented with either glucose, galactose or trehalose.

first: Jonathon

last: Baker

first: Elizabeth

last: Lindsay

first: Thao

middle: T

last: To

first: Erik

last: Hendrickson

first: Xuesong

last: He

first: Wenyuan

last: Shi

first: Jeffrey

last: McLean

first: Robert

middle: G

last: Quivey Jr


title: Differential Gene Expression Analysis of Human Cumulus Cells as a Predictor of Pregnancy

city: İstanbul

first: Hüseyin Okan

last: Soykam

address: Teknopark İstanbul, Sanayi Mh. Teknopark Blv. No: 1/4A, Kuluçka Merkezi, Pendik, 34906, İstanbul

department: Bioinformatics

country: Turkey

institute: Epigenetiks Genetik Biyoinformatik Yazılım A.Ş.

summary:
The objective of this study was to provide valuable insights into the determination of clinical pregnancy and live birth outcomes in the context of differential gene expression analysis of cumulus cells as predictors of clinical pregnancy and/or live birth after single embryo transfers.
This study was performed with the consideration that each oocyte and each group of cumulus cells surrounding different oocytes might have different genetic expression patterns that might affect human reproduction.
Differential gene expression analysis of cumulus cells was performed in 10 clusters of cumulus cells obtained from 10 cumulus-oocyte complexes of 10 patients. Same procedures related to the oocyte maturation, microinjection, and microarray analyses were applied to the group of cumulus cells, individually.
The results of the microarray analyses were enriched according to the clinical pregnancy and live birth outcomes of the patients.
In conclusion, our data indicated significant differences in gene expression related with a variety of signaling pathways; the RAS signaling, the mitogen-activated protein kinases signalling, the ERBB signaling, the RAP1 signaling, the transcription factor nuclear factor-kb signaling, the transforming growth factor-b signaling pathways and neurological signaling pathways such as glutamatergic synapse, cholinergic synapse, dopaminergic synapse, GABAergic synapse, long-term potentiation, the neuroactive ligand-receptor interaction pathways.
Circadian entrainment pathway was also affected in both clinical pregnancy and live birth at different significance level. These pathways can be exploited to identify biomarkers related to clinical pregnancy and live birth outcomes.

overall_design:
This prospective case study included 10 women (aged 23-35 years) who were referred to a 3rd level reference center university hospital for idiopathic infertility and implemented Assisted Reproductive Technologies. The total sample size was 10 oocyte-cumulus complexes obtained over a period of 14 months between October 2011 and December 2012. Cumulus cells gene expressions in 10 clusters of cumulus cells obtained from 10 cumulus-oocyte complexes of 10 patients were individually evaluated by microarrays using a NimbleGen Human Gene Expression 12x135K Microarray Kit (NimbleGen, Roche, Germany). Although the number of cumulus cells belonging to the same oocyte was very few, the oocytes and the cumulus cells sourrounding the same oocyte were analysed individually. The cumulus cells from each oocyte that developed an embryo that were transferred, applied with microarray analysis.
Cumulus cells gene expressions were individually evaluated by microarrays in10 clusters of cumulus cells obtained from 10 cumulus-oocyte complexes of 10 different paitents using a NimbleGen Human Gene Expression 12x135K Microarray Kit (NimbleGen, Roche) according to the manufacturer’s instructions. Twelve-sample hybridization was performed on a single microarray slide, with three probes per gene. Total RNA was isolated using an RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. cDNA synthesis from total RNA was carried out using a Superscript Double Chain cDNA Synthesis Kit (Invitrogen Life Technologies, Carlsbad, CA, USA). cDNA was marked using a Single Color DNA Labeling Kit (NimbleGen, Roche, Germany). cDNA was hybridized using the NimbleGen Hybridization System. Washing and drying of the array were carried out with a NimbleGen MS 2000 Microarray Scanner, and raw probe expression data was collected from microarray images using DEVA software.

first: Sirin

last: Demiray

first: Ozlem

middle: Y

last: Dilsiz

first: Nazan

last: Goker

first: Erol

last: Tavmergen

first: Nilufer

last: Calimlioglu

first: Huseyin

middle: O

first: Osman

middle: U

last: Sezerman

first: Gulperi

last: Oktem


title: Agilent SurePrint G3 Human V2 GE 8×60K microarray-BEAS-2B cells treatment with NiCl2

city: Taichung

first: Jiunn-Liang

last: Ko

address: 110, Sec. 1, Chien-Kuo N. Road

country: Taiwan

institute: Institute of Medicine, Chung Shan Medical University

summary: To investigate the effects of nickel on gene expression in BEAS-2B cells.

overall_design: NiCl2 mediated gene expression in BEAS-2B cells was measured at 48 h after exposure to doses of 0 and 0.5 mM.

first: Chih-Hsien

last: Wu


title: HmiOA4.1 microarrays-BEAS-2B cells treatment with NiCl2

summary: To investigate the effects of nickel on miRNAs expression in BEAS-2B cells.

overall_design: NiCl2 mediated miRNA expression in BEAS-2B cells was measured at 48 h after exposure to doses of 0 and 0.5 mM.


title: De novo transcriptome characterization of Nitraria sibirica Pall. under salt stress

city: beijing

first: Huanyong

last: Li

address: xiangshan road

institute: Chinese  academy of forestry

summary: We will use high-throughput sequencing technology to study gene expression under NaCl treatment, screen for differential expressed genes, and then analyze the gene regulation features. Nitraria sibirica Pall. seedlings were treated by 0, 100 and 400 mM NaCl with 3 replicates，and the leaves were harvested after treated 3 days. Extracting total RNA of leaves and then sequencing by Illumina HiSeq 2000 sequencing platform. Our study provides a basis for the study of salt-tolerant gene resources in Nitraria sibirica Pall.

overall_design: Total RNA were extracted from Nitraria sibirica Pall. leaves which treated by 0, 100 and 400 mM NaCl for 3 days with 3 replicates.

first: Huaxin

last: Zhang


title: Murine mature B Cells: Control vs. Notch1 Signaling Activated

city: Kyoto

first: Hiroshi

last: Arima

address: 54 Shogoin Kawahara-cho, Sakyo-ku

department: Department of Hematology and Oncology

institute: Graduate School of Medicine, Kyoto University

summary: Transcriptional profiling of murine splenic mature B cells that have experienced activation-induced cytidine deaminase (Aicda) gene expression comparing control untreated B cells with B cells in which transgenic Notch1 intracellular domain (NICD1) gene, coding for an active form of Notch1, began to be expressed after Aicda promoter-driven expression of Cre recombinase. B cells that have experienced Aicda promoter activation were visualized by Cre-inducible expression of red fluorescent protein (RFP) which was inserted in the Rosa26 locus. Total RNA was extracted from splenic CD19+ RFP+ B cells isolated from mice using an RNeasy Mini kit (Qiagen, Hilden, Germany). Equal amounts of total RNA derived from 3 control mice and 3 mice with conditional activation of Notch1 signaling in mature B cells were pooled and submitted for gene expression microarray analysis. Goal was to determine the effects of conditional activation of Notch1 signaling in mature B cells.

overall_design: Two-condition experiment, mature B cells vs. Notch1-activated mature B cells. Biological replicates: Equal amounts of total RNA from 3 mice per group were pooled together.

first: Momoko

last: Nishikori


title: Identification of rapamycin as an autophagy inducer to treat PANC-1 cells [miRNA]

city: Nanning

first: Qiao

last: Yu

address: Shuangyong road, qingxiu district，nanning

institute: First Affiliated Hospital of Guangxi Medical University

summary: The function and mechanism of autophagy in pancreatic cancer remained elusive owing to its complex biological process and multi-molecular involvement including non-coding RNAs. Here, we, from the view of mRNA, circRNA, lncRNA and miRNA, investigate the molecular mechanism of autophagy induction on human pancreatic cancer cells

overall_design: The autophagy-induced model was constructed with PANC-1 cells treated by rapamycin. It was indicated that 100µM rapamycin was the best choice to induce the autophagy of PANC-1 in humans.

first: Dan-ming

last: Wei

first: Rong-quan

last: He

first: Meng-tong

last: Jiang

first: Peng

last: Lin

first: Jie

last: Ma

first: Hong

last: Yang

first: Dian-zhong

last: Luo

first: Yi-wu

last: Dang

first: Gang

last: Chen


title: Gene regulation by elevated c-di-AMP levels in Streptococcus pneumoniae

city: Albany

first: Guangchun

last: Bai

address: New Scotland Ave

department: DIMD

institute: Albany Medical College

summary: Streptococcus pneumoniae harbors two cyclic di-AMP (c-di-AMP) phosphodiesterases Pde1 and Pde2. Previously, we demonstrated that deletion of one or both of these proteins leads to growth retardation in culture media, defects in the bacterial stress response, and attenuation in mouse models of disease. All of these phenotypes are due to increased levels of c-di-AMP, since the nature and break down products of each protein are different, and mutations that lower c-di-AMP levels partially restore growth and stress tolerance in these mutants. However, how c-di-AMP mediates pneumococcal stress resistance and virulence is unknown. To establish how c-di-AMP affects the transcriptome, RNA-Seq analysis was employed to compare gene expression between wild-type and Δpde1Δpde2 (ST2734) pneumococci. Overall, the competence regulon was upregulated in the Δpde1Δpde2 mutant.

overall_design: The goal of this research was to determine c-di-AMP-responsive genes in Streptococcus pneumoniae. We prepared RNA samples of the wild-type and Δpde1Δpde2 strains with three independent biological replicates. RNA samples were treated with DNase to remove contaminated DNA. rRNA was removed using Ribo-Zero magnetic kit (Epicentre). cDNA library was then generated using ScriptSeq Complete Kit for Bacteria (Epicentre). Samples 1 to 6 were amplified with index PCR primers 1to 6, respectively, from Script Seq Index PCR primers (Epicentre). RNA-Seq was performed at the Next Generation Sequencing and Expression Analysis Core of University of Buffalo.

first: Tiffany

last: Zarrella

first: Dennis

last: Metzger


title: Expression data from primary sqWAT-MSC cells from mouse

city: Berlin

first: Cornelius

last: Fischer

state: Berlin

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine (MDC)

summary:
GATA2 is a transcription factor that is required for hematopoietic stem cell (HSC) differentiation. GATA2 is also expressed in mesenchymal cells and blocks differentiation of both white and brown adipocytes by interfering with C/EBP activity and PPARγ expression. By studying genome-wide binding sites of endogenous GATA2 in mesenchymal stem cells (MSC), we discovered a previously unrecognized function of GATA2 in the regulation of skeletal development-related genes. In contrast to hematopoietic stem cells, canonical GATA2 binding motifs in MSCs co-localized with motifs for transcription factors of the FOX and HOX family, known regulators of skeletal development. Consistently, ectopic GATA2 expression in MSCs regulated many osteoblast-related genes. Ectopic GATA2 blocked, whereas GATA2 deletion enhanced differentiation of osteoblastic precursors. GATA2 expression inhibited bone morphogenetic protein (BMP)-2 induced SMAD1/5/8 activity, a pathway that drives osteoblastogenesis. MSC-specific deletion of GATA2 in mice affected both numbers and osteogenic potential of bone-residing precursors without disturbing normal skeletal development. In adult mice, MSC-specific GATA2 deficiency affected trabecular bone structure and its mechanical properties. blood phenotype? In summary, our study identified GATA2 as a novel regulator of osteoblast differentiation and bone morphology, suggesting a role of GATA2 in MSC lineage determination that goes beyond adipocyte differentiation.
Microarrays analysis was done to determine gene expression changes between sqWAW-MSC control cells and sqWAT-MSC cells with Gata2 over-expression.

overall_design: This dataset consists of two sample groups: sqWAT-MSC cells infected with empty (control) or GATA2-expressing retroviruses (GATA2 over-expression). Each sample group consists of three replicates samples.

first: Alexander

last: Tolkachov

first: Thomas

last: Ambrosi

first: Chung

last: Han

first: Matthias

last: Münzner

first: Susanne

last: Mathia

first: Marjo

last: Salminen

first: Georg

last: Seifert

first: Mario

last: Thiele

last: Duda

first: Sascha

last: Sauer

first: Tim

middle: J

last: Schulz

first: Michael

last: Schupp


title: Nasonia Tiling Microarray Experiments for Expression Profiling Sexual Development (Gonads)

status: Public on Apr 15 2018

city: Augusta

first: Justin

last: Choi

state: GA

address: 1410 Laney Walker Blvd.

department: Cancer Center

institute: Georgia Regents University

type: Expression profiling by genome tiling array

summary:
A key feature of Nasonia are their form of sex determination, called haplodiploidy. Females are diploid and develop from fertilized eggs, whereas males are haploid and develop parthenogenetically from unfertilized eggs. This form of sex determination is exploited by this experiment, by knowing the sex of the organisms from the earliest stages of development, so to trace the transcriptomes of sexual development of an insect.
We conducted three replicates each using RNA from independent biological extractions of male and female early embryo (0-10 hrs), late embryo (18-30 hrs), 1st instar larvae, and pupae. Additional experiments were performed comparing transcription in adult males, adult females, testis and the female reproductive tract.

overall_design: We conducted two-color competitive hybridizations that measure differential expression from three replicates, each using RNA from independent biological extractions. Transcriptional active regions (TARs) were defined by stringing together overlapping probes showing fluorescence above a 1% false positive rate (FPR). Positive probes were joined into a TAR if they were adjacent (maxgap=0, no intermittent non-positive probe) and a TAR's length had to be at least 45 bp (minrun=45, mid-point first positive probe to mid-point last positive probe, resulting in at least 3 adjacent positive probes for a TAR). The data analysis to measure differential expression of Official Gene Set (OGS) 2.0 annotated genes (http://arthropods.eugenes.org/EvidentialGene/nasonia/), their exons and of unannotated TARs was performed using the statistical software package R and Bioconductor with additions and modifications. The signal distributions across chips, samples and replicates were adjusted to be equal according to the mean fluorescence of the random probes on each array. All probes including random probes were quantile-normalized across replicates. Expression-level scores were assigned for each predicted gene based on the median log2 fluorescence over background intensity of probes falling within the exon boundaries.

first: John

middle: K

last: Colbourne

first: Jacqueline

last: Lopez

first: Jeong

last: Werren


title: Gene expression profiling of mammary epithelial cells from mice transiently exposed to tamoxifen

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: The tumor suppressor gene p53 is frequently mutated in human breast cancer and is a marker for poor prognosis and resistance to chemotherapy. Transplantation of p53-null mouse mammary epithelium into syngeneic wild-type mice leads to normal mammary gland development followed by spontaneous mammary tumors that recapitulate many of the phenotypic, molecular, and genetic features of human breast cancer. Using this genetically engineered mouse model, we have examined the molecular mechanisms underlying tamoxifen-dependent tumor prevention. To determine whether the changes observed in the ERα cistrome after tamoxifen exposure are reflected in changes in estrogen responsive gene signatures in p53-null mammary epithelial cells (MECs), we performed global gene expression analysis by microarray profiling of MECs isolated from control and tamoxifen-exposed mice 4 weeks after tamoxifen withdrawal and treated with E2 for 8h. We identified 245 differentially regulated genes (P<0.01 and FC>1.4). Of these, 177 genes (72%) were persistently upregulated and 68 genes (28%) were persistently downregulated after transient exposure to tamoxifen. These results indicate that transient exposure to tamoxifen leads to lasting intrinsic changes in gene expression profiles of p53-null mammary epithelial cells that persist after tamoxifen withdrawal.

overall_design: Two experimental groups: Tamoxifen-treated group and control group. We used triplicate pools of mammary glands from control or tamoxifen-treated mice (5 mice per pool) for preparation of MEC’s total RNA isolation followed by Affymetrix array profiling using Affymetrix GeneChip Mouse Exon 1.0 ST array.

first: Murugesan

last: Palaniappan

first: Yiqun

last: Zhang

first: Orla

last: Conneely


title: Effect of Sidt2 deficiency on skeletal muscle

city: Shanghai

first: Huiwen

address: Kongjiang Road 1665#

institute: Xinhua Hospital

summary:
To study the effect of Sidt2 protein deficiency on skeletal muscle, we developed skeletal musclespecific Sidt2 gene knockout mouse model using Cre under the control of the MCK promoter
We used microarrays to detail the changes of gene expression.

overall_design: Skeletal muscles from Sidt2f/f and Sidt2f/fCre mice  of two-month-old were compared.

first: Guoying

last: Chang


title: The hypertrophy of the ligamentum flavum is assosciated with activation of the unfolded protein respone

city: Tokushima

first: Masatoshi

last: Morimoto

address: 3-18-15 Kuramoto

institute: Institute of Biomedical Sciences Tokushima University Graduate School

summary: To investigate the gene expression compared the hypertrophic ligament of elderly with non-hypertrophic ligament of young

overall_design: compare the gene expression between the ligamentum flavum of young and elderly

first: Shoichi

last: Oyadomari


title: Nasonia Tiling Microarray Experiments for Expression Profiling Sexual Development (Pupa)


title: Transcriptomic study on protective effects of Danhong Injection against cerebral ischemia/reperfusion-induced damage

city: Hangzhou

first: shujing

last: zhang

address: Xihu district

department: College of Pharmaceutical Sciences

institute: Zhejiang University

summary: This study compared the gene expression change of rat brain (cerebral ischemia reperfusion model) before and after Danhong injection treatment

overall_design: The Sprague Dawley (SD) rats were  subjected to cerebral ischemia reperfusion. After 2 h of occlusion, the nylon suture was pulled out. Animals were Tail vein injected drugs for 14 days after which surgical procedure for the common carotid arteries and reperfusion was performed. Then, the animals that designed to be injected Danhong injection for 14 days.  1. Sham group: sham-operated group  2. Model group:the ischemia-reperfusion group  3. Danhong group:administered with Danhong injection+ ischemia-reperfusion group

first: Shujing


title: Effects of NiCl2 on gene and miRNA expression in BEAS-2B cells

first: Jiunn-Liang

last: Ko

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

overall_design: Refer to individual Series


title: Nasonia Tiling Microarray Experiments for Expression Profiling Sexual Development (Embryo10)


title: Nasonia Tiling Microarray Experiments for Expression Profiling Sexual Development (Adult)


title: Nasonia Tiling Microarray Experiments for Expression Profiling Sexual Development (Larva)


title: Exon skipping variations modulate stress-inducible inflammation

city: London

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

institute: UCL

summary: Psychological stress reactions can stimulate mammalian immune functions due to yet unknown mechanisms. We hypothesized that these involve massive post-stress alternative splicing modulations in peripheral blood mononuclear cells (PBMCs). RNA was extracted from PBMCs of BALB/C mice following unpredictable repeated foot shocks. Among the tested group, five mice exhibiting the maximal circulation glucocorticoids were selected for the stress group. PBMC RNA of 5 BALB/C mice served as the control group. Through linear regression analysis of all the reciprocal junction pairs represented on the microarrays and the Ensembl database, 496 alternative splicing events were detected. The stressed mice showed 65% exon skipping out of total splicing event changes compared to controls. The detected genes exhibited functional enrichment (through DAVID EASE analysis) in alternative splicing (47%), cellular response to stress (12%), lymphocyte activation (8%), stress-induced proteins (2%) and heat-shock-induced proteins (2%). Specifically, exon skipping modifications in the Hnrnph1 and CLK1 splicing-related transcripts were accompanied by stress-inducible inclusions in the immune response-related IRF-1 gene. Our findings demonstrate dependence on exon skipping and independence from glucocorticoid and innate immunity for the stress-inducible exacerbation of immunity and open new venues for preventing post-trauma inflammatory crisis.

overall_design: 11 samples were analyzed. Mouse Junction Array (MJAY) expression data was obtained from the RNA of PBMCs from 5 stressed and 5 control BALB/C mice, with 1 restained stressed sample. Detection of exon inclusion events was conducted through both junction- and exon-level analyses on summarized and normalized junction and exon interrogating probesets (JUC/PSR). The junction-level expression data was analyzed through a linear regression approach on all the array represented reciprocal junction pairs (through adopted AltAnalyze code), and the exon-level expression data was analyzed through a splicing-index analysis approach.The functional relevance of the detected events was deduced through comparison to all the Ensembl transcripts of each gene (e.g., alternative terminus, truncation, nonsense-mediated decay, etc). Protein/motif predictions for significant probesets and over-representation scores were calculated for each impacted microRNA-binding site.

first: Hermona

first: Adi

last: Gilboa-Geffen

first: Shani

last: Shenhar-Tsarfaty

first: Nir

last: Weiskopf


title: Nasonia Tiling Microarray Experiments for Expression Profiling Sexual Development (Embryo18)

first: Justin

last: Choi

first: John

first: Jacqueline

first: Jeong


title: Nasonia Tiling Microarray Experiments for Expression Profiling Sexual Development

last: Colbourne


title: The molecular characterisation of mitochondrial DNA deficient oocytes using a pig model

status: Public on Apr 11 2018

city: Melbourne

first: Tesha

last: Tsai

state: Vic

address: 27-31 Wright Street, Clayton

country: Australia

institute: Hudson Institute of Medical Research

summary: Pig oocytes were stained with Brilliant cresyl blue to identify mtDNA deficient oocytes.

overall_design: RNA sequencing was performed on pooled oocytes (n=5 per group) and single oocytes to determine differences between mtDNA-normal and mtDNA-deficient oocytes.

last: St. John


title: Comparison of atrial appendage tissues of patients with Valvular Heart Disease and patients with Valvular Heart Disease-Atrial Fibrillation

status: Public on Apr 12 2018

city: Chengdu

first: nini

last: rao

state: Sichuan

address: No.4, Section 2, North Jianshe Road

institute: University of Electronic Science and Technology of China

summary: Atrial fibrillation (AF) is the most common heart arrhythmia disease. The greatest risk of atrial fibrillation is stroke, and stroke caused by valvular heart disease with atrial fibrillation (AF-VHD) is more serious. the development mechanism from VHD to AF-VHD is not yet clear. The research on expression profiles of lncRNA and mRNA is helpful to explore molecular mechanism in patients with valvular heart disease who develop atrial fibrillation.

overall_design: the atrial appendage tissues of five AF-VHD and five SR-VHD (sinus rhythm, SR) patients  were obtained from patients undergoing heart surgery

first: Nini

last: Rao

first: Wei

last: Zeng


title: Gene expression profiling of novel hematopoietic stem cell subpopulations defined by CD35 expression and progenitor populations in human adult hematopoiesis

status: Public on Apr 13 2018

city: Fukuoka

first: Kohta

last: Miyawaki

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

institute: Kyushu University

summary: Cannonical hematopoietic stem cell (HSC) population is phenotypically defined as Lin- CD34+ CD38- CD45RA- CD90+ in human adult bone marrow. We recently identified novel HSC subpopulation defined as CD35+ HSCs. We performed microarray analysi to clarify the characteristics of CD35+ HSCs in comparison with other stem/progenitor populations. As compared to CD35- HSCs and progenitor populations, CD35+ HSCs showed lower expression of cell-cycle- or lineage-affiliated genes.suggesting their dormant or immature state.

overall_design: To undertake gene expression profiling of the newly identified HSC and other stem/progenitor populations, we purified target populations by FACS Aria III. Extracted RNA from these populations were subjected to Agilent microarray analysis.

first: Takashi

last: Jiromaru


title: Comparative study of interruption of TLR and NF-kB signaling pathways in lung epithelial cell by Mycobacterium tuberculosis strains [NFkB]

city: Tehran

first: Shima

last: Hadifar

address: 12th Farvardin Ave, Jomhhoori St

department: Mycobacteriology and Pulmonary Research

country: Iran

institute: Pasteur Institute of Iran

summary: comparing different lineages of M.tb strains (lineages 3 and 4) in interrupting of epithelial signalling pathways in A549 cell line, from TLRs and NFkB signalling pathways to specific cytokine secretion

overall_design: qPCR gene expression profiling.  Alveolar epithelial cell infected separately  by two M.tb strains . Equal amount total RNA from each infected cell was pooled prior to gene expression analysis.

first: Farzam

last: Vaziri

first: Ava

last: Behrouzi

first: Seyed

middle: D

last: Siadat

first: Shohreh

last: Khatami

first: Fatemeh

last: Rahimi Jamnani

first: Abolfazl

last: Fateh


title: Comparative study of interruption of TLR and NF-kB signaling pathways in lung epithelial cell by Mycobacterium tuberculosis strains


title: Genome-wide gene expression disturbance by single a  A1/C1 chromosome substitution line  in  Brassica rapa restituted from natural B. napus

status: Public on Apr 09 2018

city: Wuhan P.R. China

first: Bin

last: Zhu

address: No.1,Shizishan Street · Hongshan District · Wuhan · Hubei Province · 430070 · P.R.China

department: College of Plant Science and Technology

institute: Huazhong Agricultural University

summary: Alien chromosome substitution lines are vital germplasm for breeding and genetic mapping. Previously, a whole set of nine Brassica rapa-oleracea monosonic alien addition lines (MAALs, C1-C9) was established in the background of natural B. napus genotype “Oro”, after the restituted B. rapa (RBR) for Oro was realized. Herein, a monosomic substitution line with one alien C1 chromosome (Cs1) in the RBR complement was selected in the progenies of MAAL C1 and RBR, by the PCR amplification of specific gene markers and fluorescence in situ hybridization. Cs1 exhibited the whole plant morphology similar to RBR except for the defective stamens without fertile pollen grains, but it produced some seeds and progeny plants carrying the C1 chromosome at high rate besides those without the alien chromosome after pollination by RBR. The viability of the substitution and its progeny for the restituted B. rapa diploid further elucidated the functional compensation between the chromosome pairs with high homoeology. To reveal the impact of such aneuploidy on genome-wide gene expression, the transcriptomes of MAAL C1, Cs1 and euploid RBR were analyzed. Compared to RBR, Cs1 had sharply reduced gene expression level across chromosome A1, demonstrating the loss of one copy of A1 chromosome. Both additional chromosome C1 in MAAL and substitutional chromosome C1 in Cs1 caused not only cis-effect but also prevalent trans-effect differentially expressed genes. A dominant gene dosage effects prevailed among low expressed genes across chromosome A1 in Cs1, and moreover, dosage effects for some genes potentially contributed to the phenotype deviations. Our results provided novel insights into the transcriptomic perturbation and gene dosage effects on phenotype in chromosome substitution related to one naturally evolved allopolyploid.

overall_design: The newly expanded third leaves without petioles from six plants of each genotype were collected and immediately stored in liquid nitrogen for RNA extraction. Three samples with three replicates were sequenced via  Illumina HiSeqTM 3000.

first: Yang

last: Xiang

first: Pan

first: Xianhong

last: Ge

first: Zaiyun

last: Li


title: Acquired paternal inheritance fatty liver transcriptomes induced by high-fat diet

city: Changchun

first: yonghong

last: zhang

state: Jilin Province

address: No.2699 Qianjin Street

institute: Jilin University

summary: Many acquired traits related to fat metabolism are inherited, and nutritional factors can induce fatty liver in chickens. We found that the paternal fatty livers induced by high-fat diet in Jingxing-Huang chickens were inherited, but the molecular mechanisms of inherited fatty liver in chickens are far from clear. The goals of this study are to compare liver transcriptome profiling (RNA-seq) in F1 generation to screen candidate genes for acquired fatty liver. Compared to birds without fatty liver in the control group, the paternal group exhibited altered hepatic gene expression profiles, including up-regulation of several key genes involved in fatty acid metabolism, lipid metabolism and glucose metabolism (ACACA, FASN, SCD, ACSL5, FADS2, FABP1, APOA4 and ME1). This study uniquely revealed that acquired fatty liver in cocks can be inherited. The hepatic gene expression profiles were altered in chickens with the inherited phenotype of acquired paternal fatty liver and several genes could be candidate biomarkers.

overall_design: Liver mRNA profiles for paternal inheritance group and control group of F1 generation were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

first: Jie

last: Wen

first: Yonghong

last: Zhang


title: To the limit and beyond: Comparative "Omics"-approaches give insights into stress adaptation and pathogenicity of basal fungal pathogens (Lichtheimia spp.)

status: Public on Apr 10 2018

city: Jena

first: Konstantin

last: Riege

address: Beutenbergstraße 11

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

summary: The study consists of the pathogens Lichtheimia corymbifera, Lichtheimia ramosa and non-pathogen Lichtheimia hyalospora untreated (control, CTRL) and during HSP90 inhibition (Geldanamycin, GDA), endoplasmic reticulum stress (Dithiothreitol, DTT), thermal stress (42°C, HEAT) and heat stress upon a concentration of 0.5 M NaCl (L. hyalospora only)

sample_organism:
Lichtheimia corymbifera
Lichtheimia hyalospora
Lichtheimia ramosa

overall_design: Insights into stress adaption and pathogenicity of mucormycotic agents by RNA-Seq of mycelia: Spores in SUP medium incubated - 16h growth + 6h HEAT, HEAT+NaCl - 20h growth + 2h GDA, DTT - 22h growth CTRL

first: Volker

last: Schwartze

first: Tilman

middle: E

last: Klassert

first: Marina

last: Marcet-Houben

first: Minou

last: Nowrousian

first: Ulrike

last: Binder

first: Igor

last: Grigoriev

first: Morten

last: Grøtli

first: Andrii

last: Gryganskyi

first: Markus

last: Fleischauer

middle: H

last: Gräler

first: Fabian

last: Horn

first: Jörg

last: Linde

first: Anna

last: Lipzen

first: Hea-Reung

last: Park

first: Asaf

last: Salamov

first: Patricia

last: Sieber

first: Jason

last: Stajich

last: Tamás

first: Andrew

last: Tritt

first: Sascha

last: Winter

first: Sebastian

last: Böcker

first: Toni

last: Gabaldón

first: Stefan

last: Schuster

first: Manja

last: Marz

first: Cornelia

last: Lass-Flörl

first: Hortense

last: Slevogt

first: Kerstin

last: Voigt


title: Gene expression in tobacco (Nicotiana) nectaries

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

summary: Nectaries are the glands responsible for nectar secretion. To understand the genetic programming underlying nectar production, floral nectaries of six Nicotiana species at four different time points (floral stage 6,9, and 12, a post-secretory stage) in biological triplicate were collected, with RNA being isolated and subjected to Illumina RNA-seq analysis.

sample_organism:
Nicotiana glauca
Nicotiana plumbaginifolia
Nicotiana rustica
Nicotiana benthamiana
Nicotiana clevelandii
Nicotiana bonariensis

overall_design: RNA-seq of nectaries from six species of Nicotiana. This series includes RNA-seq of leaf, ovary and sepal tissue from Nicotiana plumbaginifolia.

first: Clay

last: Carter

first: Adel

middle: A

last: Guirgis

first: Fredy

last: Silva

first: Robert

middle: W

last: Thornburg


title: Gene expression of nucleolin or TRA2B4-silencing HCT116 cells

status: Public on Apr 06 2018

city: Toskushima

first: Yuki

last: Kuwano

address: Kuramoto-cho

department: Pathophysiology

institute: The University of Tokushima Graduate School

summary: TRA2β4 is transcribed from the human transformer 2β(TRA2B) gene and overexpressed in colon cancer cells. Nucleolin is one of RNA-binding proteins to regulate cell survival and proliferation. In this study, TRA2β4 and Nucleolin levels were reduced in colon cancer HCT116 cells and gene expression levels were measured using microarray analysis.

overall_design: Ten nM of TRA2β4 or Nucleolin siRNA was transfected into HCT116 cells for 48 hours and then gene expression was measured by human whole-genome microarray (Agilent Technology).


title: Comparison of transcriptional profiles between naive, primed and ground state pluripotency in mouse embryonic stem cells of the same genetic background

city: Ghent

first: Sabitri

last: Ghimire

address: De Pintelaan 185

department: Reproductive Medicine

country: Belgium

institute: Ghent University Hospital

summary: Derivation of naive state of mouse embryonic stem cells (mESCs) in LIF+serum (LS) culture condition is strain dependent, whereas derivation of ground state mESCs is readily possible from all strains tested so far in “2i” culture condition. ESCs can be derived from the post-implantation stage mouse embryos (EpiSCs), showing primed characteristics. In the present study, we characterized and compared the transcriptional profile of naïve, primed and ground state mESCs. Considering the importance of genetic background of mouse model for ESCs derivation in conventional culture conditions, all ESCs lines used in the study were derived from the same strain of mice. We found distinct transcriptional profiles between naive, primed and ground state mESCs. Primed state mESCs exhibit lower expression of pluripotency markers along with higher expression of lineage specific markers compared to naive and ground state mESCs. We also demonstrate that the differentiation propensity of ESCs to specific germ layer varies depending on the pluripotency state of ESCs.

overall_design: Embryonic stem cells were derived from 129ola mice in naïve (LIF +serum, from pre-implanatation stage embryo ), primed (Activin A + bFGF, epiblast of E6.5 embryos) and ground state (2i+LIF and 2i+SB431542+LIF, pre-implanation stage embryo) of pluripotency. 4 lines from each condition was used for micro array analysis.

first: Jitesh

last: Neupane

first: Matthias

last: Roost

first: Jasper

last: Anckaert

first: Dieter

last: Deforce

first: Pieter

last: Mestdagh

first: Jo

last: Vandesompele

first: Margot

last: Van der Jeught

first: Susana

last: Chuva de Sousa Lopes

first: Petra

last: De Sutter

first: Bjorn

last: Heindryckx


title: Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [MoEx-1_0-st array]

city: Charleston

first: Michael

last: Ostrowski

state: SC

address: 86 Jonathan Lucas street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

summary:
Eavluation of temporal expression kinetics during mouse osteoclast differentiation evaluated by microarray.
We overlayed gene expression data with correspoding DNA binding data from MITF and PU.1 ChIP-seq to evaluate gene regulatory networks in osteoclasts.

overall_design: Either, mouse myeloid precurosrs or human osteoclast precurosrs were treated with osteoclast differentiation medim for 1.5 days and 3 days and gene expression compared to precurosrs treated with CSF-1 alone.

first: Sudarshana

middle: M

last: Sharma


title: Generation of splice switching oligonucleotides targeting the Cockayne syndrome group B gene product in order to change the diseased cell state

city: Saito-Asagi, Ibaraki

first: Yooksil

last: SIN

state: Osaka

department: Center for Drug Design

institute: NIBIOHN

summary: Cockayne syndrome (CS) is a severe disorder with no effective treatment. The Cockayne syndrome group B (CSB) gene is one gene responsible for CS and also causes UV sensitive syndrome (UVSS), a disorder that causes mild symptoms. How the CSB gene determines a patient’s fate is unknown, but one intriguing point is that in UVSS patient cell, there are nonsense mutations in both alleles at the same position in each upstream region of the PiggyBac transposable element derived 3 (PGBD3) inserted region. In contrast, in CS patient cells, there is at least one allele with several mutations downstream of the PGBD3 inserted region, or there are homozygous mutations in exon 1. Here, we designed and synthesized 24 splice switching oligonucleotides (SSOs) to skip exon 3 in CSB mRNA. Use of these SSOs induced a frame shift in order to generate an alternative stop codon at the upstream region of the PGBD3 invasion site. As a result, a reduction of mitochondrial membrane potential following H2O2 treatment in CS cell was recovered. It was demonstrated that up-regulation of several gene expression brought about by SSOs are related to mitochondrial dysfunction in CS cells.

overall_design: In this study, we investigated whether it was possible to get Cockayne syndrome (CS) cells to mimic UV sensitive syndrome (UVSS) cell by using splice switching oligonucleotides (SSOs). Thus, we needed to assess whether the states of SSO-transfected cells were close to CS or UVSS cells. One of the way to assess that, a microarray analysis was performed to define the differences in gene expression states between CS and UVSS. Gene expression states of each patient cell lines were compared, WI-28 VA13 sub 2 RA (normal) vs UVS1KO (UVSS), CS1AN (AN) vs UVS1KO (UVSS) and CS1BE (BE) vs UVS1KO (UVSS) (n=4).

last: Sin

first: Futaba

last: Makimura

first: Masafumi

last: Saijo

first: Satoshi

last: Obika


title: A CLK3-HMGA2 alternative splicing axis impacts human hematopoietic stem cell molecular identity throughout development [HSC and PROG miRNA profiling]

status: Public on Apr 05 2018

city: Cambridge

last: Guo

state: MA

address: 415 Main St

institute: Broad Institute

summary: While gene expression dynamics have been extensively catalogued during hematopoietic differentiation in the adult, less is known about transcriptome diversity of human hematopoietic stem cells (HSCs) during development. To characterize transcriptional and post-transcriptional changes in HSCs during development, we leveraged high-throughput genomic approaches to profile miRNAs, lincRNAs, and mRNAs. Our findings indicate that HSCs manifest distinct alternative splicing patterns in key hematopoietic regulators. Detailed analysis of the splicing dynamics and function of one such regulator, HMGA2, identified an alternative isoform that escapes miRNA-mediated targeting. We further identified the splicing kinase CLK3 that, by regulating HMGA2 splicing, preserves HMGA2 function in the setting of an increase in let-7 miRNA levels, delineating how CLK3 and HMGA2 form a functional axis that influences HSC properties during development. Collectively, our study highlights molecular mechanisms by which alternative splicing and miRNA-mediated post-transcriptional regulation impact the molecular identity and stage-specific developmental features of human HSCs.

overall_design: miRNA profiling of hematopoietic stem cells (HSC) and progenitor cells (PROG) from fetal liver (FL), cord blood (CB) and bone marrow (BM) and control HPC cells differentiated from IPSC cells.

first: Davide

last: Cacchiarelli

first: Marcella

last: Cesana


title: Comparative study of interruption of TLR and NF-kB signaling pathways in lung epithelial cell by Mycobacterium tuberculosis strains [TLR]

first: Shima

last: Hadifar

first: Farzam

last: Vaziri

first: Ava

last: Behrouzi

first: Seyed

last: Siadat

first: Shohreh

last: Khatami

first: Fatemeh

last: Rahimi Jamnani

first: Abolfazl

last: Fateh


title: Identification of direct transcriptional target genes of ExoS/ChvI two-component signaling in Sinorhizobium meliloti

status: Public on Apr 07 2018

city: Stanford

first: Melanie

last: Barnett

state: CA

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

summary: We performed transcriptional profiling with chvI gain-of-function (EC220) and reduced-function (EC69) strains. The chvI gain-of-function strain that we used contains a dominant gain-of-function chvI allele in addition to wild-type chvI. We identified genes that, relative to their expression level in the wild type, are both upregulated in the chvI gain-of-function strain and downregulated in the reduced-function strain or vice versa.

platform_organism:
Sinorhizobium meliloti
Medicago truncatula

overall_design: Gene expression profiling of Sinorhizobium meliloti Rm1021-derived strains, with wild type or mutant chvI alleles, using custom Affymetrix GeneChips

first: Esther

last: Chen

first: Sharon

middle: R

last: Long


title: Transcriptome of Phaseolus vulgaris nectaries and leaves

first: Marshall

last: Hampton

summary: Comparative RNA-Seq study of expression in Phaseolus vulgaris nectaries

overall_design: RNA-seq of extrafloral nectaries, floral nectaries and leaf tissue from Phaseolus vulgaris cv Blue Lake 274.

first: Clay

last: Carter


title: Neuro-specific HuR-deficient mice spontaneously develop motor neuron disease

city: Cleveland

first: Tomasz

last: Herjan

state: Ohio

address: 9500 Euclid Avenue

department: Immunology

institute: Cleveland Clinic Foundation

summary:
To study the neuron-specific function of HuR, we generated inducible, neuron-specific HuR-deficient mice of both sexes. These mice developed a phenotype consisting of poor balance, decreased movement, and decreased strength
Genome-wide microarray and RT-PCR analysis further indicated that HuR deficiency in neurons resulted in altered expression of genes in the brain involved in cell growth The additional enriched GO terms in the brain tissues of neuron-specific HuR-deficient mice were largely related to inflammation, including interferon-induced genes and complement components.

overall_design: We generated conditional neuron-specific HuR-deficient mice (Thy1Cre-ERT2-EYFPHuRf/f, designed as KO) and control mice (Thy1Cre-ERT2-EYFPHuRf/+, designed as wild type, WT). Cre expression was induced through Tamoxifen administration to conditional neuron-specific HuR-deficient mice (Thy1Cre-ERT2-EYFPHuRf/f) and control mice (Thy1Cre-ERT2-EYFPHuRf/+) of either sex at 10 and 11 weeks of age (Fig. 1A). Cre-YFP expression was highly induced 21 days after first tamoxifen administration. Then RNA was extractedfrom  total brain tissues from neuron-specific HuR-deficient and control mice to perform Mouse Gene 2.0 ST microarray.


title: Differential Regulation of Genes Involved in Root Morphogenesis and Cell Wall Modification is Associated with Salinity Tolerance in Chickpea

status: Public on Apr 03 2018

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Plenty Road

department: School of Science

institute: RMIT University

summary: In this study, the root tissues from the salt tolerant genotype (JG 11) and the salt sensitive genotype (ICCV 2) were analyzed using RNA sequencing to identify genes/pathways associated with salt tolerance/sensitivity in the both genotypes.

overall_design: The salt sensitive and salt tolerant genotypes were subject to 40 mM of NaCl treatment and the root tissues at two developmental stages were collected and sequenced to profile the differential genes expression in response to the salt stress.

first: Mayank

last: Kaashyap


title: different expression of RNAs between breast cancer and benign tissue

city: Wenzhou

first: jiang

last: yang

address: The First Affiliated Hospital of Wenzhou Medical University

summary: To find differentially expressed RNAs between breast cancer and benign tissue, we have conducted whole genome microarray expression profiling as a discovery platform to identify genes that play a key role in the breast cancer progression. Primary cancer tissues and paired adjacent noncancerous tissues were snap-frozen in liquid nitrogen immediately after resection and were used to perform genome expression analysis.

overall_design: Comparing to benign tissue, gene expression in human breast cancer tissue was measured. Three independent experiments were performed.

first: Xiaoqu

last: Hu

first: Feiyan

last: Xie


title: Long noncoding RNAs/mRNAs expression profiling for 10 human HCC samples

status: Public on Apr 04 2018

city: Jingmen

first: Qian

last: Zhu

state: Hubei

address: 67 Xiangshan Avenue

department: Department of Hepatobiliary Surgery

institute: Jingmen First People's Hospital

summary: To determine the lncRNA expression profile in HCC and matched non-tumor tissues, we used lncRNA microArray analysis form Arraystar to examine the expression of lncRNAs in HCC and matched non-tumor tissues. Goal was to determine the different gene expression between HCC and matched noncancerous tissue.

overall_design: Tissue based experiment: 5 HCC tissue, 5 matched noncancerous tissue

first: Zhu

last: Qian

first: Duan

last: Rui