title: Gene expression data from human subcutaneous adipose tissue

status: Public on Nov 14 2014

city: Guelph

first: David

middle: M

last: Mutch

address: 50 Stone Road East

department: Human Health & Nutritional Sciences

institute: University of Guelph

summary:
Obesity is a heterogeneous conditions comprising obese individuals with metabolic disorders (termed metabolically unhealthy obese; MUO) and obese individuals who are metabolically healthy (termed metabolically healthy obese; MHO).
We used microarrays to examine differences in subcutaneous adipose tissue gene expression from lean healthy (LH), metabolically healthy obese (MHO), and metabolically unhealthy obese (MUO) individuals.

overall_design: Subcutaneous adipose tissue samples from the periumbilical region were obtained under local anesthesia and after an overnight fast. 50-100 mg of adipose tissue was homogenized and total RNA was extracted after homogenisation in TRIzol reagent using a tissue homogenizer.

first: Flavia

last: Badoud


title: Gene expression profiling of myxoid liposarcomas (training set INT-A)

status: Public on Oct 30 2014

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: FUS-CHOP and EWS-CHOP balanced translocations characterize myxoid liposarcoma which encompasses myxoid (ML) and round cell (RC) variants initially believed to be distinct diseases. Currently, myxoid and RC liposarcoma are regarded to represent the well differentiated and the poorly differentiated ends, respectively, within spectrum of myxoid liposarcoma where the fusion proteins blocking lipogenic differentiation play a role in tumor initiation while molecular determinants associated to progression to RC remain poorly understood. Activation of AKT pathway sustained by PIK3CA and PTEN  mutations and growth factor receptor signalling such as RET and IGF1R have been recently correlated with the increasing of aggressiveness and RC.  Aim of the present study is to elucidate molecular events involved in driving round cell progression analyzing two small series of MLS selected to be representative of the two end of the gamut: the pure myxoid (0% of RC component) and RC with high cellular component (≥80%).

overall_design: The training series (INT-A) was made up of formalin-fixed paraffin embedded samples obtained from 12 patients. The diagnoses were confirmed by means of FISH analysis, which revealed CHOP rearrangement, or by RT-PCR searching for the transcript type. Different molecular variants of the fusion transcript have been described by Powers MP et al. (Mod Pathol. 2010).

first: L

first: S

last: Pilotti


title: The epigenetic modifier EZH2 controls melanoma growth and metastasis through silencing of distinct tumour suppressors

status: Public on Nov 12 2014

city: Zurich

first: Daniel

last: Zingg

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

summary: Increased activity of the epigenetic modifier EZH2 has been associated with different cancers. However, evidence for a functional role of EZH2 in tumourigenesis in vivo remains poor, in particular in metastasising solid cancers. Here we reveal central roles of EZH2 in promoting growth and metastasis of cutaneous melanoma. In a melanoma mouse model, conditional Ezh2 ablation as much as treatment with the preclinical Ezh2 inhibitor GSK503 stabilises the disease through inhibition of growth and virtually abolishes metastases formation without affecting normal melanocyte biology. Comparably, in human melanoma cells, EZH2 inactivation impairs proliferation and invasiveness, accompanied by re-expression of tumour suppressors connected to increased patient survival. These EZH2 target genes suppress melanoma growth and prevent EMT / metastasis in vivo revealing the dual function of EZH2 in promoting tumour progression. Thus, EZH2-mediated epigenetic repression is highly relevant especially during advanced melanomagenesis, which makes EZH2 a promising target for novel melanoma therapies.

overall_design: 2 different melanoma cell lines, each of which was treated with either siControl or siEZH2. For each group 3 biological replica were analysed.

first: Lukas

last: Sommer


title: Expression data from ABA up-regulated rice under drought stress

status: Public on Oct 14 2014

city: Guangzhou

first: Guohui

last: Zhu

state: Guangdong

address: Wushan Rd, Tianhe

department: College of Life Sciences

country: China

institute: South China Agricultural University

summary: To understand the molecular mechanism of drought stress resistance mediated by OsABA8ox3 gene, we checked the genome-wide expression profile changes in the OsABA8ox3 RNAi and WT seedlings using the Affymetrix GeneChip under the normal condition and drought stress. A total of 1436 genes showed greater than 2-fold higher expression levels in both WT and RNAi-9 seedlings after drought stress, and most of them had higher up-regulated folds in RNAi-9 seedlings than that of WT.

overall_design: Gene expressions in the OsABA8ox3 RNAi and WT seedlings under the normal and drought stress conditions.

first: Shanlan

last: Cai


title: Genome-wide analysis of primary and secondary angiosarcomas using RNA extracted from formalin-fixed parafinembedded samples.

status: Public on Aug 22 2014

city: Lund

first: Emelie

last: Styring

address: Skanes University Hospital

department: Dept of Orthopedics

country: Sweden

institute: Lund University

summary:
Angiosarcomas are highly malignant tumors that develop as primary angiosarcomas of unknown cause or as secondary angiosarcomas, most often following radiation therapy for breast cancer. These subsets are morphologically indistinguishable, which motivates our aim to identify genetic classifiers for diagnostic and therapeutic application.
We applied the 18k whole-genome c-DNA-mediated annealing, selection, extension, and ligation (WG-DASL) assay for expression profiling of 26 primary and 29 secondary angiosarcomas.
Primary and secondary angiosarcomas differed by 103 significantly de-regulated genes with up-regulation of RET, KIT, FLT4, MYC and RASGRP3 and down-regulation of CDKN2C in secondary angiosarcoma. Functional annotation analysis demonstrated involvement of multiple target genes in the receptor protein tyrosine kinase pathway.
Up-regulation of RET and down-regulation of CDKN2C characterize secondary angiosarcoma, which implies a mechanistic basis for the evaluation of RET-kinase inhibitors in the treatment of these highly aggressive tumors.

overall_design:
Total RNA obtained from primary and secondary angiosarcoma samples from formalin-fixed parafin-embedded samples were compared using WG-DASL.
Biological replicates (two samples from the same patient, different parts of the tumor or different operation specimens)
Technical replicates (two samples from the same patient and same tumor sample, analyzed in different areas of the bead chip)

first: Jojanneke

last: Seinen

first: Mev

last: Dominguez-Valentin

first: Henryk

last: Domanski

first: Mats

last: Jönsson

first: Fredrik

last: Vult von Steyern

first: Harald

middle: J

last: Hoekstra

first: Albert

last: Suurmaijer

first: Mef

last: Nilbert


title: Expression data from rice panicles of osmads1 mutant and wild type

status: Public on Oct 06 2014

city: Shanghai

first: Hu

last: Yun

state: Shanghai

address: 800 Dongchuan RD. Minhang District, Shanghai, China

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

summary:
OsMADS1 in rice is an important transcription factor in controlling flower development, not only in flower organs development, but also in floral meristem determinacy. Early flower panicle we used is a high expression stage for OsMADS1.
We used microarrays to detail the global gene expression underlying functions of OsMADS1 in rice flower development.

overall_design: Rice panicles in length of 2 mm and 5-7 mm were collectecd for RNA extraction and hybridization on Affymetrix microarrays.Rice panicles in length of 2 mm is the stage for the initiation of inner floral organ development and in length of 5-7 mm is the late stages for floral organ development.Though comparing the microarray data of osmads1 and wild-type (control) at these two stages, we can find the functions of OsMADS1 in the early and late flower development stages. Three biological repeats were used. And totally 12 samples were analyzed.


title: Expression data from human keratinocytes stimulated with streptococcal M1 protein

status: Public on Oct 03 2014

first: Sandra

middle: Therese

last: Persson

address: Tornavägen 10

department: Department of Clinical Sciences

summary:
We used microarray analysis to investigate if keratinocytes excert an immuno-inflammatory response towards streptococcal M1 protein.
Keratinocytes respond to M1 protein by activating pathways to induce the production of inflammatory signaltransducers, AP-1 and NFkB transcription factor subunits, together with inflammatory mediators such as IL-8, CCL20 and IL-1 family proteins etc.

overall_design: HaCaT cells were cultured in serum-free media, without calcium, until 80% confluency. Cells were incubated 6 h in absence or presence of M1 protein before RNA extraction. The integrity of RNA quality was analysed by an Bioanalyzer. Out of 12 samples, 3 M1 stimulated and 3 control samples were chosen for hybridization on Affymetrix Human 2.0 ST array.

first: Laura

last: Wilk

first: Matthias

last: Mörgelin

first: Heiko

last: Herwald


title: Genome-wide genotyping and CNV scan in IgA Nephropathy patients.

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

institute: University of Bari

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Immunoglobulin A Nephropathy (IgAN) is a complex multifactorial disease whose genetic bases remain unknown.  Distinct linkage and genome-wide association studies in both familial and sporadic IgAN suggest that there is a strong genetic component in IgAN. In this context, an intriguing role could be ascribed to copy number variants (CNVs) that have been recognized as an important source of genetic variation in humans. Here, we performed a whole-genome screening of CNVs in IgAN patients, their healthy relatives and healthy subjects (HS). A total of 217 individuals consisting of 51 IgAN cases and 166 healthy relatives were included in the initial screening. The high-throughput analysis of structural genetic variations, to find concordant aberrations across classes of samples, identified 178 IgAN-specific aberrations,  specifically 114 loss and 64 gain. Several CNVs overlapped with regions evidenced by previous genome-wide genetic studies. Moreover, we found that IgAN patients characterized by deteriorated renal function carried low copy numbers of a CNV in chromosome 3 (chr3_loss:52031010-52260722). This CNV contained the TLR9 gene whose expression significantly correlated with the loss aberration in patients with progressive renal damage. Conversely, IgAN patients with normal renal function had no chr3_loss:52031010-52260722 and the TLR9 mRNA was expressed at the same level as in HS, still maintaining a strong correlation with the CNV. In conclusion, here we performed the first genome-wide CNV study in IgAN identifying some structural variants specific to  IgAN patients and providing a collection of new candidate genes and loci that could help to dissect the complex genomic setting of the disease. Moreover, we identified a specific CNV, spanning the TLR9 gene, which could explain the disease severity in IgAN patients.

overall_design: To perform a genome-wide CNV study in IgAN identifying some structural variants specific to  IgAN patients and providing a collection of new candidate genes and loci that could help to dissect the complex genomic setting of the disease.

first: Sharon

middle: N

last: Cox


title: Gene expression profiling of circulating tumor cells in breast cancer

status: Public on Nov 21 2014

first: Maurizio

last: Callari

address: Via Amadeo, 42

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

summary: CTCs are the purpoted intermediates of metastatic dissemination and are likely to contain cellular clones responsible for disease progression representing a preferred source for identification of druggable targets. Unfortunately a molecular characterization of CTCs is seriously hampered by their low numbers even in metastatic patients and by the elevated contamination of isolated CTCs with leukocytes. With the final goal of providing a reliable assay allowing to obtain valuable information on CTC features in the clinical setting, we have developed a method based on capture with beads linked to EpCAM and to MUC1 exploiting a commercially available kit and performing an extensive gene expression profiling with the DASL platform.

overall_design:
For spike-in experiments, low pre-defined numbers of cells derived from established breast cancer cell lines (MCF7 and MDA-MB-468) were spiked into 5 mL of whole blood of healthy donor and captured using AdnaTest EMT-1/StemCell Select kit. Total RNA isolated from the captured cells together with total RNA isolated from the same in vitro cultered cells was processed in duplicate or triplicate onto Illumina Whole-Genome DASL HT platform. Finally, gene expression profiling was carried out on CTCs isolated from blood of 7 patients with advanced breast cancer.
According with the characteristics of the study, data normalization was not applicable

first: Emanuela

last: Fina

first: Vera

last: Cappelletti

first: Callari

last: Maurizio

first: Francesca

last: D'Aiuto

first: Maria

middle: G

last: Daidone


title: Expression data from rice lesion mimic mutant spotted leaf 5 (spl5)

status: Public on Oct 02 2014

city: JinHua

first: JIN

last: BIN

state: ZheJiang

address: YingBin Road 688#

department: College of Chemistry & Life Sciences

institute: Zhejiang Normal University

summary:
The rice lesion mimic, spotted leaf 5 (spl5), created by γ-ray radiation, has spontaneous HR-like lesions on its leaves and shows enhanced resistance to rice blast and bacterial blight pathogens. Some genes were differentially expressed in this mutant compared with its WT control ZF802, and these genes were also associated with some important signaling pathways, such as defense response, oxidation-reduction process and stress response.
We analyzed the transcriptional profiling of spl5 mutant and WT using the microarray, in order to reveal the signal pathway of SPL5 gene in regulation of disease resistance.

overall_design: Rice leaves were selected at lesion stages of spl5 mutant for RNA extraction and hybridization on Affymetrix microarrays. The lesions in rice leaves were belong to HR phenotype, which was one of the important reasons for rice disease resistance. In order to realize which genes were associated with the degree of lesions and mediated the disease resistance, we put the leaves of spl5 mutant into two categories, based on the degree of lesion formation: few lesions (FL), leaf area with 10-20% lesions and many lesions (ML), leaf area with 70-80% lesions.

first: Jin

last: Bin

first: Chen

last: Xifeng

first: Ma

last: Bojun


title: Expression data from +Pi and -Pi treeatment between WT and spx1spx2 double mutant

city: Hangzhou

first: Chuanzao

last: Mao

address: 866 Yu Hang Tang Road

institute: Zhejiang University

summary:
Fourteen days plants growth under hydroponic +P condition (200 µM) were treated with +P(200µM) or –P (no phosphate) for another 7 days, shoot of plants from 3 biological repeats were sampled for Affymetrix microarray analysis.
We used microarrays to detail the global programme of gene expression underlying +Pi and -Pi condition between WT and spx1spx2 double mutant.

first: Zhiye

last: Wang


title: Identification of rice ethylene-response mutants and characterization of mhz1, mhz4 and mhz5 in distinct ethylene response and yield trait regulation

status: Public on Sep 24 2014

city: Los Angeles

first: Xiang

last: Lu

state: CA

address: 10833 Le Conte Ave

department: Department of Molecular and Medical Pharmaacology

country: USA

institute: University of California, Los Angeles

summary: Ethylene plays major roles in adaptive growth of rice plants in water-saturated soil; however, ethylene signaling in rice is largely unclear. Here, we report identification and characterization of ethylene-response mutants based on distinct ethylene-response phenotypes of dark-grown rice seedlings.

overall_design: The seeds were soaked in tap-water and germinated at 37°C in the dark for two days (change the water daily). For ethylene treatment, we reduced the amount of water to 1.5-1.7cm below the seeds.Three-day old seedlings were treated with ethylene (10 ppm) for 8 hours at 28°C in the dark. Seedling grown in the air was used as control. We isolated RNA from roots and shoots of wild-type and mutant.

first: Biao

last: Ma

first: Jingsong

last: Zhang


title: Identification of rice ethylene-response mutants and characterization of mhz2 and mhz8 in distinct ethylene response and yield trait regulation


title: Expression data from OsSIK2-overexpression and mutant rice seedlings

summary:
Receptor-like kinases (RLKs) play important roles in plant development and defense responses; however, their functions in other processes remain unclear. Here, we report that OsSIK2, an S-domain RLK from rice, is involved in abiotic stress and senescence process, integrating stress signals into developmental program for adaptive growth.
We used microarrays to detail the gene expression in OsSIK2-overexpression and mutant lines from 14-day-old rice seedlings and identified distinct regulated genes.

overall_design: We sought to obtain distinct regulated genes by OsSIK2. To that end,the aerial parts of different rice seedlings,including OsSIK2-overexpression lines, mutant and respective controls, were harveted for total RNA extraction and hybridization on Affymetrix microarrays.

first: Lijuan

last: Chen


title: Quinacrine Overcomes Resistance to Erlotinib by Inhibiting FACT, Nuclear Factor-kappa B and Cell Cycle Progression in Non-Small Cell Lung Cancer

status: Public on Jun 19 2014

city: Cleveland

first: George

last: Stark

state: OH

address: 9500 Euclid Avenue

department: Cancer Biology

institute: Cleveland Clinic Lerner Research Institute

summary:
Erlotinib is a tyrosine kinase inhibitor (TKI) that is approved as a second-line monotherapy in patients with advanced non-small cell lung cancer (NSCLC). In these patients, erlotinib prolongs survival but its benefit remains modest since many tumors express wild-type EGF receptor (wtEGFR) lacking a TKI-sensitizing mutation, develop a second-site EGFR mutation, e.g., EGFR-L858R/T790M, or activate an alternate receptor tyrosine kinase, e.g., through MET amplification. To test potential drug combinations that could improve the efficacy of erlotinib, we combined erlotinib with quinacrine, which inhibits the FACT (facilitates chromatin transcription) complex that is required for nuclear factor-κB (NF-κB) transcriptional activity. In A549 (wtEGFR), H1975 (EGFR-L858R/T790M) and H1993 (MET amplification) NSCLC cells, the combination of erlotinib and quinacrine was highly synergistic, as quantified by Chou-Talalay combination indices. The combination inhibited colony formation, induced cell cycle arrest and apoptosis, and slowed xenograft tumor growth. Quinacrine decreased the level of active FACT subunit SSRP1 and suppressed NF-κB-dependent luciferase activity. Knockdown of SSRP1 decreased cell growth and sensitized cells to erlotinib.
Transcriptomic profiling showed that quinacrine, alone or in combination with erlotinib, significantly affected cell cycle-related genes that contain binding sites for transcription factors that regulate SSRP1 target genes. As potential biomarkers of drug synergy, we identified genes that were more strongly suppressed by the combination than by either single treatment, and whose increased expression predicted poorer survival in lung adenocarcinoma patients. Combination of quinacrine and erlotinib is synergistic in NSCLC through suppression of FACT, resulting in inhibition of cell cycle progression.

overall_design: RNA was isolated from cells treated with 1 μM erlotinib, 3 μM or 5 μM quinacrine or a combination of both for 6, 12, 24, or 48 h using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions. Microarray analysis was performed using the Affymetrix Human Gene 2.1 ST Array at the Gene Expression & Genotyping Core Facility at Case Comprehensive Cancer Center. Raw CEL files were pre-processed using the Affymetrix Expression Console Software 1.30 with Robust Multi-array Average (RMA) normalization (background correction, quantile normalization and log2 transformation). Probes were annotated using the HuGene 2.1 st hg19 probeset annotation files downloaded from the Affymetrix website.

first: Josephine

middle: K

last: Dermawan

first: John

last: Pink

first: Goutham

last: Narla

first: Neelesh

last: Sharma


title: Epigenetic Reprogramming Modulates Malignant Properties of Human Liver Cancer Cells

status: Public on May 26 2014

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

summary: Reversal of DNA hypermethylation and associated gene silencing is  an emerging cancer therapy approach. In this context we have addressed the  impact of epigenetic alterations and local microenvironment on the  functional and transcriptional reprogramming of hepatic cancer stem cells. (CSCs) using the DNMT1 inhibitor Zebularine (ZEB). We show for the first  time that cellular context is a critical determinant in the response to  DNMT1 inhibition resulting in either a long term epigenetically driven  malignant reprogramming or an effective antitumor therapeutic  reprogramming. Furthermore, permanent reduction of DNMT1 protein level  renders the HCC cell lines insensitive to both DNMT1 inhibition and  cellular context. These results emphasize the importance of decoding the mechanisms involved in therapeutic application of DNA demethylating agents.

overall_design: Huh7 and PLC treated with ZEB, and Huh7 depleted for DNMT1

first: Chiara

last: Raggi

first: Snorri

middle: S

last: Thorgeirsson


title: Gene-expression profiles of paired biopsies and explanted liver from hepatitis C virus (HCV)-infected individuals

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary:
OBJECTIVE: The number of patients with HCV-related cirrhosis is increasing, leading to a rising risk of complications and death. Prognostic stratification in patients with early-stage cirrhosis is still challenging. We aimed to develop and validate a clinically useful prognostic index based on genomic and clinical variables to identify patients at high risk of disease progression.

DESIGN: We developed a prognostic index, comprised of a 186-gene signature validated in our previous genome-wide profiling study, bilirubin (>1 mg/dL) and platelet count (<100 000/mm3), in an Italian HCV cirrhosis cohort (training cohort, n=216, median follow-up 10 years). The gene signature test was implemented using a digital transcript counting (nCounter) assay specifically developed for clinical use and the prognostic index was evaluated using archived specimens from an independent cohort of HCV-related cirrhosis in the USA (validation cohort, n=145, median follow-up 8 years).

RESULTS: In the training cohort, the prognostic index was associated with hepatic decompensation (HR=2.71, p=0.003), overall death (HR=6.00, p<0.001), hepatocellular carcinoma (HR=3.31, p=0.001) and progression of Child-Turcotte-Pugh class (HR=6.70, p<0.001). The patients in the validation cohort were stratified into high-risk (16%), intermediate-risk (42%) or low-risk (42%) groups by the prognostic index. The high-risk group had a significantly increased risk of hepatic decompensation (HR=7.36, p<0.001), overall death (HR=3.57, p=0.002), liver-related death (HR=6.49, p<0.001) and all liver-related adverse events (HR=4.98, p<0.001).

CONCLUSIONS: A genomic and clinical prognostic index readily available for clinical use was successfully validated, warranting further clinical evaluation for prognostic prediction and clinical trial stratification and enrichment for preventive interventions.

overall_design: Paired core needle liver biopsy specimens obtained with time interval ranging from 1 month to 7.5 years from three individuals, and liver tissues from right and left lobes of explanted liver with chronic HCV infection from one individual.

first: Lindsay

last: King

first: Claudia

last: Canasto-Chibuque

first: Kara

last: Johnson

first: Shun

last: Yip

first: Xintong

first: Kensuke

last: Kojima

first: Manjeet

last: Deshmukh

first: Anu

last: Venkatesh

first: Poh

last: Tan

first: Augusto

last: Villanueva

first: Angelo

last: Sangiovanni

first: Venugopalan

last: Nair

first: Milind

last: Mahajan

first: Masahiro

last: Kobayashi

first: Hiromitsu

last: Kumada

first: Massimo

last: Iavarone

last: Colombo

first: Scott

middle: L

last: Friedman

first: Josep

last: Llovet

first: Raymond

middle: T

last: Chung


title: Expression data from additional fertilization rice seeds

status: Public on Aug 04 2014

city: Tokyo

first: Keiko

last: Midorikawa

address: 1-1-1, Yayoi, Bunkyo-ku

country: Japan

institute: The University of Tokyo

summary:
Carbon (C) and nitrogen (N) contents of grain-filling stage are keys item that determined the growth of rice, and also the quality of seed. Therefore, to elucidating the mechanism of C/N signaling in a seed is an important problem for crops whose seed is used as food like rice.
The DNA microarray analysis with the rice seed which was performed the additional fertilizer at the time of heading, in order to clarify how C/N signal change of the rhizosphere in seed production stage affects a seed component on a gene expression level.

overall_design: Fertilization was supplied at the same time of plantation and performed middle fertilizing 37 days after germination. 400 mg of ammonium chloride (NH4 Cl) was supplied at the time of heading to the “ + NH4 Cl ” group. Rice seeds were selected from 6 plants for RNA extraction, and hybridization on Affymetrix microarrays. We sought to understand the change of gene expression by the additional fertilization.

first: Tomoyo

last: Narikawa


title: Gene expression-based analysis of extra-cerebral metastases of patients with cerebrotropism (defined here as development of brain metastasis within < 6 months of stage IV disease), compared to patients who did not develop brain metastases for >18 months

status: Public on Aug 18 2014

city: New Haven

first: Fabio

last: Parisi

address: 462 Humphrey Street

institute: Yale School of Medicine

summary:
To test the association between gene expression and cerebrotropism the Wilcoxon rank-sum test was utilized and revealed over 400 genes differentially expressed between thw two patient groups
Please note that cerebrotropism is defined here as development of brain metastasis within < 6 months of stage IV disease

overall_design:
In this study we utilized a well-annotated  cohort of metastatic melanoma cases to acquire expression profiles of a total of 9,829 unique genes

Cerebrotropism Status (provided in each sample characteristics field):
1 represents early cerebrotropic patients (patients who developed CNS metastases within 6 months of diagnosis of metastatic disease )
0 represents non-cerebrotropic patients (patients who did not develop brain metastases for over 18 months.


title: Human oocytes reprogram adult somatic cells to pluripotent stem cells [Illumina]

status: Public on Aug 12 2014

city: New York

first: Dieter

last: Egli

state: NY

address: 1150 St. Nicholas Avenue, room 607B, New York NY 10032

institute: Columbia University

summary: The stem cell lines were generated according to the principle described in Noggle et al., Nature 2011, Oct 5;478(7367):70-5. doi: 10.1038/nature10397.  Title: Human oocytes reprogram somatic cells to a pluripotent state.  Abstract: The exchange of the oocyte's genome with the genome of a somatic cell, followed by the derivation of pluripotent stem cells, could enable the generation of specific cells affected in degenerative human diseases. Such cells, carrying the patient's genome, might be useful for cell replacement. Here we report that the development of human oocytes after genome exchange arrests at late cleavage stages in association with transcriptional abnormalities. In contrast, if the oocyte genome is not removed and the somatic cell genome is merely added, the resultant triploid cells develop to the blastocyst stage. Stem cell lines derived from these blastocysts differentiate into cell types of all three germ layers, and a pluripotent gene expression program is established on the genome derived from the somatic cell. This result demonstrates the feasibility of reprogramming human cells using oocytes and identifies removal of the oocyte genome as the primary cause of developmental failure after genome exchange. The major difference to Noggle et al. are that these new stem cell lines are tetraploid rather than diploid. The main technical difference is the addition of cytochalasinB during artificial activation, preventing extrusion of the second polar body, thereby resulting in the retention of a diploid oocyte genome, rather than a haploid one.

overall_design: Adult somatic cells were transferred into non-enucleated oocytes and then activated in the presence of cytochalasinB. Addition of cytochalasinB inhibits extrusion of the second polar body, resulting in tetraploid eggs. The efficiency of development to the blastoycst stage is described in: Yamada et al., 2014, Human oocytes reprogram adult somatic nuclei of a type 1 diabetic to diploid pluripotent stem cells, Nature. 2014 Jun 26;510(7506):533-6. doi: 10.1038/nature13287. Blastocysts developing from these were used for the derivation or pluripotent stem cell lines. Gene expression analysis was performed to demonstrate transcriptional reprogramming. These cell lines contain both somatic and oocyte genomes.

first: Mark

last: Sauer


title: Pyrrole-imidazole polyamide targeted to the REL/ELK1 overlapping sequences in the EVI1 minimal promoter

status: Public on Jul 28 2014

city: Kyoto

first: Junetha

last: Syed

state: Kyoto

address: Kitashirakawa-Oiwakecho,Sakyo-Ku

department: Chemistry, Graduate School of Science

institute: Kyoto University

summary: Pyrrole-imidazole polyamides (PIPs) have been shown to inhibit gene expression by interrupting the DNA-protein interface. Human Ectopic viral integration site 1 (EVI1) is an oncogenic transcription factor which plays a key role in many aggressive forms of cancer. We have developed a novel pyrrole–imidazole polyamide, PIP1 targeting the REL/ELK1 binding site in the EVI1 minimal promoter that can significantly repress the expression of EVI1 in MDA-MB-231 cells. Whole-transcriptome analysis revealed that a fraction of EVI1-driven genes were modulated by PIP1.

overall_design: Global expression changes in MDA-MB-231 cells were evaluated after treating the cells with PIP1 and DMSO for 48 hours. The vehicle DMSO is used as a negative control. Each condition is performed in technical replicates.

first: Hiroshi

last: Sugiyama


title: Expression data from early and late vegetative stages from rice hybrid and its parents

status: Public on Mar 30 2014

city: New Delhi

first: Sanjay

last: Kapoor

state: Delhi

address: Benito Juarez Road

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi South Campus

summary:
Heterosis is a complex phenomenon governed by many phenotypes in combination. In comparative account of the different stages a better understanding regulating this phenomenon in terms of gene action can be ascertained.
We used microarrays to ascertained the kind and extent of gene actions in the different developmental stages to reach to the conclusion of contribution of different mode of gene actions.

overall_design:
A total of 45 arrays representing in triplicates of each five developmental stages of an Indica hybrid and its parents five vegetative developmental stages. Indica hybrid (MRP5401) has been take along with its parents (female parent PMS80 (B Line) and male parent PR319 (R line)) and five stages are selected  for rna extraction and hybridization on Affymetirx microarray comprising young leaf (Leaves of 14-days-old seedling), young root (Roots of 14-days-old seedlings), Leaves of 40-60-days-old plants, Roots of 40-60-days-old plants and Flag Leaves of 90-days-old plants. Further these stages are named accordingly as YL_B, YL_H, YL_R (Leaves of 14-days-old seedlings of B parent, hybrid and R parent), YR_B, YR_H, YR_R (Roots of 14-days-old seedlings of B parent, hybrid and R parent), ML_B, ML_H, ML_R (Leaves of 40-60-days-old plants of B parent, hybrid and R parent), BMR, HMR, RMR (Roots of 40-60-days-old plants of B parent, hybrid and R parent) and BFL, HFL, RFL (Flag leaves of 90-days-old B parent, hybrid and R parent).
Development course

first: Vinay

last: Baranwal

first: Manupriya

last: Manupriya

first: Pavan

last: Umate

first: Venugopal

last: Mikkilineni

first: Usha

middle: B

last: Zehr

first: Akhilesh

last: Tyagi


title: Human proliferating and differentiating keratinocytes treated with retinoic acid or 3,4-didehydroretinoic acid

status: Public on Aug 01 2014

city: Uppsala

first: Hans

last: Törmä

address: Dag Hammarskjölds väg 20

department: Dept of Medical Sciences

institute: Uppsala University

summary:
Targets of Retinoic Acid (RA) and 3,4-didehydroretinoic acid (ddRA) were identified in primary human epidermal keratinocytes grown in the presence of atRA or ddRA for 4 and 24 hours.
Retinoids (natural forms and synthetic derivatives of vitamin A) are used as therapeutic agents for numerous skin diseases such as keratinization disorders (e.g. ichthyoses) and psoriasis. Two endogenous ligands for retinoic acid receptors exist, retinoic acid (atRA) and 3,4-didehydroretinoic acid (ddRA). In primary human epidermal keratinocytes many transcriptional targets for atRA are known, whereas the targets for ddRA are  unknown. In an attempt to determine the targets, we compared the effect of atRA and ddRA on transcriptional profiles in undifferentiated and differentiating human primary keratinocytes. First, as expected, many genes were induced or suppressed in response to keratinocyte differentiation.  Furthermore, the two retinoids affected substantially more genes in differentiated keratinocytes (more than 350) than in proliferating keratinocytes (20). In differentiating keratinocytes markers of cornification were suppressed suggesting a de-differentiating effect by the two retinoids. When comparing the expression profile of atRA to that of ddRA, no differently regulated genes were found. The array analysis also found that a minor number  of miRNAs and a large number of non-coding transcripts were changed during differentiation and in response to the two retinoids. Furthermore, the expression of all, except one, genes known to cause autosomal recessive congenital ichthyosis (ARCI) were found to be induced by differentiation.  These results comprehensively document that atRA and ddRA exert similar transcriptional changes in keratinocytes and also add new insights into the molecular mechanism influenced by retinoids in the epidermis. Furthermore, it suggests which ARCI patients could benefit from therapy with retinoids.

overall_design: Proliferating and differentiated keratinocytes were harvested after 4 and 24 hours after treatment with atRA, ddRA and vehicle for RNA extraction and hybridization on Affymetrix microarrays. Triplicate samples were generated for each time point and each treatment.

first: Anna

last: Bergström

first: Ghazaleh

last: Ghiasifarahani

first: Berit

last: Berne


title: Microarray data of genome-wide gene expression profile in osmads6-1

status: Public on May 12 2014

first: dabing

last: zhang

address: Dongchuan Road

institute: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University,China

summary: to investigate gene expression profile in osmads6-1 flowers at stage Sp6, unsing the wild type as control.

overall_design: 6 samples: 3 osmads6-1 and 3 wild-type

first: Yun

last: Hu

first: Dabing

last: Zhang


title: Distinct DNA-based epigenetic switches trigger transcriptional activation of silent genes in human dermal fibroblasts (Affymetrix)

status: Public on Dec 31 2013

first: Junichi

last: Taniguchi

address: Kitashirakawa-Oiwakecho, Sakyo-Ku

department: Department of Chemistry, Graduate School of Science

summary: Artificial epigenetic switches are of increasing demand owing to the critical role of the dynamic epigenome in orchestrating genome-wide transcriptional activation. Recently, we divulged that certain epigenetically active small molecules called SAHA-PIPs containing the cell permeable pyrrole-imidazole polyamides (PIPs) as DNA recognition module and a histone deacetylases inhibitor SAHA as functional module, is capable of triggering targeted transcriptional activation of pluripotency and germ cell genes in mouse and human fibroblasts, respectively. Through microarray studies and functional analysis, here we demonstrate the first ever example about the remarkable ability of 32 different SAHA-PIPs to trigger transcriptional activation of their own unique set of genes and noncoding RNAs. QRT-PCR studies validated that certain SAHA-PIPs could induce several therapeutically important genes including KSR2 and SEMA6A to suggest its potential use as reagents capable of targeted transcriptional activation and as probe(s) to identify the functional relevance of the uncharacterized genes.

overall_design: Gene induction by a SAHA-PIP and SAHA was measured after treating human dermal fibroblasts at 48 h time-point. Experiment includes a vehicle (DMSO) treatment as a negative control.

first: Ganesh

last: Pandian


title: Genomic aberrations predicts survival in clear cell renal cell carcinoma

status: Public on Jul 01 2014

city: Umeå

first: Linda

last: Köhn

address: Building 6M

department: Medical Biosciences/pathology

institute: Umeå University

summary: Detailed genetic profiling of clear cell Renal Cell Carcinoma (ccRCC) has shown that these tumors are characterized by large genetic heterogeneity with some genomic regions commonly affected by structural changes. Loss on chromosomes 3p and 14q, and gain on 5q and 7 are examples of alterations commonly reported in ccRCC. However, there is no consensus regarding the potential prognostic information carried by the identified alterations. We report on poorer outcome for patients with gain on 5q and 7, and loss on 9p, 9q and 14q. These aberrations were in addition found more frequently in metastasized tumors, suggesting that they are markers for advanced disease. Furthermore, the presence of ≥ 4 common aberrations was associated with decreased survival time. Shorter relative telomere length (RTL) has been associated with loss of chromosomal regions in ccRCC tumors, but we found no significant associations between tumor RTL and chromosomal deletions. However, significantly lower tumor-to-nontumor (T/N) RTL ratio was detected for patients with loss on 4q and 9p. Finally, we found a minimum region (MR) of genetic loss of 1.4 Mbp on chromosome 9p and this region contains only one gene, the tumor suppressor candidate 1 gene (TUSC1). TUSC1 has been implicated in lung carcinogenesis and our result further strengthens its role in tumorigenesis.

overall_design: Seventy-four ccRCC tumors and 22 paired normal kidney cortex and blood samples were genotyped on Illuminas HumanCytoSNP-12 bead chips.

first: Ulrika

last: Svenson

first: Emma

middle: A

last: Evelönn

first: Börje

last: Ljungberg

first: Göran

last: Roos


title: Chromosomal analysis of products of conception

status: Public on Jul 13 2015

city: San Carlos

first: Jennifer

last: Dikan

state: California

address: 201 Industrial Road, Suite 410

institute: Natera

summary:
Results of an unbiased series of 2833 fresh products of conception samples (in conjunction with maternal blood samples for comparison)  that were tested using a 300K Illumina SNP array.  we report on the rate and type of whole aneuploidies, UPD, partial aneuploidies, copy number variants found in our series as well as the rate of maternal cell contamination vs. true fetal results.
2833 consecutive fresh products of conception samples and corresponding maternal and/or paternal blood samples were analyzed using a SNP array plus informatics algorithms for the purpose of detecting causal chromosome abnormalities.  Hypothesized advantages of using SNP microarray with Parental SupportTM informatics over the traditional standard G-banded karyotyping include:  direct testing without need for cell culture, faster turn-around time, low failure rate, the ability to detect or rule out maternal cell contamination (MCC), and the detection of small segmental changes, uniparental disomy (UPD) and parent of origin of any aneuploidies.  Results showed a 22% MCC rate. In the 78% of samples with true fetal results, 60% had abnormalities with single aneuploidy being the most common.  Separate evaluation of the samples to determine the resolution of the SNP array with informatics showed the ability to detect copy number variations (CNVs) as small as 1 MB or less, with 1.4% of samples revealing a clinically relevant microdeletion or duplication.

overall_design: 2833 fresh products of conception samples were analyze using no controls, no replicates, and no reference samples.

first: Brynn

last: Levy

first: Styrmir

last: Sigurjonsson

first: Barbara

last: Pettersen

first: Melissa

last: Maisenbacher

first: Zachary

middle: P

last: Demko

first: Ruth

last: Lathi

first: Rosina

last: Tao

first: Vimla

last: Aggarwal

first: Matthew

last: Rabinowitz


title: Expression data from rice plants showing hybrid weakness syndrome

status: Public on Jan 22 2014

city: Yangzhou

first: Chen

last: Chen

state: Jiangsu

address: 12 E. Wenhui Rd.

department: Agricultural College

institute: Yangzhou University

summary:
Reproductive  barriers perform a vital role during speciation. Hybrid weakness, the poor development of hybrids compared to their parents, hinders gene exchange between different species at the postzygotic stage. The molecular and evolutionary mechanisms of hybrid weakness are poorly understood. Here, we report that two incompatible dominant loci (Hwi1 and Hwi2) involving three genes determine the high temperature-dependent expression of hybrid weakness in interspecific hybrids of rice. Hwi1 comprises two indispensable wild rice (Oryza rufipogon)-specific leucine-rich repeat receptor-like kinase (LRR-RLK) genes, 25L1 and 25L2, for inducing hybrid weakness, and the genes possibly undergo balancing selection. Hwi2, a rare allele that is predominantly distributed in indica rice (Oryza sativa), encodes a secreted putative subtilisin-like protease. Functional analysis indicated that pyramiding of Hwi1 and Hwi2 activates the autoimmune response in the basal nodes of hybrids, interrupting root formation and then impairing shoot growth, likely due to immune signal is transmitted from the basal nodes to the above-ground parts. Considering the nature of RLK activity of Hwi1 and the protease activity of Hwi2, we propose that a certain endogenous signaling molecule produced by Hwi2 is perceived by Hwi1 to activate autoimmunity through ligand-receptor signal transduction. These findings bring new insights into our understanding of reproductive isolation and may benefit rice breeding to maximally utilize invaluable genes from wild rice.
We conducted microarray analysis to unravel the global changes in gene expression of a pair of NILs (nearly isogenic lines).

overall_design: Plants were cultivated at constant 20°C for 20 days and then shifted to constant 30°C conditions. The basal nodes of NIL(Hwi1) and NIL(hwi1) were harvested immediately before the temperature shift (set as the 0 point) or at 3, 7 or 15 days after the shift. Three biological replicates (each comprising basal nodes from 15–20 individuals) were used for each time point.

first: Hong-Xuan

last: Lin


title: Gene expression analysis in response to various hormone treatments

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

institute: Jawaharlal Nehru University

summary:
Hormones effect various plant developmental processes by altering gene expression. The expression of several genes is regulated by plant hormones and many of these genes are regulated commonly and specifically by various hormones.
We used microarrays to study the global effect of plant hormones on rice gene expression and identify the genes involved in operlapping and specific transcriptional responses.

overall_design: Rice seedlings of IR64 variety were grown hydroponically for 7-days in a culture room with a daily photoperiodic cycle of 14h light and 10h dark. Seedlings were incubated in water (control) or 50 µM solution of indole-3-acetic acid (auxin, IAA) and benzyl aminopurine (cytokinin, BAP) and 100 µM solution of abscisic acid (ABA), 1-aminocyclopropane-1-carboxylic acid (ethylene derivative, ACC), salicylic acid (SA) and jasmonic acid (JA) for 3h. The 5 micrograms of total RNA sample isolated from each tissue sample was processed for microarray analysis according to Affymetrix protocol. Two biological replicates for each sample (two controls, IAA, BAP, ABA, ACC, SA and JA) were used for microarray analysis.

first: Garg

last: Rohini

first: Jain

last: Mukesh


title: Transcriptome analysis of hrf1 transformed rice revealed crosstalk between disease resistance and drought tolerance mediated by Harpin

status: Public on Dec 29 2013

city: Nanjing

first: Zhang

last: Lei

address: Weigang 1

institute: Nanjing Agricultural University

summary: Harpin proteins from Gram-negative plant pathogenic bacteria can activate distinct signaling pathways and cause multiple effects in plants. In this document, we observed the transcriptome profile in transgenic NJH12 and wide type R109 using a customized 57 k rice cDNA microarray and found 225 differentially expressed transcripts related to the responses to biotic and abiotic stresses, including programmed cell death (PCD), defense responses associated with the recognition of pathogen-derived elicitors secondary metabolite biosynthesis, and defense signalling pathways mediated by abscisic acid (ABA), reactive oxygen species (ROS), nitric oxide (NO), polyamines (PAs) and Ca2+, suggesting that the disease resistance and drought tolerance mediated by Harpin protein in hrf1-expressing NJH12 rice has a crosstalk through several signaling pathways.

overall_design: The homozygous T3 NJH12 line is a transgenic rice line generated by transforming rice cultivar R109 with hrf1-containing pBMH9 using Agrobacterium-mediated transformation (Shao et al., 2008). Three T3 progeny of the transgenic NJH12 used in this study were grown in a sterile incubator at 28 ℃ in the greenhouse with a 16 h light/8 h dark cycle. Rice leaves were collected at the four-leaf stage and stored in liquid nitrogen prior to RNA extraction. Wild-type rice R109 was used as the negative control. The experiments for each transgenic line and wild type were repeated three times by three independently grown sets of plants for preparing RNA samples used for independent hybridization to the microarrays. Total RNA was extracted with TRIZOL reagent (Invitrogen, Gaithersburg, MD). The RNA quality was assessed by formaldehyde agarose gel electrophoresis and concentration was quantitated by spectrophotometric analysis. Total RNA was kept at −80 ℃ and sent to the Affymetrix core facility, where quality-control analysis was carried out before cDNA synthesis from the mRNA, labeling (through synthesis of cRNA with incorporation of biotinylated ribonucleotide analogs), and hybridization to the GeneChip Rice Genome Array (Affymetrix). This chip contains 57, 381 probe sets to query 51, 279 transcripts, which was designed based on the 59, 712 gene predictions of TIGR’s osa1 version 2.0 release. The chip was washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 400, followed by scanning on a GeneChip Scanner 3000 (Affymetrix). The results were quantified and normalized using MicroArray Suite 5.0 (GCOS1.4) software (Affymetrix). The gene annotation and pathway identiﬁcation were performed according to the method described by Shi et al. (2006) and Miao et al. (2010b).

first: Lei

last: Zhang

first: Min

last: Shao

first: Wenqi

last: Li

first: Shanshan

last: Xiao

first: Zhidan

last: Wu

last: Chang

first: Guang

last: Wang

first: Xuewen

last: Gao

first: Fengquan

last: Liu


title: Cell-type specific transcriptome analysis to study germline development and reproduction in apomictic Boechera gunnisoniana- ATH1 arrays

status: Public on Jun 01 2014

city: Glarus

first: Marc

middle: William

last: Schmid

address: Hauptstrasse 34

institute: MWSchmid GmbH

summary: Apomixis differs from sexual reproduction only in three major aspects: While the sexual megaspore mother cell undergoes meiosis, the apomictic initial cell omits or aborts meiosis (apomeiosis); the unreduced egg cell of apomicts forms an embryo without fertilization (parthenogenesis), and formation of functional endosperm requires specific developmental adaptations. Currently, our knowledge about the gene regulatory programs underlying apomixis is scarce. We used the apomict Boechera gunnisoniana, a close relative of Arabidopsis thaliana, to investigate the transcriptional basis underlying apomeiosis and parthenogenesis. Here, we present the first comprehensive reference transcriptome for reproductive development in an apomictic species. To compare sexual and apomictic development at the cellular level, we then used a combination of laser-assisted microdissection with microarray and RNA-Seq analysis. Our study yields important new insights into the transcriptional basis underlying apomixis.

overall_design: Cell-type specific transcriptome profiles were generated from the apomictic initial cell (2 biological replicates), surrounding sporophytic tissues (sporo_nucellus; 2 biological replicates), egg cell, central cell and synergid cells (one sample each) from the triploid pseudogamous obligate apomict Boechera gunnisoniana by heterologous hybridization on the Affymetrix ATH1 arrays.

first: Anja

last: Schmidt

first: Ueli

last: Grossniklaus


title: Microarray analysis of transcriptional responses to alkali stress in two rice genotypes

status: Public on May 16 2014

city: Changchun

first: Yunhong

state: Jilin province

address: Renmin street 5268

institute: Northeast Normal University

summary: To investigate possible genetic basis of alkali tolerance in rice, we generated an introgressed rice line (K83) with significantly enhanced tolerance to alkali stress than its recipient parental cultivar (Jijing88). By using microarray analysis, we examined global gene expression profiles in K83 and Jijing88, found more than 1,200 genes were constitutively differentially expressed in K83 compared with Jijing88, with 572 up- and 654 down-regulated. Upon alkali treatment, a total of 347 genes in K83 were found up- and 156 down-regulated in K83, compared with 591 and 187 respectively in Jijing88.

overall_design: Seven-day-old uniform-sized seedlings grown in hydroponic medium were transferred to fresh hydroponic medium alone or containing 50 mM alkali salts. Shoots were harvested 24 h after transfer and 10 shoots were pooled for microarray analysis.

first: Xiuyun

last: Lin

first: Bao


title: SNP data from human fibroblasts and induced Pluripotent Stem cells from Parkinson's Disease patients

status: Public on Dec 18 2013

city: Oxford

first: Sally

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

summary:
We have generated human induced Pluripotent Stem cells (hiPSc) from Parkinson's Disease patients, using retrovirus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation to dopaminergic neuronal clutures and downstream functional assays.
Fernandes H.J.R., Hartfield E.M., Badger J., Christian H. C., Emmanoulidou E., Vowles J., Evetts S., Vekrellis K., Talbot K., Hu M.T., James W., Cowley S.A., and Wade-Martins, R.   Heterozygous glucocerebrosidase mutations in Parkinson's increase autophagic demand, but decrease capacity, in induced pluripotent stem cell-derived dopaminergic neuronal cultures.  submitted for publication

overall_design: human iPSc lines were derived from human dermal fibroblasts from 2 Parkinson's Disease patients with heterozygous glucocerebrosidase mutations (GBA N370S) mutations,  and 2 idiopathic Parkinson's Disease patients. SNP datasets from the 2 control individuals used in this study have been published previously [PMID 23951090  GSE45472; PMID:24586273  GSE43904]

first: H

last: Fernandes

first: E

last: Hartfield

first: J

last: Badger

middle: C

last: Christian

last: Emmanoulidou

last: Vowles

first: S

last: Evetts

first: K

last: Vekrellis

last: Talbot

first: M

last: Hu

first: W

last: James

first: R

last: Wade-Martins


title: A Gene Expression Profiling of Early Rice Stamen Development that Reveals Inhibition of Photosynthetic Genes by OsMADS58

status: Public on Dec 17 2013

city: Beijing

first: Rui

last: Chen

address: 5 Yiheyuan Road, Haidian District

institute: Peking University

summary:
Plant organ formation, or organogenesis is the process in which the primordium derived from shoot apical meristem develops into an organ with a given shape and proper function, through a series of cell division and differentiation.
To decipher the genetic program underling plant organ formation, we targeted early rice stamen development that covers most important events in male organ formation and germ cell initiation in plants.

overall_design: Totally, seven samples were used in this experiment. Stamens of stages 2-6 was collected through microdissection under microscope. And to ensure the stamen primordia collected are at corresponding stages, rice panicles were cut in half longitudinally, one half for paraffin sectioning to confirm developmental stages and the other half for preparing GEP samples. Samples of primordial and just-expanded third leaves were used as controls because leaf and stamen are homolog organs. RNA was extracted and amplified with Two-Cycle Eukaryotic Target Labeling Assay kit, and then hybridized to microarrays. Three biological replicates were applied for each sample.

first: Liping

last: Shen

first: Donghui

last: Wang

first: Fugui

first: Hongyun

last: Zeng

first: Zhishan

first: Yiben

last: Peng

first: Yanan

first: Xing

last: Tang

first: Minghua

last: Deng

last: Yao

first: Jingchu

last: Luo

first: Zhihong

last: Xu

first: Shunong

last: Bai


title: Rice Submergence Stress Response

status: Public on Dec 15 2013

city: Lincoln

first: Harkamal

last: Walia

state: NE

address: Agronomy and Horticulture

institute: University of Nebraska

summary: Two rice genotypes, M202 (intolerant) and M202(Sub1), a tolerant genotype, were submerged for 1 day and 6 day and sampled for identifying differentially expressed genes.

overall_design: 4 samples. M202- 1 day and 6 day; M202(Sub1)- 1 day and 6 day

first: Pamela

last: Ronald


title: Human oocytes reprogram adult somatic cells to pluripotent stem cells

status: Public on Apr 27 2014

first: Dieter

last: Egli

summary: The transfer of somatic cell nuclei into oocytes can give rise to pluripotent stem cells, holding promise for autologous cell replacement therapy. Though reprogramming of somatic cells by nuclear transfer was first demonstrated more than 60 years ago, only recently have human diploid embryonic stem cells been derived after nuclear transfer of fetal and neonatal fibroblasts. Because of the therapeutic potential of developing diploid embryonic stem cell lines from adult cells of normal and diseased human subjects, we have systematically investigated the parameters affecting efficiency and developmental potential in their derivation. We found that improvements to the oocyte activation protocol, including the use of both a kinase and a translation inhibitor, and cell culture in the presence of histone deacetylase inhibitors enable development of diploid cells to the blastocyst stage. Developmental efficiency varied significantly between oocyte donors, and was inversely related to the number of days of hormonal stimulation required to reach mature oocytes, while the daily dose of gonadotropin or the total number of MII oocytes retrieved did not affect developmental outcome. The use of diluted Sendai virus in calcium-free medium during nuclear transfer improved developmental potential, while the use of concentrated Sendai virus induced an increase in intracellular calcium and caused premature oocyte activation. Using these modifications to the nuclear transfer protocol, we successfully derived diploid pluripotent stem cell lines from both postnatal and adult somatic cells of a type 1 diabetic subject.

overall_design: The goal of this experiment was to determine if human oocytes have the ability to reprogram a somatic cell genome in the absence of the oocyte genome. Our previous research had indicated that human oocytes can reprogram adult somatic cells if the oocyte genome remains present (Noggle et al. Nature 2011, doi:10.1038/nature10397). The data presented here is part of a new series of experiments aimed at obtaining diploid cells after somatic cell nuclear transfer into enucleated oocytes. In this experiment, adult somatic cells were transferred into enucleated oocytes and thereafter cultured in the presence of 240ng/ml scriptaid for 17 hours. Samples were cultured until cleavage stage and then collected for microarray analysis.

first: Mark

last: Sauer


title: Post dose-dense (dd) MVAC tumors

status: Public on Feb 10 2014

city: Houston

first: Woonyoung

last: Choi

address: 1515 Holcombe

institute: Md Anderson Cancer center

summary: post dd MVAC tumors were used for the validation of bladder cancer subsets

overall_design:
dd MVAC cohort consisted of 20 post-treatment tumors were used to validate the bladder cancer subsets

Please note that the GEO accession number for the corresponding pretreatment sample (with matching TURBT Information) is provided in the sample description field.

first: Sima

last: Porten

first: I-ling

last: Lee

first: Elizabeth

last: Plimack

first: Jean

last: Hoffman-Censitis

first: David

last: McConkey


title: Tumors with neoadjuvant chemotherapy

summary: Using whole genome mRNA expression profiling of primary human tumors and unsupervised hierarchical cluster analyses,  3 novel molecular subsets (basal, luminal and p53-like subsets) of muscle-invasive bladder cancer (MIBC) were identified.  23 MVAC treated samples were used for the validation of three MIBC subsets

overall_design:
MVAC cohort consisted of 23 FFPE pretreatment tumors (TURs) from a Phase III clinical trial were used to validate 3 molecular subsets including basal, luminal and p53-like subsets
We used Illumina cDNA-mediated Annealing, Selection, Extension, and Ligation (DASL) assay that is specifically designed for the gene expression of RNA that is extracted from FFPE.


title: Gene expression profiling of urothelial carcinoma

summary: Identification of bladder cancer subsets

overall_design: 128 FFPE bladder tumors were used to validate the bladder cancer subsets


title: Gene expression profiling in sinonasal sarcoma

status: Public on Apr 17 2014

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

summary: Analyses of gene expression profiling in sinonasal sarcoma (SNS) harboring PAX3-MAML3 fusion gene or PAX3 rearrangement and other types of tumors without having such fusion or rearrangement. The results provide important information for further investigations of the PAX3-MAML3 fusion functions in SNS.

overall_design: Total RNA was obtained from FFPE tissues of 41 tumors including 8 SNS (6 with PAX3-MAML3 fusion and 2 with PAX3 rearrangement only) and 33 cases from other 10 different types of tumors. Gene expression profiling of fusion group including 8 SNA vs.non-fusion group including 33 control tumors were analyszed.

first: Andre

last: Oliveira

first: Xiaoke

last: Wang


title: OsJMJ705 preferentially activates stress-responsive genes

status: Public on Dec 10 2013

city: wuhan

first: zhong

last: xiaochao

address: shizishan road No.1

institute: NCPGR

summary:
Histone methylation is important epigenomic information for gene regulation and genome activity
To evaluate genome-wide effect of OsJMJ705  on gene expression, we used the Affymetrix microarray technologies to analyze the transcriptomes of the wild type, over-expression plants and the T-DNA mutant. Gene ontology (GO) analysis revealed that up-regulated genes were significantly enriched for the categories of stress-responsive genes.

overall_design: To evaluate genome-wide effect of OsJMJ705  on gene expression, we used the Affymetrix microarray technologies to analyze the transcriptomes of the wild type, over-expression plants and the T-DNA mutant 14 days after germination under normal growth conditions. Two biological repeats were performed. Gene expression changes between the samples were analyzed by AffylmGUI package from the R software.

first: Li

last: Tiantian

first: Zhou

last: Daoxiu


title: Reduced lymphoid lineage priming promotes human hematopoietic stem cell expansion

status: Public on Dec 01 2013

city: Boston

first: Peter

last: van Galen

state: Massachusetts

address: 4 Blackfan Circle

department: Hematology

institute: Brigham and Women's Hospital / Broad Institute of MIT and Harvard

summary: Hematopoietic stem cells (HSCs) must balance self-renewal and lineage differentiation to regenerate the hematopoietic system throughout life. HSCs exhibit lineage-associated gene expression that keeps them responsive to demands of mature blood production. However, it is not known whether this process, termed lineage priming, directly influences HSC self-renewal. We investigated the link between stemness and lineage priming by attenuating the early lymphoid transcription factor E47 through ID2 over-expression (OE). Transcriptional profiling of ID2 OE HSCs showed down regulation of B-cell factors including EBF1 and FOXO1 with a concomitant increase in stemness programs and myeloerythroid factors including CEBPA and GATA1. This resulted in myeloid commitment bias from the earliest stages of differentiation. HSC self-renewal was strongly affected by this lineage perturbation resulting in an 11-fold expansion of HSCs. Thus, early lymphoid transcription factors antagonize human HSC self-renewal, providing a direct link between differentiation program priming and the maintenance of stem cell self-renewal.

overall_design: Three independent lineage depleted CB samples were transduced with P-CTRL or P-ID2 and injected into 5 mice (30 mice total). From every group of 5 mice, human lin- cells were isolated and GFP+CD34+CD38-CD45RA- HSPCs were sorted by FACS.

first: Antonija

last: Kreso

first: Erno

last: Wienholds

first: Elisa

last: Laurenti

first: Kolja

last: Eppert

first: Eric

last: Lechman

first: Nathan

last: Mbong

first: Craig

last: April

first: Jian-Bing

last: Fan

first: John

middle: E

last: Dick


title: Copy number profiling of 36 human melanoma tumors on Affymetrix 100K SNP arrays

status: Public on Oct 15 2013

city: South San Francisco

last: Haverty

address: 1 DNA Way

institute: Genentech, Inc.

summary: Fresh frozen Melanoma patient samples  were profiled on Affymetrix GeneChip Mapping 100K Set Arrays

overall_design: Profiling of 36 melanoma tumors

first: Christy

last: Ong

first: Zora

last: Modrusan

first: Klaus

last: Hoeflich


title: DNA microarray data from root of transgenic rice Huahui 1 (HH1) and its parent Minghui 63 (MH63)

status: Public on Oct 16 2013

first: Jie

last: Zhao

address: No. 2 Yuan Ming Yuan West Street

institute: Institute of Plant Protection, Chinese Academe of Agricultural Sciences

summary:
DNA microarray analysis has been proved to be an effective method in investigating unintended effects in genetically modified (GM) crops. However, unintended effects of GM plants in leaves through DNA microarray analysis has many researches, but research of unintended effects of GM plants of the underground portion has few. In this study, DNA microarray analysis was used to detect DEG in  underground portions between transgenic rice HH1 and its non-transgenic control MH63.
We used microarrays to study unintended effects in root of transgenic rice Huahui 1.

overall_design: Samples were collected from root of HH1 and MH63  at 30-day old and were used for RNA extraction and hybridization on Affymetrix microarrays. We selected diferentially expressed genes and common significantly changed pathways hoping to as a clue to  investigate unintended effects of HH1 root.

first: Fangjun

last: Qi

first: Zhao

last: Jie


title: Nitrogen-efficient rice over-expressing alanine aminotransferase at three different N concentrations

status: Public on Oct 25 2013

city: Edmonton

first: Perrin

middle: Hudson

last: Beatty

state: Alberta

address: G425 Biological Sciences

department: Biological Sciences

country: Canada

institute: University of Alberta

summary:
Oryza sativa cv. Nipponbare was engineered to over-express a barley alanine aminotransferase (alaAT) gene using the promoter (OsANT1) from a rice aldehyde dehydrogenase gene that expresses in roots.
We use biotechnology to improve the nitrogen use efficiency of rice by over-expressing alaAT in a tissue specific (root) manner. The AlaAT enzyme is a reversible aminotransferase that is linked to both C and N metabolism since it uses pyruvate plus glutamate to produce alanine and 2-oxoglutarate, and visa versa.

overall_design:
Transcriptome data from the roots and shoots of rice plants at maximum tillering, grown hydroponically on either 0.5, 2 or 5 mM NH4+ as the nitrogen source.
Wildtype rice (Nipponbare) and two independent OsANT1:HvAlaAT rice transgenic lines (AGR1/7, and AGR3/8) were grown hydroponically with either 0.5, 2 or 5mM NH4+ as the nitrogen source, to the reproductive stage. Tissue samples were taken at active and maximum tillering from root and shoot, at mid-day of the plants' day/night cycle. The RNA from root and shoot at maxiumum tillering was used for mcroarray analysis. Please read Beatty et al., 2009, PLant Biotechnology Journal 7, pp562-576 for detailed about these transgenic lines. The results from this variable N study were reported in a manuscript submitted to Botany, July 2013

middle: H

first: Allen

last: Good


title: Gene expression analysis of rice seedling under potassium deprivation

status: Public on Sep 14 2013

city: NEW DELHI

first: GIRDHAR

middle: KUMAR

last: PANDEY

state: DELHI

address: BENITO JUAREZ ROAD

department: Plant Molecular Biology

institute: Delhi University South Campus

summary:
Potassium is one of the essential macronutrients required for plant growth and development. It plays a major role in different physiological processes like cell elongation, stomatal movement, turgor regulation, osmotic adjustment, and signal transduction by acting as a major osmolyte and component of the ionic environment in the cytosol and subcellular organelles.
We used whole genome microarrays to determine the transcriptomic profile of rice seedlings exposed to short-term K+ deficiency followed by K+ resupply.

overall_design: Potassium treated seedlings were used for RNA extraction and hybridization on Affymetrix rice Genechip  by microarrays. Three biological replicates of each sample were used for microarray analysis. We wanted to know the altered expression patterns of potassium-responsive genes majorly involved in metabolic processes, stress responses, signaling pathways, transcriptional regulation, and transport of multiple molecules including K+. Seeds of indica rice were surface sterilized and grown hydroponically in rice growing medium. Plants were grown in the rice growth room under the condition of 16 h light/8 h dark (28°C) photoperiod with 70 % humidity. After 5 days of normal growth, one half of the rice seedlings were transferred to nutrient media with normal concentration of potassium (KP, 0.409 mM K2SO4) and other one half to medium without potassium (KM, 0 mM).  After 5 days, potassium (0.409 mM K2SO4) was resupplied to the plants grown in KM medium for 6 h.

first: Alka

last: Shankar

first: Amarjeet

last: Singh

first: Poonam

last: Kanwar

first: Ashish

last: Srivastava

first: Amita

last: Pandey

first: Penna

last: Suprasanna

first: Sanjay

last: Kapoor

first: Girdhar


title: Affymetrix SNP array data for acute-type adult T-cell leukemia (ATL) samples

status: Public on Jan 31 2014

city: miyazaki city

first: kentarou

last: nagai

state: miyazaki

department: medical

institute: Miyazaki university

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: We recently mapped 605 chromosomal breakpoints in 61 ATL cases by spectral karyotyping and identified chromosome 14q11 as one of the most common chromosomal breakpoint regions. To map the precise location of chromosomal breakpoints at 14q11, we performed single-nucleotide polymorphism (SNP)-based comparative genomic hybridization on leukemia cells from acute-type ATL patients.

overall_design: Copy number analysis of Affymetrix 50K SNP arrays was performed for leukemic cell samples from10 acute-type ATL patients.

first: Kazuhiro

last: Morishita


title: SALT-RESPONSIVE ERF1 expression profiling in rice roots

status: Public on Sep 17 2013

city: Potsdam

first: Jos

last: Schippers

address: Am Muehlenberg 1

department: Plant Signaling

country: Germany

institute: MPIMP-golm

summary: To identify genes that are regulated by SERF1, we performed expression profiling on roots of serf1 and  wild-type plants under standard growth conditions.

overall_design: Plants were grown for  4 weeks at (day/night) 26/22°C, 75/70% relative humidity with a day-length of 12 h and a light intensity of 700 µmol m-2 s-1. Seeds of serf1 T-DNA lines and Nipponbare wild type were placed on hydroponic boxes with full-strength Yoshida medium (Yoshida et al., 1971) using styrofoam adaptors.  For each genotype 3 biological replicates were seperately isolated and measured.

first: Romy

last: Schmidt

first: Bernd

last: Mueller-Roeber


title: Transcription profiling of Basmati T-DNA insertional mutant lines

status: Public on Dec 31 2013

city: Roorkee

first: Anjali

last: Awasthi

state: Uttarakhand

address: Department of Biotechnology

department: Biotechnology

institute: Indian Institute of Technology Roorkee

summary: The aim of this study was to look for the changes at the transcriptome level caused by the same T-DNA cassette in three mutants of Basmati 370 with different phenotypes. The comparative analysis of differentially expressed genes was conducted individually and collectively for all three mutants.

overall_design: RNA from Basmati mutants OsPE, Osoc and Ossl grown under optimal conditions were analyzed in two different biological replications (A and B) making total six samples.

first: Priyanka

last: Paul

first: Amit

last: Rai

first: Santosh

last: Gupta

first: R

last: Prasad

first: Harcharan

last: Dhaliwal

first: Tilak

middle: R

last: Sharma


title: A global analysis of QTLs for expression variations in rice flag leaf at heading date

status: Public on Feb 05 2014

first: wang

last: Jia

address: shizhishan

institute: hzau

summary: Analyses of QTLs for expression levels (eQTLs) of the genes reveal genetic relationship between expression variation and the regulator, thus unlocking the information for identifying the regulatory network. In this study, we used Affymetrix GeneChip Rice Genome Array to analyze eQTLs in rice flag leaf at heading date from 210 recombinant inbred lines (RILs) derived from a cross between Zhenshan 97 and Minghui 63. In the study, we attempted to construct the regulatory network by identifying putative regulators and the respective targets using an eQTL guided co-expression analysis with a recombinant inbred line population of rice.

overall_design: The ability to reveal the regulatory architecture of the genes at the whole genome level by constructing the regulatory network is critical for understanding the biological processes and developmental programs of the organism. Here we conducted an eQTL guided function-related co-expression analysis for identifying the putative regulators and constructing gene regulatory network.  The Affymetrix Genechip rice Genome Array was used to investigate their dynamic transcript levels. one replicates were sampled from each RIL, three for parents, and three replicates for each parent resulting in a dataset of 216 microarrays.

first: Jia

last: Wang

first: Huihui

last: Yu

first: Weibo

last: Xie

first: Xiaoyu

last: Weng

first: Caiguo

last: Xu

first: Xianghua

last: Li

first: Jinghua

last: Xiao

first: Qifa

last: Zhang


title: Overexpression of OsMADS29 in Oryza sativa var. PB1

status: Public on Sep 05 2013

city: New Delhi

first: Sanjay

last: Kapoor

address: Benito Huarez MArg

institute: University of Delhi, South Campus

summary: Overexpression of MADS29 results in severely dwarfed phenotype, resulting from a shift in auxin-cytokinin ratio in favor of cytokinins. To see the extent of change in gene expression in the leaves of the transgenic plants, whole genome transcript analysis was carried out using microarray.

overall_design: Three biological  replicates of MADS29 OX (overexpression) lines and Wild Type PB1 (control) plants were used for microarray study

first: Saraswati

last: Nayar

first: Rita

first: Akhilesh

last: Tyagi


title: Silencing of OsMADS29 in Oryza sativa var. PB1

summary: RNAi mediated suppression of MADS29 severely affects seed set; the surviving seeds are smaller in size with reduced grain filling, abnormal starch grains and aberrant embryo development. To identify the affected pathways  due to suppression of this transcription factor in the transgenic seeds, transcriptome analysis using microarray was carried out.

overall_design: Three biological replicates of MADS29 RNAi (silencing) lines and Wild Type PB1 (control) plants were used for microarray study


title: Expression data from Oryza sativa 3037 (wild-type) and sd37 (mutant) seedlings

status: Public on Jul 09 2013

first: zhang

last: jie

address: Datun Road

institute: BVRC

summary:
We characterized a rice (Oryza sativa L ssp. indica cultivar 3037) semi-dwarf mutant sd37, in which CYP96B4 gene (Cytochrome P450 96B subfamily) was identified as the target gene by map-based cloning and complementation test. A point mutation in CYP96B4 leads to a substitution of Thr to Lys in the SRS2 region. The sd37 leaves, panicles and seeds are all smaller compared with those of wild-type, and histological analysis showed that the decreased cell number was the main reason for the dwarf phenotype.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up- and down- regulated genes during this process.

overall_design: Two-week old seedlings of sd37 and wild-type rice plants were selected and three biological replicates were generated and evaluated.

first: Jie

first: Xiaoqiang

last: Liu

first: Shuyu

last: LI

first: Zhukuan

last: Cheng

first: Chuanyou


title: Salivary microRNAs May Be A Valuable Biomarker To Detect Resectable Pancreatic Cancer

city: Guangzhou

first: Zijun

address: No.106,zhongshan 2nd round

institute: Guangdong General Hospital

summary: Early surgery is vital in the treatment of highly fatal pancreatic cancer (PC). But there is no valuable and non-invasive biomarker to screen PC currently. Studies showed many salivary molecules can detect several systemic diseases. We aimed to investigate whether salivary microRNAs (miRNAs) can act as a biomarker to detect resectable PC.

overall_design: By Agilent microarray salivary miRNAs were profiled from saliva samples from 8 patients with resectable PC and 8 healthy controls. Candidate biomarkers discovered from the profile were subjected to validation by qPCR.


title: Genome-wide analysis of gene expression within vitiligo lesional skin with active inflammation

status: Public on Dec 12 2013

city: Worcester

first: John

last: Harris

state: MA - Massachusetts

address: 364 Plantation St

department: Medicine - Dermatology

institute: UMass Medical School

summary: Vitiligo skin samples with an active inflammatory infiltrate were selected for gene expression profiling in order to identify inflammatory pathways that drive depigmentation in vitiligo.

overall_design: Total RNA was isolated from 10 deidentified human samples from formalin fixed, paraffin-embedded skin, 5 from vitiligo patients and 5 from controls. Control skin was age- and site-matched excision tips without pathology.


title: Gene expression analysis of microvesicular hyperplastic polyps and sessile serrated polyps/adenomas

city: Cleveland

first: Rish

last: Pai

state: Ohio

address: 9500 Euclid Avenue, L25

department: PLMI

institute: Cleveland Clinic

summary: In this study we compared gene expression of precancerous SSA/Ps and benign MVHPs with particular focus on genes involved in colorectal cancer.  We also identify genes whose expression can be used to differentiate SSA/Ps and MVHPs.  These results provide insight into the development of SSA/Ps and illustrates differences between these related colonic polyps.

overall_design: Total RNA from 6 samples of normal colon, 6 microvesicular hyperplastic polyps, and 6 sessile serrated adenomas/polyps were compared

first: Pai

last: Rish


title: Transcription profiling of wild type Basmati 370 and its T-DNA insertional mutant OsAPC6.

first: Anjali

last: Awasthi

summary: The aim of this study was to look for the changes at the transcriptome level caused by the  insertion of a T-DNA in mutant of Basmati 370 with dwarf phenotype. The comparative analysis of differentially expressed genes was conducted individually and collectively for both.

overall_design: RNA from wild type Basmati 370 and its mutant OsAPC6 grown under optimal conditions were analyzed in two different biological replications (A and B) making total four samples.

first: Priyanka

last: Paul

first: Amit

last: Rai

first: Santosh

last: Gupta

first: R

last: Prasad

first: Harcharan

last: Dhaliwal

first: Tilak

last: Sharma


title: Molecular interaction between PHO2 and GIGANTEA reveals a new crosstalk between flowering time and Pi homeostasis in rice

status: Public on Jul 01 2013

city: Bundoora

first: Reena

last: Narsai

address: 5 Ring road

country: Australia

institute: La trobe University

summary:
Using a yeast to hybrid screen, it was found that PHO2, a key regulator of phosphate homeostasis, could interact with GIGANTEA, a key regulator of flowering time. In addition, mutant analysis revealed that both the pho2 and gi mutants shared similar phenotypes, both at the phosphate and flowering time levels.
We used microarrays to analyse the effects of each mutation (pho2 or gi) on global gene expression, and assessed the proportion of genes similalry regulated in both mutants, in both shoots and roots.

overall_design: Wild-type (Nipponbare), pho2 and gi knock-out rice plants were grown to 21-days before harvesting root and shoot separately.


title: affy_compartimentation_rice_albumen_embryon-Transcriptomic study of the rice seed compartimentation during germination

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

summary: affy_rice_2011_03 - affy_compartimentation_rice_albumen_embryon - During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination. -We germinate rice seeds of the first sequenced rice cultivar i.e. Nipponbare during 0, 4, 8, 12, 16 and 24h of imbibition in sterile distilled water. Germination occurs under constant air bubbling, in the dark at 30°C. These rice seeds are then manually dissected into embryo and endosperm fractions. -The embryo-derived samples are abbreviated in “E” while the endosperm samples are abbreviated “A”. The germination time-point is indicated after the letter (e.g. E8 for embryo samples harvested after 8 hours of germination). Finally, the biological repetition number is indicated before the letter and the time digit (e.g. 1-E8 for an embryo sample from the first repetition at 8 hours of imbibition).

overall_design: 36 arrays - rice; organ comparison,time course

first: Pascal

last: Gamas

first: Stephanie

last: Huguet

first: MARC

last: GALLAND

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Novel miRNA profiles as biomarkers for renal cell carcinoma and upper tract urothelial carcinoma

status: Public on Jun 18 2013

city: Athens

first: George

middle: I

last: Lambrou

state: Attiki

address: Thivon & Levadeias

department: First Department of Pediatrics

country: Greece

institute: National and Kapodistrian University of Athens

summary: We investigated the expression profiles of microRNAs (miRNA) in 26 renal cell carcinoma (RCC) FFPE tissues (3 chRCC, 5 papRCC and 18 ccRCC), 4 urothelial cell carcinomas of the upper urinary tract (UT-UCs) and 20 normal kidneys by using the miRCURY LNA™ microRNA Array, 6th gen (Exiqon, Woburn MA), containing capture probes that target all miRNAs for all species registered in the miRBASE version 16.0. Real-time PCR (qRT-PCR) using appropriate endogenous controls was performed in order to validate the microarray results of the 27 most differentially expressed (DE) miRNAs. We identified 434 miRNAs that were significantly deregulated in all tumours compared to the normal kidney tissues. Overall, 126 miRNAs (29%) showed increased expression and 303 miRNAs (69.8%) had decreased expression in RCCs and UT-UCs vs. the normal kidneys. Specifically, 374, 420, 421 and 409 miRNAs were 90% consistently down-regulated in ccRCC, papRCC, chRCC and UT-UC, respectively. Unsupervised two-way hierarchical clustering (HCL) with Euclidian distance accurately discriminated between RCC and UT-UC. Apart from one chRCC sample that was clustered with ccRCCs, HCL also managed to successfully classify the 3 RCC subtypes among them. Furthermore, it showed that ccRCC is more closely related to papRCC and that both are distinct from chRCC or UT-UC. Ninety-four miRNAs were co-upregulated among ccRCC, papRCC and chRCC; and 11, 44 and 24 miRNAs were specifically up-regulated in each one of the three RCC subtypes (ccRCC, chRCC and papRCC), respectively. On the other hand, 222 miRNAs were co-down-regulated in the three RCC subtypes, whereas 16, 18 and 5 miRNAs were specifically down-regulated in ccRCC, chRCC and papRCC, respectively. When the DE miRNAs in each RCC subtype were combined with those in UT-UC, we identified 89 and 206 miRNAs, respectively, that were up- and down-regulated in all tumor types. miRNA profiling can distinguish between RCC and UT-UC as well as among distinct RCC subtypes. Our data validicate that miRNA expression tends to be down-regulated in RCC versus the normal kidney tissue.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: We used 18 ccRCC, 3 chRCC, 5 papRCC, 4 UT-UC, 1 undifferentiated carcinoma and 19 normal tissue samples for miRNA profiling. Total RNA (0.5 µg) from each sample and reference was labeled with Hy3™ fluorescent label, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit (Exiqon, Woburn MA). The Hy3™-labeled samples were hybridized to the miRCURY LNA™ microRNA Array, 6th gen (Exiqon, Woburn MA), using an Agilent hybridization SureHyb chamber and gasket slide kits. After hybridization, the microarray slides were scanned at 10 μm using the High-Resolution Microarray Scanner (Agilent Technologies) and stored in an ozone free environment. The image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA). Raw microarray data were filtered, background corrected and quantile normalizated. Normalized data were further extracted, pre-processed and sorted with Microsoft Excel®. MicroRNAs were considered to be significantly differentially expressed if they obtained a p-value<0.05 and a FDR<0.05

first: Apostolos

last: Zaravinos

first: Nikos

last: Mourmouras

first: Krinio

last: Giannikou

first: Dimitris

last: Delakas

first: Constantinos

last: Deltas


title: Expression analysis of genes affected by dehydration-responsive transcription factor Os02g31890 from rice.

status: Public on Nov 30 2013

city: Postdam

first: Salma

last: Balazadeh

department: Stitt

institute: MPIMP

summary:
Os02g31890 encodes a dehydration-responsive transcription factor (named ´ARID´) from rice (Oryza sativa, cv. Dongjin).
Expression profiling was performed 90 min after the start of dehydration stress in roots of Oryza sativa wild-type plants (cv. Dongjin) and a knock-out (i.e. arid) mutant.

overall_design: Wild-type rice plants and a line carrying a T-DNA insertion in the third exon of the transcription factor gene (arid mutant) were subjected to dehydration stress for 90 min. Well-watered wild-type and T-DNA insertion plants were used as controls. Total RNA was extracted from roots and subjected to expression profiling using rice Affymetrix microarrays.

first: Masood

last: Soltaninajafabadi

first: Slobodan

last: Ruzicic

first: Bernd

last: Mueller-Roeber


title: Expression data from human glioma cancer stem cell (CSC) specimens following knockdown of GREM1

status: Public on Jun 03 2014

first: Kenneth

last: Yan

state: OH

address: 2111 E. 96th Street

department: Stem Cell Biology & Regenerative Medicine

institute: Cleveland Clinic Lerner Research Institute

summary:
CSCs differentially secrete the BMP antagonist Gremlin1 compared to non-stem glioma populations.  Knockdown of Gremlin1 decreases CSC proliferation and tumorigenicity, establishing Gremlin1 as an essential effector for CSC maintenance.
We used a microarray to determine the gene expression programs that are activated downstream of Gremlin1 that might be responsible for CSC maintenance.

overall_design: Glioma CSC cultures from two distinct patient-derived specimens (528 and 3691) were transduced with lentivirus expressing non-targeting scrambled shRNA or one of two distinct Gremlin1 shRNAs (shGrem1_485 and shGrem1_2456) for 72 hours (total of six samples).  RNA was extracted for array hybridization.

first: Jeremy

middle: N

last: Rich


title: Expression data from leaf of plant overexpressing OsXa5 in japonica rice (cv. Ishikari-shiroge (I-S))

city: Hangzhou

first: Yan

middle: Qiu

state: Zhejiang

address: Shiqiao Road 198#

department: Institute of Virology and Biotechnology

institute: Zhejiang Academy of Agricultural Sciences

summary:
A candidate gene was cloned and overexpressed to explore its potential function in bacterial blight (BB) resistance. Due to it was the susceptible allele of xa5 gene in rice, it was designated as OsXa5.
We used microarrays to detail the global reprogram of gene expression in OsXa5-overexpressing plants.

overall_design: To find out pathways and genes related to this candidate gene, microarray analysis were carried out with OsXa5-overexpressing plants. Three independent replicates were performed for overexpressing plants, and the wild type plants (japonica rice cv. Ishikari-shiroge) were used as control.

last: Qiu

first: Xuming

last: Wang

first: Chengqi

first: Jianping

last: Chen


title: SNP data from OX1 human fibroblasts and induced Pluripotent Stem cells

status: Public on Mar 26 2013

city: Oxford

first: Sally

last: Cowley

address: South Parks Road

institute: University of Oxford

summary:
human induced Pluripotent Stem cells (hiPSc) and their differentiated progeny have great potential for modelling disease. To realise this potential, robust protocols need to be developed for deriving authentic differentiated cell lineages and these lineages need to be rigorously characterised. We have generated hiPSc using retrovirus-mediated delivery of reprogramming factors, and have used them for assessing the efficiency of a defined protocol for differentiation to monocytes and macrophages. hiPSc lines have been screened using SNP array to assess chromosomal stability, and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets.
van Wilgenburg B, Browne C and Cowley SA, submitted for publication

overall_design: human iPSc lines were derived from normal human dermal fibroblasts.

first: Bonnie

last: van Wilgenburg

first: Cathy

last: Browne


title: ovation-Transcriptomic study of rice seed ageing

status: Public on Sep 01 2013

first: stephanie

last: huguet

summary: affy_rice_2012_01 - ovation - One of the key questions for future agriculture will be to save agronomical relevant biodiversity. To do so, it is important to select the best crop cultivars that will germinate efficiently (good seed vigor) and for a long period of time (good seed longevity). Surprisingly, while mankind rely heavily on cereals, very few studies have identified genes positively related to cereal seed vigor and longevity. To close this scientific gap, we aimed to identify genes positively involved in rice seed vigor and longevity. We thus used a “controlled deterioration treatment (Tesnier et al., 2002) to mimic natural seed ageing. Seeds are first equilibrated at 25°C and 85% relative hygrometry during three days. Then, during 15 days, three different batch of seeds are either (i) kept at 25°C and 85% RH (control seeds), (ii) placed at 40°C and 85% RH (loss of seed vigor) or (iii) placed at 45°C and 85% RH (loss of germination capacity). Finally, seeds are equilibrated at 25°C and 32% RH during three days. Using this CDT treatment, we obtained rice seeds with contrasted seed vigor or germination capacity. We extracted the total RNA from the embryos and we analysed their transcriptome using the Affymetrix Rice Genome Array.-We applied a Controlled Deterioration Treatment (CDT) to seeds from the reference rice cultivar Nipponbare. First, all seeds are equilibrated at 25°C and 85% relative hygrometry. Then, depending on the treatment, seeds are placed at 25, 40 or 45°C in 85% relative hygrometry before being finally equilibrated at 25°C and 32% relative hygrometry. The germination of the three seed batches was measured during five days with one measure every 8h. Seeds placed at 25°C during the whole experiment were similar to control seeds kept in the fridge and germinated at nearly 100% in 48h. Seeds placed at 40°C during 15 days germinate at 74% but show altered seedling phenotypes (loss of seed vigor). Finally, seeds placed at 45°C do not germinate.

overall_design: 6 arrays - rice; treated vs untreated comparison

first: Stephanie

last: Huguet

first: MARC

last: GALLAND

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Mechanotransduction regulates adipose estrogen output and its impact on tumor cell growth

status: Public on Mar 04 2013

city: San Antonio

first: Keith

last: Ashcraft

state: TX

address: 8403 Floyd Curl Dr.

institute: UT Health Science Center San Antonio

summary: Adipose stromal cells (ASCs) are the primary source of local estrogens in adipose tissue, aberrant production of which promotes estrogen receptor-positive (ER+) breast cancer.  Here we show that extracellular matrix (ECM) rigidity and cell contractility are two opposing determinants for estrogen output of ASCs.  Using synthetic ECMs and elastomeric micropost arrays with tunable rigidity, we find that increasing matrix compliance induces transcription of aromatase, a rate-limiting enzyme in estrogen biosynthesis.  This mechanical cue is transduced sequentially by Discoidin Domain Receptor 1 (DDR1), c-Jun N-terminal kinase 1 (JNK1), and phosphorylated JunB, which binds to and activates two breast cancer-associated aromatase promoters.  In contrast, elevated cell contractility due to actin stress fiber formation dampens aromatase transcription.  Mechanically stimulated stromal estrogen production enhances estrogen-dependent transcription in ER+ tumor cells and promotes their growth.  This novel mechanotransduction pathway underlies communications between ECM, stromal hormone output, and cancer cell growth within the same microenvironment.

overall_design: Total RNA was isolated from primary adipose stromal cells after 2d culture or 3d Collagen gel for 21 hours. Triplicates for each conditioned were analyzed

first: Rong

last: Li

first: Sagar

last: Ghosh


title: Identification of rice ethylene-response mutants and characterization of MHZ7 in distinct ethylene response and yield trait regulation

status: Public on Apr 04 2013

city: beijing

first: Jinsong

last: Zhang

address: No.1 West Beichen Road,Chaoyang District

institute: IGDB

summary: Ethylene plays major roles in adaptive growth of rice plants in water-saturated soil; however, ethylene signaling in rice is largely unclear. Here, we report identification and characterization of ethylene-response mutants based on distinct ethylene-response phenotypes of dark-grown rice seedlings.

overall_design: The seeds were soaked in tap-water and germinated at 37°C in the dark for two days (change the water daily). For ethylene treatment, we reduced the amount of water to 1.5-1.7cm below the seeds.Three-day old seedlings were treated with ethylene (10 ppm) for 8 hours at 28°C in the dark. Seedling grown in the air  was used as control. We isolated RNA from roots and shoots of wild-type and mutant.

first: Biao

last: Ma

first: Jin-Song


title: Genetic profiling to predict recurrence of early cervical cancer

status: Public on May 01 2013

city: Seoul

first: Yuyoung

last: Lee

address: 50 Irwon-Dong, Gangnam-Gu

country: South Korea

institute: SMC

summary:
We compared the prediction powers for disease recurrence between gene set prognostic model and clinical prognostic model developed in a single large population to see whether genetic quantitative approach will have significant prognostic role in early cervical cancer patients who underwent radical hysterectomy with or without adjuvant therapies.
Gene set model to predict disease free survival of early cervical cancer was developed using DASL assay dataset from the cohort of early cervical cancer patients who were treated with radical surgery with or without adjuvant therapies at the Samsung Medical Center of Sungkyunkwan University School of Medicine in Seoul, Korea, between January 2002 and September 2008. Clinical prediction model was also developed in the same cohort and the ability of predicting recurrence from each model was compared.

overall_design: Adequate DASL assay profiles were obtained in 300 patients and we selected 12 genes for the gene set model. When the proportions of patients were categorized as having a low or high risk by the prognostic scores using these genes from LOOCV procedure, the Kaplan-Meier curve showed significant different recurrence rate between two groups. Clinical model was developed using FIGO stage as well as post-surgical pathological findings.