title: Global regulatory networks active in Pseudomonas syringae B728 during leaf colonization and in response to target environmental stresses: the GacS, SalA, RetS, AlgU, HrpL, RpoN, RpoS, AhlR and AefR regulons

status: Public on Sep 01 2014

city: Ames

first: Gwyn

middle: A

last: Beattie

state: IA

address: 207 Science I

department: Dept of Plant Pathology & Microbiology

institute: Iowa State University

summary: The plant pathogen Pseudomonas syringae pv. syringae B728a grows and survives on leaf surfaces and in the leaf apoplast of its host, bean. Global transcriptome profiling was used to understand the contribution of distinct regulators to B728a fitness and pathogenicity.  We performed a transcriptome analysis of B728a and nine regulator mutants recovered from the surface and interior of leaves and exposed to various environmental stresses in culture. These mutants were nonpolar deletion mutants lacking a single target regulator gene: ahlR, aefR, gacS, retS, salA, rpoS, algU, hrpL and rpoN. RNA was collected from cells of these strains that were exposed to five treatments in vitro, namely a basal medium, sodium chloride to confer an osmotic stress, hydrogen peroxide to confer an oxidative stress, iron limitation, and nitrogen limitation, and were recovered from two bean (Phaseolus vulgaris L.) leaf sites, namely epiphytic sites after leaf surface inoculation and 72 h of growth and apoplastic sites after leaf infiltration and 48 h of growth. The results indicated that the quorum-sensing regulators AhlR and AefR influenced few genes in planta or in vitro. In contrast, GacS and a downstream regulator SalA formed a large regulatory network that included a branch that regulated diverse traits and was independent of plant-specific environmental signals, and a signal-dependent branch that positively regulated secondary metabolite genes and negatively regulated the type III secretion system. RetS functioned almost exclusively to repress secondary metabolite genes in cells in culture but not on leaves. SalA functioned as a central regulator of iron status, based on its reciprocal regulation of pyoverdine and achromobactin genes, and also sulfur uptake, suggesting a role in the iron-sulfur balance. Among the sigma factors examined, AlgU influenced many more genes than RpoS, and most AlgU-regulated genes depended on RpoN. RpoN differentially impacted many AlgU- and GacS-activated genes in cells recovered from apoplastic versus epiphytic sites, suggesting differences in environmental signals or bacterial stress status in these two habitats. Collectively, our findings illustrate a central role for GacS, SalA, RpoN and AlgU in global regulation in B728a in planta and a high level of plasticity in their response to distinct environmental signals.

overall_design:
RNA was collected from cells of B728a and nine regulator mutants following exposure to seven treatments. Each treatment was performed using two biological replicates, with B728a, ∆rpoS, ∆algU, ∆hrpL and ∆rpoN examined in one laboratory, designated lab A, B728a, ∆ahlR and ∆aefR examined in lab B, and B728a, ∆retS, ∆gacS and ∆salA examined in lab C.  Experimental methods were standardized across the three laboratories.  For the in vitro treatments, exponential cells from two independent cultures were each exposed to the five treatments.  For each treatment, the cells originating from the two cultures were pooled and the RNA was extracted; this was repeated in its entirety and the two RNA pools were combined.  The resulting RNA representing four independent cultures served as a single biological replicate.  Two biological replicates for each strain in each treatment were generated in this manner, with B728a included as a strain in each of the laboratories.
Epiphytic populations of B728a and the nine regulator mutants were established following spray inoculation onto bean leaves and subsequent incubation; the epiphytic cells recovered from 400 to 600 leaves inoculated at one time served as a biological replicate, and the procedure was repeated to provide two biological replicates.  Due to the availability of facilities, all of the epiphytic treatments were conducted at a single laboratory, lab B, with cultures provided from each of the other laboratories, and the cell pellets were returned to those laboratories for RNA extraction and analysis.
Apoplastic B728a populations were established following vacuum infiltration into bean leaves and subsequent incubation; the apoplastic cells recovered from 40 to 80 leaves inoculated at one time served as a biological replicate, and two biological replicates were generated at each of the three laboratories.
The RNA from all treatments was submitted to Roche Nimblegen, Inc where it was labeled and hybridized to an ORF-based microarray that included 5,071 ORFs and 61 putative sRNAs, with each ORF represented by 14 60-mer nucleotide probes.  The fluorescence intensity for each probe was measured and subjected to robust multiarray averaging, which included adjustment for the background intensity, log2 transformation, quantile normalization and median polishing, and a robust estimated mean value was determined for each ORF and putative sRNA on the array.

first: Xilan

last: Yu

middle: P

last: Lund

first: Russell

last: Scott

first: Jessica

last: Greenwald

first: Angela

middle: H

last: Records

first: Dan

last: Nettleton

last: Lindow

first: Dennis

middle: C

last: Gross


title: Analysis of gene expression changes when KLF6 is overexpressed in HepG2 cells

status: Public on Aug 22 2014

city: Newcastle Upon Tyne

first: Gary

last: Beale

state: Tyne and Wear

address: Framlington place

department: NICR

country: United Kingdom

institute: Newcastle University

summary: KLF6 was overexpressed using an adenoviral delivery system. Overexpression was confirmed at 12, 24, 48 and 72 hours post infection by RT-PCR and Western Blot analysis. Codelink Whole genome microarrays were used to analyse changes in expression resulting from KLF6 overexpression.

overall_design: RNA Samples were taken at 48 and 72 hours from samples oeverexpressing KLF6 and the empty vector control pBabe

first: Helen

last: Reeves

first: Pamela

last: Macdonald


title: Gene expression profile associated with PTB-mediated transdifferentiation of human fibroblast cells into neurons

status: Public on Sep 22 2014

city: London

first: Yuming

last: Wang

address: South Mimms

department: Mechanisms of Transcription Laboratory

institute: Cancer Research UK

summary:
Fibroblasts can be directly converted into neurons in vitro by depletion of nPTB, the reprogramming process induces neuronal gene expression while inhibits fibroblast gene expression. Human fibroblasts lacking CSB can not be converted into neurons, unless CSB gene was introduced. This study characterizes the CSB-dependent gene expression alterations during reprogramming.
Using Nimblegen microarray we identified differentially expressed genes in induced neurons from wild type CSB reconstituted fibroblasts, and we proved that the difference in gene expression after reprogramming was not observed in CS1AN cells.

overall_design: The Nimblegen human 12 x 135K gene expression array was used to define gene expression profiles in PTB-depleted human fibroblasts lacking CSB or expressing reconstituted CSB.

first: Probir

last: Chakravarty

first: Jesper

last: Svejstrup


title: Broad shifts in gene expression during early postnatal life are associated with shifts in histone methylation patterns

status: Public on Aug 04 2014

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

country: USA

institute: NIDDK/NIH

type: Expression profiling by genome tiling array

summary: During early postnatal life, extensive changes in gene expression occur concomitantly in multiple major organs, indicating the existence of a common core developmental genetic program. This program includes hundreds of growth-promoting genes that are downregulated with age in liver, kidney, lung, and heart, and there is evidence that this component of the program drives the widespread decline in cell proliferation that occurs in juvenile life, as organs approach adult sizes. To investigate epigenetic changes that might orchestrate this program, we performed chromatin immunoprecipitation-promoter tiling array to assess temporal changes in histone H3K4 and H3K27 trimethylation (me3) at promoter regions throughout the genome in kidney and lung, comparing 1- to 4-wk-old mice. We found extensive genome-wide shifts in H3K4me3 and H3K27me3 occurring with age in both kidney and lung. The number of genes with concordant changes in the two organs was far greater than expected by chance. Temporal changes in H3K4me3 showed a strong, positive association with changes in gene expression, assessed by microarray, whereas changes in H3K27me3 showed a negative association. Gene ontology analysis indicated that shifts in specific histone methylation marks were associated with specific developmental functions. Of particular interest, genes with decreases in H3K4me3 with age in both organs were strongly implicated in cell cycle and cell proliferation functions. Taken together, the findings suggest that the common core developmental program of gene expression which occurs in multiple organs during juvenile life is associated with a common core developmental program of histone methylation.  In particular, declining H3K4me3 is strongly associated with gene downregulation and occurs in the promoter regions of many growth-regulating genes, suggesting that this change in histone methylation may contribute to the component of the genetic program that drives juvenile body growth deceleration.

overall_design: Tissues samples were collect from Lung (1 and 4 week old) and Kindey (1 and 4 week old) respectively with four biological replications of mice that were collected, frozen in liquid nitrogen, and stored at -70 °C

first: Julian

last: Lui

first: Weiping

first: Jeffrey

last: Baron


title: Transformation of quiescent adult oligodendrocyte precursor cells into malignant glioma through a multi-step reactivation process

status: Public on Sep 09 2014

city: Eugene

first: Rui

middle: Pedro

last: Galvao

state: Oregon

address: 1229 University of Oregon

institute: University of Oregon

summary: How malignant gliomas arise in a mature brain remains a mystery, hindering the development of preventive and therapeutic interventions. We previously showed that oligodendrocyte precursor cells (OPCs) can be transformed into glioma when mutations are introduced perinatally. However, adult OPCs rarely proliferate compared to their perinatal counterparts. Whether these relatively quiescent cells have the potential to transform is unknown, which is a critical question considering the late onset of human glioma. Additionally, the events taking place between initial mutation and a fully developed tumor mass (pre-malignant phase) are particularly poorly understood in glioma. Here we used a temporally controllable Cre transgene to delete p53 and NF1 specifically in adult OPCs, and demonstrated that these cells consistently give rise to malignant gliomas. To investigate the transforming process of quiescent adult OPCs, we then tracked these cells throughout the pre-malignant phase, which revealed a dynamic multi-step transformation, starting with rapid but transient hyper-proliferative reactivation, followed by a long period of dormancy, then final malignant transformation. Using pharmacological approaches, we discovered that mTOR signaling is critical for both the initial OPC reactivation step and late stage tumor cell proliferation, and thus might be a potential target for both glioma prevention and treatment. In summary, our results firmly establish the transforming potential of adult OPCs, and reveal an actionable multi-phasic reactivation process that turns slowly dividing OPCs into malignant gliomas.

overall_design: 44K Mouse Development Oligo Microarrays from Agilent Technologies were used for microarray analysis. For each experiment, total RNA was fluorescently labeled and hybridized directly against a common reference sample generated from the RNA pool of four WT P17 mouse brain neocortex.

first: Anita

last: Kasina

first: Robert

middle: S

last: McNeill

first: Jordan

middle: E

last: Harbin

first: Oded

last: Foreman

first: Roel

middle: G

last: Verhaak

first: Akiko

last: Nishiyama

first: C

middle: R

last: Miller

first: Hui

last: Zong


title: Gene expression profile during SH-SY5Y neuroblastoma differentiation

summary:
Neuroblastoma cells SH-SY5Y undergoes a morphology change upon retinoic acid (RA) treatment, the neurite outgrowth characteristic in undividing cells is accompanied by cell cycle arrest and neuronal markers expression, controlled by a precise dynamic molecular circuits. Depletion of CSB in SH-SY5Y cells leads to differentiation defects. This study examines the temporal gene expression profile during differentiation.
Using Nimblegen microarray we characterized the gene expression profiles before and after RA treatment in both wild type and CSB-KD SH-SY5Y cells, and we identified the difference in gene expression between wild type and CSB-KD cells underlying the differentiation defects induced by CSB depletion.

overall_design: The Nimblegen human 12 x 135K gene expression arrays were used to define gene expression profiles of wild type and CSB-KD SH-SY5Y cells before and after RA treatment during a nine-day culture period.


title: Bacteroides fragilis in vivo gene expression

status: Public on Aug 07 2014

city: Greenville

first: Charles

middle: Jeffrey

last: Smith

state: NC

address: 600 Moye Blvd.

department: Microbiology & Immunology

institute: East Carolina University

summary: Compare BF638R gene expression during growth in vivo in a rat tissue cage/artificial abscess model, to cells grown in vitro in minimal defined media with either glucose or mucin glycans as sole carbon/energy source

overall_design: 11 chip study with 8 technical replicates on each chip comparing gene expression in vivo in a rat tissue cage model over an 8 day period to in vitro cultures grown to mid-log phase in defined media

middle: J

first: Yanlu

last: Cao


title: Direct genesis of functional rodent and human Schwann cells from skin mesenchymal precursors (rat)

status: Public on Aug 01 2014

city: Toronto

first: Freda

state: ON

address: 555 University Avenue

country: Canada

institute: Hospital for Sick Children

summary: Recent reports of directed reprogramming have raised questions about the stability of cell lineages.  Here, we have addressed this issue, focusing upon skin-derived precursors (SKPs), a dermally-derived precursor cell.  We show by lineage tracing that murine SKPs from dorsal skin originate from mesenchymal and not neural crest-derived cells.  These mesenchymally-derived SKPs can, without genetic manipulation, generate functional Schwann cells, a neural crest cell type, and are highly similar at the transcriptional level to Schwann cells isolated from the peripheral nerve.  This is not a mouse-specific phenomenon, since human SKPs that are highly similar at the transcriptome level can be made from facial (neural crest-derived) and foreskin (mesodermally-derived) dermis, and the mesodermally-derived SKPs can make myelinating Schwann cells.  Thus, non-neural crest-derived mesenchymal precursors can differentiate into bona fide peripheral glia in the absence of genetic manipulation, suggesting that developmentally-defined lineage boundaries are more flexible than widely thought.

overall_design: We obtained 3 independent samples of nerve Schwann cells, SKP-derived Schwann cells, and Dorsal Trunk SKPs, each, from adult SD rats.  Primary cells were isolated and cultured, and RNA was collected from those cultured samples.  RNA samples deriving from these cells were analyzed on the Affymetrix Rat Gene 1.0 ST Array.

first: Matthew

last: Krause

first: Shaalee

last: Dworski

first: Konstantin

last: Feinberg

first: Karen

last: Jones

first: Adam

last: Johnston

first: Smitha

last: Paul

first: Maryline

last: Paris

first: Elior

last: Peles

first: Darius

last: Bagli

first: Christopher

last: Forrest

first: David

last: Kaplan

middle: D


title: lncRNA and mRNA expression data in peripheral blood sampled from MDD patients

status: Public on Oct 20 2014

city: TaiYuan

first: Zhifen

last: Liu

state: Shanxi

address: 85 Jiefang South Road

department: Psychiatry

country: China

institute: 1st hospital of Shanxi Medical University

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

summary:
Long noncoding RNAs (lncRNAs) are pervasively transcribed and have a direct role in the regulation of genes involved in neural plasticity and cognitive function. Moreover, alterations in the expression of several lncRNAs have been observed in some psychiatric disorders. However, changes in the expression of regulatory lncRNAs in MDD have not yet been reported.
Using microarrays, we profiled the expression of 51513 lncRNAs and 35123 mRNAs in peripheral blood sampled from MDD patients as well as demographically-matched controls.

overall_design: This study recruited a total of 10 patients and 12 coupled healthy controls. The patients were recruited from outpatients of the department of psychiatry at the First Hospital of Shanxi Medical University and the controls were recruited from the community nearby. All participants were Chinese of Han origin and came from the same geographic areas in northern China.


title: Real-time quantitative PCR analysis of mRNA from the colon of WT, Nod2-/-, Pglyrp3-/-, and Pglyrp3-/-Nod2-/- mice treated with oral DSS

status: Public on Aug 08 2014

city: Gary

first: Roman

last: Dziarski

state: IN

address: 3400 Broadway

institute: Indiana University School of Medicine-Northwest

summary: Wild type (WT), Nod2-/-, Pglyrp3-/-, and Pglyrp3-/-Nod2-/- mice (BALB/c) were treated with oral 5% dextran sodium sulfate (DSS) for 48, 72, or 96 hrs, their colons were removed and homogenized, and RNA was isolated using the TRIZOL method. Quantitative reverse transcription real-time PCR (qRT-PCR) was used to quantify the amounts of mRNA in the colon using the inflammatory gene expression RT2 Profiler PCR Array from Qiagen/SA Biosciences.

overall_design: qRT-PCR gene expression profiling

first: Fareeha

last: Zulfiqar

first: Xuefang

last: Jing

first: Shin

middle: Y

last: Park

first: Dipika

last: Gupta


title: Gene expression profile of fibroblasts derived from CS patient

first: Yuming

last: Wang

summary:
As the causative gene for cockayne syndrome, CSB has a well-characerized function in transcription-coupled nucleotide excision repair. However, the complex neurological abnormalities that affect CS patients can not be simply explained by the DNA repair defects. CSB is also involved in RNAP II transcription regulation. This study characterizes the gene expression signatures affected by CSB protein.
Using Nimblegen microarray we identified differentially expressed genes in human fibroblasts derived from CS patients as compared to CSB reconstituted cell lines (wild type).

overall_design: The Nimblegen human 12 x 135K gene expression array was used to define gene expression profiles in human fibroblasts either lacking CSB or expressing exogenous CSB. Two independent CSB-deficient cell lines and two independent CSB wild type cell lines were tested in this study.

first: Probir

last: Chakravarty

first: Jesper

last: Svejstrup


title: MiRNA expression data from SOX2 knock-out 2102Ep and NTera-2 human embryonal carcinoma cell lines

status: Public on Aug 15 2014

city: Dublin

first: Sebastian

last: Vencken

address: Catherine McAuley Centre, Nelson Street

department: Clinical Research Centre

country: Ireland

institute: University College Dublin

type:
Expression profiling by RT-PCR
Other

summary:
SOX2 is an oncogene and a core pluripotency transcription factor. SOX2 has multiple roles in various malignancies, in the maintenance of pluripotency and during various stages of embryonic development. Human embryonal carcinoma cells express SOX2 and the loss of this results in their differentiation.
We silenced SOX2 in two human embryonal carcinoma cell lines and measured the differential expression of 754 unique mature miRNAs. This revealed the deregulation of many oncomiRs, tumour suppressor miRNAs and developmental miRNAs, including those belonging to the C19MC cluster.

overall_design: A specific and validated siRNA against SOX2 was chemically transfected in undifferentiated 2102Ep and NTera-2 embryonal carcinoma cell lines. After three days of incubation under normal growth conditions we used Applied Biosystems TaqMan Low Density Arrays A/B cards to measure mature miRNA expression in three biological replicates of each cell line which we compared to miRNA expression in identical samples transfected with a non-targeting, scrambled control siRNA. SOX2 silencing was validated using qRT-PCR and Western blot prior to whole-genome expression analysis.

middle: F

first: Praveen

last: Sethupathy

first: Gordon

last: Blackshields

first: Cathy

last: Spillane

first: Salah

last: ElBaruni

first: Orla

last: Sheils

first: Michael

last: Gallagher

first: John

last: O’Leary


title: Expression data of articular and growth plate cartilage zones in 10-day-old rat proximal tibial epiphysis

status: Public on Aug 16 2014

city: Stockholm

last: Chau

address: Astrid Lindgren Children's Hospital, Q2:08

department: Department of Women's and Children's Health

country: Sweden

institute: Karolinska Institutet

summary:
Articular and growth plate cartilage have comparable structures consisting of three distinct layers of chondrocytes, suggesting similar differentiation programs and therefore similar gene expression profiles.  To address this hypothesis and to explore transcriptional changes that occur during the onset of articular and growth plate cartilage divergence, we used microdissection of 10-day-old rat proximal tibial epiphyses, microarray analysis, and bioinformatics to compare gene expression profiles in individual layers of articular and growth plate cartilage.
We found that many genes that were spatially upregulated in intermediate/deep zone of articular cartilage were also spatially upregulated in resting zone of growth plate cartilage (overlap greater than expected by chance, P < 0.001).  Interestingly, superficial zone of articular cartilage showed an expression profile with similarities to both proliferative and hypertrophic zones of growth plate cartilage (P < 0.001 each).  Additionally, significant numbers of known proliferative zone markers (3 out of 6) and hypertrophic zone markers (27 out of 126) were spatially upregulated in superficial zone compared to intermediate/deep zone (more than expected by chance, P < 0.001 each).  In conclusion, we provide evidence that intermediate/deep zone of articular cartilage has a gene expression profile more similar to resting zone of growth plate cartilage, whereas superficial zone has a gene expression profile more similar to proliferative and hypertrophic zones.

overall_design: 10-day-old rat proximal tibial epiphyses were manually microdissected into articular cartilage superficial (SZ) and intermediate/deep (IDZ) zones and growth plate cartilage resting zone (RZ) for total RNA extraction and hybridization on Affymetrix microarrays.  We used 10-day-old animals because, at this age, the secondary ossification center has recently begun to form and divides the epiphysis into articular cartilage distally and growth plate cartilage more centrally.  The 4 SZ samples were taken from animals 5-8, respectively, whereas the 4 IDZ and 4 RZ samples were each taken from animals 1-2, 3-4, 5-6, and 7-8, respectively.

first: Ola

last: Nilsson


title: Nucleosome occupancy changes in mammalian cell differentiation and reprogramming (microarray)

status: Public on Jul 31 2014

city: Boston

first: Robert

last: Kingston

state: MA

address: 185 Cambridge Street

institute: Massachusetts General Hospital

summary: Embryonic stem cells (ESCs) and induced-pluripotent stem cells (iPSCs) self-renew and differentiate into an array of cell types in vitro and in vivo. A complex network of genetic and epigenetic pathways regulates the self-renewal and differentiation of these pluripotent cells, and the structure and covalent modifications of chromatin play a prominent role in this process. We examine nucleosome occupancy in mouse and human embryonic stem cells (ESCs), induced-pluripotent stem cells (iPSCs), and differentiated cell types using MNase-seq. To address variability inherent in this technique, we developed a bioinformatic approach that enabled the identification of regions of difference (RoD) in nucleosome occupancy between pluripotent and somatic cells. The majority of changes in nucleosomal signatures that occur in differentiation are reset during reprogramming. We conclude that changes in nucleosome occupancy are a hallmark of pluripotency and likely identify key regulatory regions that play a role in determining cell identity.

overall_design: A six chip study using total RNA recovered from three cell types with 2 replicates each

first: Jason

last: West

first: April

last: Cook

first: Burak

last: Alver

first: Mattias

last: Stadtfeld

first: Aimee

middle: M

last: Deaton

first: Konrad

last: Hochedlinger

first: Peter

last: Tolstorukov


title: TNFalpha and IL1beta stimulate differential gene expression in endometrial stromal cells

city: Vermillion

first: Kathleen

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

institute: University of South Dakota

summary: Cytokines are implicated in the development of inflammatory diseases such as endometriosis. This project was designed to test the hypothesis that specific cytokines that are secreted by macrophages, such as tumor necrosis factor α (TNFα) and interleukin 1 beta (IL1β), cause gene expression changes in endometrial stromal cells. Telomerase-immortalized human endometrial stromal cells (T-HESC) were treated with TNFα (5ng/ml) ± IL1β (1ng/ml). DNA microarray and real time RT-PCR were used to study the gene expression changes in T-HESC cells. Two hundred and nineteen genes featuring in various gene ontologies were found to be differentially expressed in T-HESC cells treated with TNFα ± ILIβ. The gene ontologies included functions expected to be associated with the development of endometriosis such as peptidases, cell adhesion, cell death/apoptosis, cell cycle, growth factors, cytoskeletal organization, defense/immune system, signal transduction, and transcriptional regulation.  The differential expression of 4 genes (interleukin 8 (IL8), interleukin 6 (IL6), IL1β and matrix metalloproteinase (MMP3) was confirmed by real time RT-PCR. All four genes were up-regulated in response to TNFα ± ILIβ in T-HESC cells. The effect of TNFα ± ILIβ on migration and invasion of T-HESC cells, as measured with Boyden chambers, was not affected by treatment with these cytokines.

overall_design:
Goal of the experiment:  To examine differential gene expression in telomerase-immortalized human endometrial stromal cells (T-HESC) in response to treatment with tumor necrosis factor alpha (TNFα) ± interleukin 1β (IL1β).
Keywords:  cytokines, endometrial stromal cells, endometriosis

Experimental factors:  cytokine treatment

Experimental design: The telomerase immortalized - human endometrial stromal cell line (T-HESC, ATCC #CRL-4003, Manassas, VA) was used for all experiments.  The cells were treated with vehicle or with the cytokines, TNFα (5ng/ml) ± IL1β (1ng/ml).  Three different passages of cells were collected for each treatment group to provide biological replicates.

Quality control steps:  The cRNA that was synthesized from each cell culture sample was used for hybridization to a single CodeLink (Applied Microarrays, Tempe, AZ) whole human genome microarray.  Only one sample was hybridized with each slide and only one dye (Alexa 647) was used so no dye swaps were necessary.  Bacterial control spikes were used as per manufacturer's instructions.

Samples used, extract preparation and labeling:
The origin of each biological sample:  The samples were cultured cells of the telomerase-immortalized human endometrial stromal cell (T-HESC) line obtained from ATCC (CRL-4003).

Manipulations of biological samples and protocols used:  The telomerase immortalized - human endometrial stromal cell line (T-HESC, ATCC #CRL-4003, Manassas, VA) was used for all experiments. The cells were routinely maintained in Dulbecco’s modified Eagle’s medium (DMEM, Sigma, St. Louis, MO) with 10% fetal bovine serum albumin (FBS, Hyclone, South Logan, UT), insulin, selenious acid, transferrin, bovine serum albumin and linoleic acid (ITS+ Premix, BD Biosciences, Bedford, MA), puromycin (Cellgro, Manassas, VA) and penicillin/ streptomycin (Hyclone, South Logan, UT). After the cells reached 80% confluence they were starved for 24 hours in T-HESC starvation medium (DMEM+ ITS+ puromycin+ penicillin/streptomycin) before treatment.  The cells were treated with vehicle or with TNFα (5ng/ml) alone, IL1β (1ng/ml) alone, or with the two cytokines combined at the same concentrations for 48 hours.  Total RNA was then isolated from the cell cultures for use in the DNA microarray experiments.  Each treatment was carried out with 3 different passages of cells.

Technical protocols:  The cultured endometrial cells were rinsed with PBS and TRI reagent (MRC) was added.  The cells were scraped into tubes and centrifuged in the presence of bromochloropropane and sodium acetate.  The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity was evaluated with the RNA 6000 NanoLabChip in an Agilent Bioanalyzer.

	Labeled cRNA was prepared using the MessageAmp II-Biotin enhanced kit (Ambion).  1.0 microgram of total T-HESC cell RNA was mixed with bacterial control RNA spikes and primed with T7 oligo(dT) primer for 10 min at 70C.  (The bacterial control spikes included araB, entF, fixB, gnd, hisB, and leuB.)  The first strand of cDNA was synthesized with first strand buffer, dNTP mix, RNase inhibitor, and reverse transcriptase for 2 h at 42C.  The second strand cDNA synthesis reaction was prepared using second strand buffer, dNTP mix, DNA polymerase mix, and RNase H; the reaction was carried out for 2h at 16C.  The double-stranded cDNA was purified on columns.  The double-stranded cDNA was mixed with T7 reaction buffer, T7 ATP, T7 GTP, T7 UTP, T7 CTP, biotin-11-UTP, and T7 enzyme mix for the synthesis of cRNA.  The cRNA synthesis reaction was terminated after 14h at 37C by purifying the cRNA on columns.  The concentration of cRNA was determined by spectrophotometry.

Hybridization procedures and parameters:  10 micrograms of cRNA was mixed with fragmentation buffer and heated to 94°C for 20 min.  The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides, and hybridized for 18 hours at 37°C.
	The slides were washed in 0.75x TNT (Tris-HCl, NaCl, Tween-20) at 46°C for 1h then incubated with streptavidin-Alexa 647 fluorescent dye for 30 min at room temperature.  The Alexa fluor was prepared in TNB blocking buffer (0.1M Tris-HCl, 0.15M NaCL, 0.5% NEN Blocking Reagent-PerkinElmer)  The slides were then washed 4 times for 5 min each in 1x TNT each and once in 0.05% Tween 20 for 20 sec.  The slides were dried by centrifugation and scanned in an Axon GenePix 4000B scanner.

first: Abha

last: Chalpe

first: Chad

last: Law

first: Jennifer

middle: N

last: Dumdie

first: Keith

last: Hansen


title: MicroRNA Expression Differences In Human Hematopoietic Cell Lineages Enable Regulated Transgene Expression (Primary cell)

city: Philadelphia

first: Paul

last: Bray

state: PENNSYLVANIA

address: 1015 Chestnut Street

department: Hematology

institute: Thomas Jefferson University

summary: miRNA content normal hematopoietic cells from 5 healthy individuals.

overall_design: In the study presented here, we report the miRNA content of highly purified normal hematopoietic cells from the same individuals. We provided the miRNA profile of peripheral blood components such as, platelets, T-cell, B-cell, granulocytes and erythrocytes.

first: Raul

last: Teruel-Montoya


title: Transcriptome analysis of medaka germ cells and gonadal somatic cells during the gonadal sex differentiation.

status: Public on Aug 31 2014

city: Okazaki

first: Toshiya

last: Nishimura

address: 5-1 Higashiyama Myodaiji-cho

country: Japan

institute: National Institute for Basic Biology

summary: Microarray analysis was performed using germ cells and gonadal somatic cells  isolated by Fluorescence Activated Cell Sorter (FACS) from XX and XY embryos at st.33 and st.35.

overall_design: Medaka germ cells (olvas-EGFP) and somatic cells (sox9b-DsRed) were isolated by FACS. The microarray experiments were done using three independent biological replicates.

first: Taro

middle: L

last: Saito

first: Jun

last: Yoshimura

first: Shinichi

last: Morishita

first: Tatsuya

last: Tsukahara

first: Shuji

last: Shigenobu

first: Minoru

last: Tanaka


title: MicroRNA Expression Differences In Human Hematopoietic Cell Lineages Enable Regulated Transgene Expression

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

overall_design: Refer to individual Series


title: Expression data measured by custom Nanostring gene set of CD4+ T cells from healthy individuals stimulated with anti-CD3/CD28 with or without IFNb or Th17 polarizing cytokines

status: Public on Aug 28 2014

first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary:
Variation in individuals' adaptive immune response is believed to influence susceptibility to complex diseases in humans. The genetic basis of such variation is poorly understood.
We measured gene expression from resting and activated CD4+ T cells derived from the peripheral blood of 348 healthy individuals. We activated the primary T cells with anti-CD3/CD28 beads.

overall_design: We collected peripheral blood from each human donor. We isolated peripheral blood mononuclear cells by Ficoll, and negatively selected for CD4+ T cells using RosettaSep. We then either left cells unstimulated or stimulated them with beads conjugated with anti-CD3 and anti-CD28 either without additional cytokines, or with IFNb, or with Th17 cocktail. Cells were harvested at 0hr, 4hr (anti-CD3/CD28 +/- IFNb) or 48hr (anti-CD3/CD28 +/- Th17) and lysed, and RNA was isolated to be profiled on NanoString.

first: Chun

last: Ye

first: Ting

last: Feng

first: Aviv

last: Regev

first: Christophe

last: Benoist


title: MicroRNA Expression Differences In Human Hematopoietic Cell Lineages Enable Regulated Transgene Expression (cell line)

summary: miRNA content of 5 different hematological cell lines

overall_design: In the study presented here, we provided the miRNA profile of different hemathological cell lines such as Meg-01, Jurkat, Raji, U937 and K562.


title: Time-course microarray study of Cryptococcus neoformans var. neoformans spore germination

city: Madison

first: Christina

last: Hull

state: WI

address: 440 Henry Mall

department: Biomolecular Chemistry, Medical Microbiology and Immunology

institute: University of Wisconsin- Madison

summary: To identify the genome-wide transcriptional changes that occur throughout germination of C. neoformans spores, we conducted a time-course microarray experiment spanning six timepoints to generate a temporal expression pattern for each known gene. Spores were placed in rich medium and allowed to germinate for 10 hours, when they start to replicate as yeast. Each time point was flash frozen in liquid nitrogen and RNA was harvested for each time point at the same time. Microarray hybridizations were conducted in a reference pool design, where each time point was mixed together in equal amounts to make a reference pool sample. Then each time point was hybrdized against the reference pool. Characterization of the genes and pathways that are regulated during germination of this ubiquitous fungal pathogen will allow us to better understand how infectious spores resume vegetative growth, a process that likely is critical for interaction between C. neoformans and a host.

overall_design: The experiment spanned six time points of germination: 0 hours (dormant spores), 2 hours, 4 hours, 6 hours, 8 hours and 10 hours. Hybridizations were conducted in a reference pool design, with  a mixture of each sample serving as the reference pool. This design results in 6 experimental comparisons: 0 Hr vs Reference pool (REF), 2 Hhr vs REF, 4 Hr vs REF, 6 Hr vs REF, 8 Hr vs Ref, and 10 Hr vs REF. Each comparison consistent of duplicate hybridizations with dye swaps. Arrays contain duplicate genomes, resulting in eight-fold coverage within each comparison. (total of 24 hybridizations)

first: Michael

last: Botts


title: Suberin degradation by Aspergillus nidulans

city: Lisboa

first: Cristina

middle: Silva

last: Pereira

address: Rua da Quinta Grande nº6

country: Portugal

institute: Instituto de Tecnologia Química e Biológica (ITQB)

summary: The study aims essentially at the characterisation of suberin degradation mechanisms by Aspergillus nidulans, at a fundamental level.  Suberin is an important protective barrier in plant, thus the study of its biodegradation significantly impacts on phytopatology.  In addition, fungal suberin degrading enzymes might provide important insights to develop new waste management, bioremediation and biodeterioration prevention strategies.

platform_organism:
Aspergillus nidulans FGSC A4
Neurospora crassa OR74A

overall_design: The Aspergillus nidulans cultures were grown for two days in mineral media containing glucose (T0).  After this time point, the extracellular media was replaced by fresh mineral media containing suberin as the sole carbon source and allowed to incubate for two (T1), four (T2) and six (T3) days.  To investigate the mechanisms by which the fungus was able to degrade suberin, the fungal transcriptome (three biological replicates) was analysed using Affymetrix microarrays.  Pair-wise comparisons were used to identify the set of genes with altered expression levels between the control (grown on glucose) and during growth on suberin for two, four or six days.

first: Jörg

last: Becker

first: Paula

last: Alves

first: Isabel

last: Martins

first: Diego

middle: O

last: Hartmann

first: Helga

last: Garcia

first: Ji

last: He


title: Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

city: Cincinnati

first: Matthew

middle: Tyson

last: Weirauch

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital

summary: The DNA sequence preferences of the vast majority of eukaryotic transcription factors (TFs) are unknown.  Using an approach designed to broadly sample both DNA-binding domain types and eukaryotic clades, we have determined DNA-binding motifs for 1,033 TFs from 131 diverse eukaryotes, encompassing 54 domain types.  Closely related orthologs and paralogs typically have very similar sequence preferences; this property allows inference of motifs for roughly one third of the 166,851 known or predicted eukaryotic TFs.  While the origins of most motifs can be dated to hundreds of millions of years ago, we also characterize more recent TF expansions.  Sequences matching the motifs are enriched upstream of TSS in most eukaryotic lineages, and at informative eQTL SNPs in Arabidopsis promoters, demonstrating their utility in mapping transcriptional networks.  The motifs are housed at http://cisbp.ccbr.utoronto.ca

overall_design: Protein binding microarray (PBM) experiments were performed for a set of 1048 diverse eukaryotic transcription factors. Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to two double-stranded 44K Agilent microarrays, each containing a different DeBruijn sequence design, in order to determine their sequence preferences. Details of the PBM protocol are described in Berger et al., Nature Biotechnology 2006.

first: Ally

first: Mihai

last: Albu

first: Hamed

last: Najafabadi

first: Atina

last: Cote

first: Alejandro

last: Montenegro-Montero

first: Philipp

last: Drewe

first: Sam

last: Lambert

first: Ishminder

last: Mann

first: Kate

last: Cook

first: Hong

last: Zheng

first: Alejandra

last: Goity

first: Harm

last: van Bakel

first: Jean-Claude

last: Lozano

first: Mary

last: Galli

first: Mathew

last: Lewsey

first: Eryong

last: Huang

first: Tuhin

last: Mukherjee

first: Xiaoting

last: Chen

first: John

last: Reece-Hoyes

first: Sridhar

last: Govindarajan

first: Gadi

last: Shaulsky

first: Albertha

last: Walhout

first: François-Yves

last: Bouget

first: Gunnar

last: Ratsch

first: Luis

last: Larrondo

first: Joseph

last: Ecker

first: Timothy

last: Hughes


title: DNA microarray analysis of global gene regulation by AdpAch in Streptomyces chattanoogensis

status: Public on Jul 29 2014

city: Hangzhou

first: Pin

last: Yu

state: Zhejiang Province

address: College of Life Sciences, Institute of Biochemistry, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China

department: College of Life Sciences

institute: Zhejiang University

summary: The effects of AdpAch on transcription of all protein-coding genes of S. griseus were evaluated by comparison of the transcriptomes of the wild-type to that of the ∆adpAch mutant strain

overall_design: We compared the pattern of gene expression of the wild-type (WT) to that of the ∆adpAch mutant strain. Mycelium was harvested after 16h, 24h, and 36h of growth and RNA was isolated from three independent cultures of each strain. For DNA microarray analysis of mutant strains, we considered a fold change of ≥2 and ≤0.5 of that of the WT strains, respectively, with a P-value <0.05 to be significant. According to these criteria, approximately 1400 genes were differentially expressed at all time points

first: Yong-Quan

last: Li


title: Transcriptome analysis of ∆scgA at three time points

status: Public on Jul 30 2014

city: HangZhou

first: zhenxing

last: zhou

state: Zhejiang

address: 388* Yuhang Tang Road

institute: zhejiang university

summary: In ∆scgA, there were more than 1000 genes displaying at least a two-fold change (P<0.05), indicating a strong disturbation of gene expression in ZJUD7.

overall_design: In this study, RNA isolated from ZJUD7 or wild type Streptomyces chattanoogensis L10 was used to acquire expression profiles of a total of 8,117 protein-coding genes in S. chattanoogensis L10, leading to the successful construction of different expression profiles between which deletion mutant and wild type S. chattanoogensis L10.

first: Zhenxing

last: Zhou

first: Yongquan


title: Expression Profiles of Primary Mouse Hepatocytes treated with Cyclosporin A and solvent control [RNA]

status: Public on Jul 24 2014

city: Maastricht

first: Wim

last: Van den Hof

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

summary: The transcriptomics changes induced in Primary Mouse Hepatocytes by Cyclosporin A after treatment for 24h and 48h

overall_design: The study investigated differential gene expression in Primary Mouse Hepatocytes mRNA following 24 and 48 hours of exposure to Cyclosporin A and solvent. Three biological replicates per compound/solvent. In total 24 arrays .


title: Expression data from the stomach of mice treated with dexamethasone.

status: Public on Jul 18 2014

city: Göttingen

first: Holger

last: Reichardt

address: Humboldtallee 34

department: Cellular and Molecular Immunology

country: Germany

institute: University of Göttingen Medical School

summary:
Glucocorticoids are used for the treatment of inflammatory conditions but they also cause many side-effects.
We used microarrays to detail the changes in gene expression induced in the stomach upon oral glucocorticoid treatment.

overall_design:
Female wildtype Balb/c mice were treated for three days with 50 mg/l dexamethasone (dex) via the drinking water.
Control mice were left untreated. The stomach was dissected and RNA prepared from the corpus.

first: Toni

last: Weinhage


title: Heterogeneity in the inter-tumor transcriptome of high risk prostate cancer

status: Public on Jul 21 2014

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

type: Genome variation profiling by genome tiling array

summary:
Background: Genomic analyses of hundreds of prostate tumors have defined a diverse landscape of mutations and genome rearrangements, but the transcriptomic effect of this complexity is less well understood, particularly at the individual tumor level. We selected a cohort of 25 high-risk prostate tumors, representing the lethal phenotype, and applied deep RNA-sequencing and matched whole genome sequencing, followed by detailed molecular characterization.

Results: Ten tumors were exposed to neo-adjuvant hormone therapy and expressed marked evidence of therapy response in all except one extreme case, which demonstrated early resistance via apparent neuroendocrine transdifferentiation. We observe high inter-tumor heterogeneity, including unique sets of outlier transcripts in each tumor. Interestingly, outlier expression converged on druggable cellular pathways associated with cell cycle progression, translational control or immune regulation, suggesting distinct contemporary pathway affinity and a mechanism of tumor stratification. We characterize hundreds of novel fusion transcripts, including a high frequency of ETS fusions associated with complex genome rearrangements and the disruption of tumor suppressors. Remarkably, several tumors express unique but potentially-oncogenic non-ETS fusions, which may contribute to the phenotype of individual tumors, and have significance for disease progression. Finally, one ETS-negative tumor has a striking tandem duplication genotype which appears to be highly aggressive and present at low recurrence in ETS-negative prostate cancer, suggestive of a novel molecular subtype.

Conclusions: The multitude of rare genomic and transcriptomic events detected in a high-risk tumors cohort offer novel opportunities for personalized oncology and their convergence on key pathways and functions has broad implications for precision medicine.

overall_design: 28 samples were analyzed, no replicates, using Agilent aCGH arrayscompetitively hybridized against a male reference pool

first: Alexander

middle: W

last: Wyatt

first: Colin

middle: C

last: Collins


title: Wild-type Zebrafish subjected to swim-training

status: Public on Jul 17 2014

city: Wageningen

first: ansa

last: fiaz

address: De Elst 1

institute: Wageningen University

summary: Genome-wide microarray analysis of the effects of swim-training on zebrafish larval development. Zebrafish were subjected to swim-training from 5 days post fertilization (dpf) until 10  dpf. Subsequently, we performed a genome-wide microarray analysis of trained and control fish at 10 dpf. The goal of the project was to investigate the effects of swim-training on the gene expression level during zebrafish larval development

overall_design: Two-condition experiment: control vs trained fish. RNA was isolated from 10 control fish and from 10 trained fish. Subsequently, each sample was labeled with Cy3 and Cy5 in order to correct for dye bias. Control-Cy3 and Trained-Cy5 were hybridized on array 1 and Trained-Cy5 and Control-Cy3 were hybridized on array 2.

first: Ansa

last: Fiaz


title: Hyperactivation of mTORC1 and mTORC2 by multiple oncogenic events causes addiction to eIF4E-dependent mRNA translation in T-cell leukemia

status: Public on Jul 15 2014

city: Hannover

first: Doris

middle: Johanna

last: Steinemann

department: Institute of Human Genetics

institute: Hannover Medical School

summary:
T-ALL cell lines versus Bl57/6J spleen
We investigated how RTK signaling might contribute to T-ALL using an established bone marrow transplantation model. To mimick tyrosine kinase signalling we expressed a constitutively active form of the TRKA receptor tyrosine kinase (ΔTrkA) in hematopoietic progenitor cells. Mice transplanted with ΔTrkA transduced cells developed T-ALL with a high penetrance.

overall_design: comparative hybridization of DNA from T-ALL clones versus reference DNA (spleen)

first: Adrian

last: Schwarzer


title: Gene expression analysis of WT and Tfap4–/– OT-I cells activated by Listeria monocytogenes expressing ovalbumin

status: Public on Jul 13 2014

city: Saint Louis

first: Takeshi

last: Egawa

state: MO

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: Gene expression of Tfap4–/– and WT OT-I T cells were compared 4 or 6 days after activation with Listeria monocytogenes infection in vivo with the ERCC spike-in RNA control.

overall_design: Naive CD8+ T cells from Tfap4–/– OT-I or control WT OT-I TCR transgenice mice were adoptively transferred to congenic host mice that were subsequently infected with Listeria monocytogenes expression ovalbumin. Activated OT-I cells were harvested 4 days or 6 days after infection and gene expression was compared using microarray.  1 μL of 1:1,000 diluted External RNA Controls Consortium (ERCC) RNA Spike-In Control Mixes (Ambion) was added to total RNA extracted from 1 x 10^5 cells prior to amplification. Gene expression was quantitated by RMA normalization to Signal intensity and signal intensities were further converted by formula obtained from linear regression of signals for spiked-in control RNA between samples to obtain cell number-normalized gene expression.

first: Chun

last: Chou


title: Global hepatic transcript data from LRH-1 hep+/+ and LRH-1 hep-/- livers

status: Public on Jul 11 2014

city: Lausanne

first: Kristina

last: Schoonjans

address: Station 15

department: SV IBI GR-SCH

country: Switzerland

institute: Ecole Polytechnique Fédérale de Lausanne

summary:
Transcript data from LRH-1 hep+/+ and LRH-1 hep-/-  livers from mice fed ad libitum and sacrificed at 7 am
We used microarrays to detail the global programme of gene expression underlying hepatic function in ad libitum fed mice.

overall_design: 17-19-week-old mice were fed ad libitum, sacrificed at 7 am, and livers snap-frozen in liquid nitorgen for RNA extraction and hybridization on Affymetrix microarrays.

first: Sokrates

last: Stein


title: Transcriptomic analysis of the role of Rim101 in the adaptation of Ustilago maydis to an alkaline environment

city: San Nicolas de los Garza

first: Elva

middle: Teresa

last: Aréchiga-Carvajal

state: Nuevo León

address: Av. Pedro de Alba

country: Mexico

summary:
Alkaline pH triggers an adaptation mechanism in fungi that is mediated by Rim101/PacCp, a zinc finger transcription factor. To identify the genes under its control in Ustilago maydis, we performed microarray analyses, comparing gene expression in a wild type strain vs a rim101/pacC mutant of the fungus. In this study we obtained evidence of the large number of genes regulated mostly directly, but also indirectly (probably through regulation of other transcription factors) by Rim101/PacCp, including proteins involved in a large number of physiological activities of the fungus. Our analyses suggest that the response to alkaline conditions under the control of the Pal/Rim pathway involves changes in the cell wall and plasma membrane through alterations in their lipid, protein, and polysaccharide composition, changes in cell polarity, actin cytoskeleton organization, and budding patterns. Also as expected, adaptation involves regulation by Rim101/PacC of genes involved in the meiotic functions, such as recombination and segregation, and expression of genes involved in ion and nutrient transport, as well as general vacuole functions.
The mutant analyzed in this study is described in PMID 15947192

overall_design: Five different oligonucleotide probes per gene (60 nt in length) per duplicate represented each of the 6,883 genes of the U.maydis genome. Accordingly, the expressed data are equivalent to 10 different assays of the expression of each gene.

first: Eduardo

last: Franco-Frías

first: José

last: Ruiz-Herrera

middle: T


title: Whole gene expression data from Gfi-1-/- and Gfi-1-/-;Id2+/- mouse bone marrow cells

status: Public on Jul 12 2014

city: Frederick

first: Jonathan

middle: R

last: Keller

address: 1050 Boyles St. P.O. Box B (Building 560, Room 12-03)

department: Mouse Cancer Genetics Program

institute: Center for Cancer Research, National Cancer Institute, NIH

summary: To understand molecular mechanisms by which reducing Id2 rescues impaired erythropoiesis and hematopoietic progenitor cell development in Gfi-1-/- mice, we compared gene expression in Gfi-1-/-;Id2+/- and Gfi-1-/- BMC using Affymetrix microarray.

overall_design: Total RNA samples from four individual Gfi-1-/- or Gfi-1-/-;Id2+/- mice were arrayed using the GeneChip Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA).

first: Wonil

last: Kim

first: Kimberly

last: Klarmann


title: Interaction between ROS and miR-451

status: Public on Jul 09 2014

city: Chicago

first: Ravi

last: Ranjan

state: IL

address: 840 S Wood St

department: Medicine

institute: University of Illinois at Chicago

summary:
Reactive Oxygen Species (ROS) could be a stress factor that affects microRNA regulation and function in macrophages.
The production of microRNAs (miRNA) is influenced by various stimuli, including environmental stresses. We hypothesized that ROS-associated stress could regulate macrophage miRNA synthesis. p47phox-/- mice have deficient NADPH oxidase activity resulting in decreased ROS production. We cultured bone marrow-derived macrophages (BMDM) from wild type (WT) and p47phox-/- mice and profiled miRNA expression using microarrays. The microarray data reveals that there are differences in the expression levels of different miRs, and our studies suggest functional crosstalk between ROS and miR-451 in the regulation of macrophage oxidant stress.

overall_design: Mouse bone marrow-derived macrophages (BMDMs) were obtained from WT (wild type) and p47phox-/- mice. MicroRNAs were isolated by using the mirVana miRNA kit, and a TaqMan rodent microRNA array (consisting of Megaplex RT Primers, Rodent Pool-A, Applied Biosystems) was used for microarray. The array enables quantitation of the expression levels of up to 380 microRNAs and controls. Rodent Pool A contains reverse transcription (RT) primers for 335 and 238 unique microRNAs for mouse and rat, respectively, plus 4 species-specific controls. The data were analyzed on RQ manager software (Qiagen, SA Biosciences) and normalized to the endogenous controls, and analyzed for fold change of miRs in WT compared to p47phox-/-.

first: Gye

last: Park

first: John

last: Christman


title: Expresion profile of TGR-1 (Myc+/+) and HO15.19 (Myc-/-) infected with a retrovirus expressing Hhex or GFP (controls)

status: Public on Jul 16 2014

city: Valencia

first: Roque

last: Bort

address: Campanar 21

department: Unidad Hepatologia Experimental

country: Spain

institute: IIS La Fe

summary: The aim of this experiment is to determine Hhex targets in the presence and absence of Myc.

overall_design: TGR-1 or HO15.19 cell lines were infected with a retrovirus expressing IRES-GFP (control) or Hhex-IRES-GFP. After infection, cells were GFP-sorted and total RNA extracted by a combination of Trizol and Rneasy columns.


title: Analysis of tumor- and stroma-supplied proteolytic networks in different metastatic tumor microenvironments identifies a critical role for cathepsin S in brain metastasis

status: Public on Jul 04 2014

city: Philadelphia

first: Robert

last: Bowman

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania School of Medicine

summary: Metastasis is a multistage process that requires cancer cells to escape from the primary tumor, survive in the circulation, seed at distant sites and colonize these foreign tissue environments. Each of these processes involves rate-limiting steps that are influenced by stromal cells of the tumor microenvironment. While the tumor microenvironment has emerged as a major regulator of cancer progression in other organ sites, our knowledge of the brain metastatic microenvironment is currently very limited. Thus, we aim to dissect signatures of tumor-stroma interactions in brain metastasis in order to identify factors that regulate the homing, seeding and outgrowth of cancer cells in this highly specialized microenvironment. We took advantage of an experimental metastasis model in which variants of the human breast cancer line MDA-MB-231 home to the brain in xenografted animals. To simultaneously capture gene expression changes in the tumor and stromal compartment, we used a dual species-specific microarray platform, the HuMuProtIn array, to discriminate between differentially expressed protease or protease inhibitor genes of human (tumor) or murine (stromal) origin.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA was isolated from early and late brain, bone and lung metastases from xenograft models of breast metastasis. RNA was also isolated from non-tumor-burdened mouse brain, bone and lung as normal tissue controls. RNA from tissue homing cell lines was isolated in vitro to serve as a control for the human-derived RNA. Samples were collected from 24 total tumor-burdened mice, with 3 replicates for each condition and control. A total of 36 samples are included here.

first: Lisa

last: Sevenich

first: Johanna

middle: A

last: Joyce


title: Real-time quantitative PCR analysis of microRNAS in islets of mice exposed to low-protein diet during gestation

city: Minneapolis

first: emilyn

middle: U

last: alejandro

state: MN

department: Integrative Biology and Physiology

institute: University of Minnesota

summary:
Maternal low-protein diet increases the susceptibility of offspring to type 2 diabetes. An insult to the pancreas during development can have long-term consequences on β-cell mass and function. Because nutrients and growth factors signaling converge on mTOR, we hypothesized that mTOR plays a central role in β-cell programming during fetal development. In this study, we revealed that newborns of dams exposed to low-protein diet (LP0.5) throughout pregnancy exhibited decreased insulin levels, β-cell fraction, and mTOR signaling. Adult LP0.5 offspring demonstrated enhanced insulin sensitivity but remained glucose intolerant due to an insulin secretory defect and not reduced β-cell mass. The insulin secretory defect was distal to Ca2+ influx, at the level of proinsulin biosynthesis and insulin content. LP0.5 islets exhibited reduced mTOR protein and increased expression of specific microRNAs. The reductions in mTOR protein and insulin secretion in LP0.5 islets were restored to normal by blockade of microRNAs 199a-3p and 342. Finally, transient activation of mTORC1 signaling in β-cells during the last week of pregnancy rescued the neonatal β-cell fraction defect and metabolic abnormalities in LP0.5 mice. These findings identify a major role of microRNAs and mTOR in β-cell programing by maternal low-protein diet.
To investigate which microRNAs are altered in islets isolated from 2-3 months old male offspring of dams fed low-protein diet (LP0.5) or control diet throughout pregnancy

overall_design: Pancreatic islets were isolated from 2-3 months old male offspring of dams fed low-protein diet (LP0.5) or control diet throughout pregnancy. Islets were isolated by collagenase digestion. The pancreas was perfused via the common duct with 1 mg/ml collagenase XI (Sigma-Aldrich) in HBSS (Life Technologies). Pancreatic digestion was carried out at 37 °C for 15 min, after which cold HBSS with 2.5% FBS (Life Technologies) was added. The suspension was centrifuged at 1000 rpm for 30s, washed 3 times with HBSS with 2.5% FBS, resuspended in RPMI complete media (RPMI 1640 with 5 mM Glucose, 10% FBS,100 IU/ml penicillin, 100 g/ml streptomycin) and poured onto a 70 µm cell strainer (BD Falcon, BD Biosciences). Islets were rinsed and handpicked. Islets were allowed to recover overnight in RPMI complete media before RNA isolation using MirVana Kit (Life Technologies).

first: Ernesto

last: Bernal-Mizrachi

first: Emilyn

last: Alejandro


title: Chromosome copy number changes in Mps1DK-driven p53 null T-ALL samples

status: Public on Jul 01 2014

city: Groningen

first: Floris

last: Foijer

address: Antonius Deusinglaan 1

department: European Institute for the Biology of Ageing

institute: University Medical Center Groningen

summary: Mps1DK and p53 loss were combined in T-cells specificely leading to early onset and highly aggressive aneuploid T-ALL. Tumors were characterized for (recurrrent) copy number changes with a focus on whole chromosome abnormalities. DNA content was compared to the DNA content of sex-matched uninfiltrated control liver samples from litter mates

overall_design: 27 Mps1DK p53f/f of Mps1DK p53f/+ tumors and 5 p53 f/f control tumors

first: Peter

middle: K

last: Sorger


title: Responses of Pelagibacterales strains to phosphate limitation

city: Corvallis

first: Paul

last: Carini

address: 220 NASH hall

institute: Oregon State U

platform_organism:
Candidatus Pelagibacter ubique HTCC1002
Candidatus Pelagibacter ubique HTCC1062
Candidatus Pelagibacter sp. HTCC7211

overall_design: Batch cultures of two different strains of P. ubique (HTCC1062 and HTCC7211) were grown in a defined artificial seawater media. Biological replicates of each strain were given no phosphate amendment, and three other cultures received an excess concentration of phosphate. Cultures were harvested for microarray analyses over a time course for the purpose of observing differences in gene expression related to phosphate limitation.

first: Stephen

middle: J

last: Giovannoni


title: Heterochromatin protein 1 secures survival and transmission of malaria parasites

city: Basel

first: Till

middle: Steffen

last: Voss

address: Socinstrasse 59

department: Medical Parasitology and Infection Biology

institute: Swiss Tropical and Public Health Institute

summary: The malaria parasite Plasmodium falciparum relies on clonally variant gene expression in order to escape immune recognition and secure continuous proliferation during blood stage infection. Here, we studied the role of heterochromatin protein 1 (HP1), an evolutionary conserved regulator of heritable gene silencing, in the biology of P. falciparum blood stage parasites. We demonstrate that conditional PfHP1 depletion de-represses hundreds of heterochromatic virulence genes and disrupts the elusive mechanism underlying mutually exclusive expression and antigenic variation of PfEMP1. Intriguingly, we also discovered that the PfHP1-dependent regulation of an ApiAP2 transcription factor controls the switch from asexual parasite proliferation to sexual differentiation. This uncovers the first mechanistic insight into the unknown pathway triggering gametocyte conversion and establishes a new concept of HP1-dependent cell fate decision in unicellular eukaryotes.

overall_design: P. falciparum 3D7 parasites expressing endogenous PfHP1-GFP-DD were grown in presence of 4nM WR/625nM Shield-1 (3D7/HP1ON) or 4nM WR (3D7/HP1OFF). RNA extracted from these samples at eleven consecutive time points each was processed for microarray analysis.

first: Nicolas

middle: B

last: Brancucci

first: Nicole

last: Bertschi

first: Lei

last: Zhu

first: Igor

last: Niederwieser

first: Wai

middle: H

last: Chin

first: Rahel

last: Wampfler

first: Ingrid

last: Felger

first: Zbynek

last: Bozdech

middle: S


title: Serum miRNA profiling by quantitative RT PCR

status: Public on Jun 27 2014

city: Hamamatsu

first: Mahesh

last: Mundalil Vasu

state: Shizuoka

address: 1-20-1 Handayama, Higashi Ward

department: Department of Psychiatry

institute: Hamamatsu University School of Medicine

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

overall_design: Refer to individual Series


title: Serum miRNA profiling by quantitative RT PCR [RT-PCR Array 2]

summary:
Initial screening, the expression of 125 mature miRNA was compared between pooled control and autism samples by two microarray analysis. The differential expression of 14 miRNA was further validated by SYBR green quantitative PCR of Individual samples. Thirteen miRNAs were differetially expressed in autistic individuals compared to the controls (8 upregulated and 5 down regulated).
miR-151a-3p, miR-181b-5p, miR-320a, miR-328, miR-433, miR-489, miR-572, and miR-663a were downregulated, while miR-101-3p, miR-106b-5p, miR-130a-3p, miR-195-5p, and miR-19b-3p were upregulated. We have identified a set of serum miRNAs that could be used as non-invasive biomarkers for autism.

overall_design: RNA from age- and gender- matched control (n=40) and autism (n=40) serum samples were pooled separately to generate four pools per group, with each pool consisting of 10 samples. miRNAs were detected and quantified using SYBR Green real-time quantitative PCR performed on ABI PRISM 7900 Sequence Detection System (SDS) [Applied Biosystems (ABI), Foster City, CA, USA]. This observed an altered expression of 14 miRNAs in the autism samples compared to that of healthy controls.


title: Global hepatic transcript data from LRH-1 WT and LRH-1 K289R livers

first: Kristina

last: Schoonjans

summary:
Transcript data from LRH-1 WT and LRH-1 K289R livers from mice fed ad libitum and sacrificed at 7 am
We used microarrays to detail the global programme of gene expression underlying hepatic function in ad libitum fed mice.

first: Sokrates

last: Stein


title: Serum miRNA profiling by quantitative RT PCR [Validation]

summary:
Initial screening, the expression of 125 mature miRNA was compared between pooled control and autism samples by two microarray analysis. The differential expression of 14 miRNA was further validated by SYBR green quantitative PCR of Individual samples. Thirteen miRNAs were differentially expressed in autistic individuals compared to the controls (8 upregulated and 5 down regulated).
miR-151a-3p, miR-181b-5p, miR-320a, miR-328, miR-433, miR-489, miR-572, and miR-663a were downregulated, while miR-101-3p, miR-106b-5p, miR-130a-3p, miR-195-5p, and miR-19b-3p were upregulated. We have identified a set of serum miRNAs that could be used as non-invasive biomarkers for autism.

overall_design: SYBR Green qPCR, performed on an ABI PRISM 7900 SDS (ABI), was used for the validation of differentially expressed 14 miRNAs.  Ten microliters of qPCR reaction mixture was prepared with a universal primer, primer assay, Template cDNA and RNase free water. All the qPCR reactions were performed in triplicate with the following cycling conditions: 95ºC →15 min, followed by 40 cycles of 94ºC →15 sec, 55ºC →30 sec and 70ºC → 30 sec.


title: Generation of a transcriptome catalog for global analysis of gene expression in Ampelomyces quisqualis during mycoparasitization

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

summary:
In this work, 454 pyrosequencing was used to build up a 3’ cDNA fragment library from a normalized library constructed from pooled RNA samples extracted at different stages of A. quisqualis mycoparasitization process (recognition, early and late parasitization). An extensive catalogue of unique transcripts was compiled and used to develop a microarray for large-scale analysis of genes involved in this mycoparasitism.
We examined the transcriptomic changes that occur during the first stage of mycoparasitism (conidial germination). Our results showed that 1,776 transcripts are regulated during germination in the presence of powdery mildew. A striking feature of the gene catalogue was the presence of a number of genes predicted to encode proteins involved in the production of, glucanases, chitinases and extracellular proteases. This suggests that A. quisqualis causes the degradation of powdery mildew macromolecular constituents to provide the carbon skeletons and energy for the synthesis of proteins and other components destined for the developing of the mycelium.

overall_design: Microarray oligo probes were designed based on 454 sequencing of 3'-ends of transcripts of a sample constituted by pooling RNAs extracted at different stages of A. quisqualis mycoparasitization process (recognition, early and late parasitization)

first: Lorenzo

last: Tosi

first: Massimo

last: Delledonne

first: Alessandro

last: Ferrari

first: Antonio

last: Chimento

first: Paola

last: Tononi

first: Monika

last: Maurhofer

first: Cesare

last: Gessler

first: Ilaria

last: Pertot


title: Genome-wide promoter methylation analysis of human osteoarthritis

city: Vienna

first: Manuela

last: Hofner

address: Muthgasse 11/2

department: Molecular Diagnostics

country: Austria

institute: Austrian Institute of Technology - AIT

type: Methylation profiling by genome tiling array

summary: Osteoarthritis (OA) is a chronic disease of the joint characterized by a progressive degradation of articular cartilage and subchondral bone.  In healthy tissue, specialized cells called chondrocytes are regulating a balanced cartilage catabolism and anabolism. By contrast osteoarthritic joints are characterized by a dramatic increase of cartilage catabolism, due to changes of gene expression patterns within chondrocytes.  To identify potential epigenetic differences regulating this process a genome-wide methylation screening of paired unaffected and osteoarthritic knee cartilage samples was performed. Therefore samples of macroscopic arthritic and non-arthritic cartilage areas of the femoral condyle of five female patients were collected and DNA isolation was performed.  For being able to investigate methylation changes on a genome-wide scale using only limited amounts of DNA a specific amplification protocol for mainly methylated DNA has been established, based on combinations of different methylation-sensitive and –independent restriction digestions. The amplified DNA was then labeled and hybridized onto Agilent “Human Promoter Whole Genome” microarrays. A random variance t-test for paired (per patient) samples was performed, identifying 1214 differentially methylated genetic targets between arthritic and non-arthritic samples. The biological relevance of these genes was then further investigated via Gene Ontology (GO) and KEGG pathway analysis.

overall_design: DNA isolated of paired arthritic and non-arthritic knee cartilage samples of five different female osteoarthritis patients (10 samples) was methylation-specifically amplified using combinations of methylation-sensitive and -insensitive restriction enzymes. Amplicons were dye labeled (Cy3) and hybridized onto 2x244k Agilent Human Promoter microarrays.

first: Florentine

last: Fürst-Moazedi


title: Immunogenic epitopes of the meningioma-associated antigen TXNDC16

city: Homburg/Saar

first: Christian

middle: Clemens

last: Harz

state: Saarland

address: Kirrberger Strasse 100

department: Department of Human Genetics

institute: Saarland University

summary: We used customized peptide arrays of 163 TXNDC16 peptides to identify immunogenic TXNDC16 epitopes and asked whether discrimination of meningioma and control sera is possible with a specific subset selection of all immunogenic epitopes.

overall_design:
CelluSpots™ peptide arrays were manufactured by Intavis (Germany) with 163 TXNDC16 spanning peptides spotted as two replicate subarrays. 15-mer peptides overlapping by 10 amino acids were covalently bound to cellulose membranes with their C-termini.

Please note that the non_normalized.txt contains Ch1 Mean values for all samples (each sequence represented in duplicates) and the identifiers in the 'index' column corresponds to those in the 'index' column in raw gpr files; sample data table contains classification values (for each sequence) described in the sample data processing field.

first: Nicole

last: Ludwig

first: Valentina

last: Galata

first: Christina

last: Backes

first: Andreas

last: Keller

first: Eckart

last: Meese


title: Profiling of human cancer breast cell lines (Affymetrix)

status: Public on Jul 10 2014

city: Boston

first: Sergey

last: Lezhnin

address: 33 AVENUE LOUIS PASTEUR

department: Molecular Profiling

institute: Merck Research Laboratories

summary: mRNA profiling data for 58 breast cancer cell lines at baseline

first: Serguei

last: Lejnine

first: Alex

last: Stoeck


title: Microarray Analysis Reveal Global Differential Transcritomes of Mesorhizobium huakuii 7653R between Bacteroids and Free-living Cells

status: Public on Jun 30 2014

city: Wuhan

first: Youguo

last: Li

state: Hebei

address: No.1,Shizishan Street · Hongshan District

department: College of Life Science and Technology

institute: Huazhong Agricultural University

summary:
Mesorhizobium huakuii 7653R is an α-proteobacterium that occurs either in a nitrogen-fixing symbiosis with its host plant, A. sinicus, or free-living in the soil.
Investigation of whole genome gene expression level changes in Bacteroids compared to the free-living cells.
Understand how M. huakuii 7653R responds to alterations in its environment and to the physiological changes that occur during bacteroid differentiation.

overall_design: Examination of mRNA levels in free-living cells and bacteroids at 32 days postinoculation

first: Jieli

last: Peng

first: Shanming

last: Wang


title: Large-scale characterization of DNA methylation changes in human gastric carcinomas with and without metastasis

status: Public on Jun 02 2014

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

summary: A large-scale characterization of the methylation states of candidate CpG islands (CGIs) throughout the gastric cancer methylome has not previously been conducted. Genome-wide DNA methylation profiles were compared between 4 metastatic and 4 non-metastatic gastric carcinomas (GCs) and their surgical margins (SMs). The GC genome showed significantly higher proportions of hypomethylation in the promoter and exon-1 regions, as well as increased hypermethylation of intragenic fragments when compared to SMs. Differential methylation was observed in CGIs near transcription start sites of 546 genes between GCs and SMs, and 601 genes between metastatic and non-metastatic GCs. From the list of differentially methylated CGIs, 68 candidate genes and 10 known tumor-related genes were selected for further characterization based on their known molecular function using DHPLC. Significant differential methylation was validated in the CGIs of 15 genes between GCs and SMs (Ps<0.05) and confirmed using bisulfite-sequencing. These genes include BMP3, BNIP3, CDKN2A, ECEL1, ELK1, GFRA1, HOXD10, KCNH1, PSMD10, PTPRT, SIGIRR, SRF, TBX5, TFPI2, and ZNF382. Hypomethylation of CGIs correlated with up-regulation of GFRA1 expression in GCs, while hypermethylation of other genes inactivated their transcription. Most importantly, prevalence of GFRA1, SRF, and ZNF382 methylation alterations were inversely and coordinately associated with GC metastasis and the patients’ overall survival throughout discovery and testing cohorts in China as well as independent validation cohorts in Japan and Korea. In conclusion, methylation changes in the CGIs of 15 genes correlated strongly with GC development. GFRA1 hypomethylation and SRF and ZNF382 hypermethylation are potential synergistic biomarkers for the prediction of GC metastasis.

overall_design: To identify differential methylation of CGIs related to GC development and metastasis, genome-wide DNA methylation changes in 8 pairs of GC and SM samples were analysed using the MCAM assay with a 99K custom-designed Agilent oligonucleotide microarray composed of 99,027 probes targeting 6,177 unique protein-coding genes containing at least two methylation-sensitive/insensitive SmaI/ XmaI restriction sites (CCC|GGG/ C|CmCGGG) as described in Shen et al, PLoS Genet 3, 2023-2036 (2007).

first: Dajun

last: Deng


title: GTF2I Mutations are Common in Thymic Epithelial Tumors

status: Public on Jun 21 2014

city: Pisa

first: Iacopo

last: Petrini

address: Via Roma 67

institute: Pisa University

summary: Within a project aim to define the genomic aberration of thymic epithelial tumors, we performed array CGH in 65 thymic epithelial tumors. Tumor samples were collected during surgery or by image-guided biopsies and immediately frozen. Section from frozen material were cut and stained with Haematoxylin and Eosin. A pathologist reviewed the slides and selected only cases with >80% of cancer cells.

overall_design: Copy number aberrations of a series of 65 thymic epithelial tumors were evaluated using array CGH. Differences in copy number aberrations between different histotypes were evaluated. Significant regions of CN aberrations were defined using GISTIC algorithms.

first: Paul

last: Meltzer

first: In

last: Kim

first: Marco

last: Lucchi

first: Gabriella

last: Fontanini

first: James

last: Gao

first: Paolo

last: Zucali

first: Fiorella

last: Calabrese

first: Adolfo

last: Favaretto

first: Rea

last: Federico

first: Jaime

last: Rodriguez-Canales

first: Robert

middle: L

last: Walker

first: Marbin

last: Pineda

first: Yuelin

last: Zhu

first: Christopher

last: Lau

first: Keith

last: Killian

first: Sven

last: Bilke

first: Donna

last: Voeller

first: Sivanesan

last: Dakshanamurthy

first: Yisong

first: Giuseppe

last: Giaccone


title: Systems analysis of the response of photosynthesis, metabolism and growth to an increase in irradiance in the photosynthesis model organism Chlamydomonas reinhardtii

status: Public on Apr 30 2014

city: Potsdam

first: Samuel

last: Arvidsson

state: Brandenburg

address: Am Muehlenberg 1

institute: Max Planck Institute of Molecular Plant Physiology

summary: Systems analysis reveals that Chlamydomonas reinhardtii responds rapidly and flexibly to an increase in light intensity. Rising metabolite levels and post-translation regulation facilitate a rapid increase in the rate of carbon fixation and a slightly delayed increase in the rate of growth, and slower changes in protein abundance adjust allocation and minimize bottlenecks in the new conditions.

overall_design: Gene expression was measured from samples of Chlamydomonas reinhardtii cell cultures at four time points (two under low, four under high light) under either low (41 µmol) or high (145 µmol) light conditions in two separate bioreactors. Three biological replicate time series were sampled.

first: Tabea

last: Mettler

first: Timo

last: Mühlhaus

first: Dorothea

last: Hemme

first: Mark-Aurel

last: Schöttler

first: Jens

last: Rupprecht

first: Adam

last: Idoine

first: Daniel

last: Veyel

first: Sunil

last: Kumar Pal

first: Liliya

last: Yaneva-Roder

first: Flavia

last: Vischi Winck

first: Frederik

last: Sommer

last: Vosloh

first: Bettina

last: Seiwert

first: Alexander

last: Erban

first: Asdrubal

last: Burgos

first: Stephanie

last: Schönfelder

first: Anne

last: Arnold

first: Manuela

last: Günther

first: Ursula

last: Krause

first: Marc

last: Lohse

first: Joachim

last: Kopka

first: Zoran

last: Nikoloski

first: Bernd

last: Mueller-Roeber

first: Lothar

last: Willmitzer

first: Ralph

last: Bock

first: Michael

last: Schroda

first: Mark

last: Stitt


title: Transcriptional changes in Aspergillus flavus-infected maize kernels

status: Public on May 14 2014

city: Raleigh

first: Gary

last: Payne

address: 851 Main Campus Drive

institute: North Carolina State University

summary: Maize kernels are susceptible to infection by the opportunistic pathogen Aspergillus flavus. Infection results in reduction of grain quality and contamination of kernels with the highly carcinogenic mycotoxin, aflatoxin. To understand host response to infection by the fungus, transcription of approximately 9,000 maize genes were monitored during the host-pathogen interaction with a custom-designed Affymetrix GeneChip® DNA array. More than 1,000 maize genes were found differentially expressed at a fold change of 2 or greater. This included the up regulation of defense-related genes and signaling pathways. Transcriptional changes also were observed in primary metabolism genes. Starch biosynthetic genes were down regulated during infection, while genes encoding maize hydrolytic enzymes, presumably involved in the degradation of host reserves, were up regulated. These data indicate that infection of the maize kernel A. flavus induced metabolic changes in the kernel, including the production of a defense response, as well as a disruption in kernel development.

platform_organism:
Zea mays
Aspergillus flavus
Aspergillus oryzae

overall_design: Maize kernels were mock inoculated at the blister (R2) or dough (R4) stage or inoculated with A. flavus at the blister (R2), milk (R3), dough (R4), or dent (R5) stage, and harvested 4 days later. Each treatment consisted of three biological replications. For each biological replication, 8 kernels were ground and RNA was isolated and further processed.

first: Andrea

last: Dolezal


title: PELP1 ChIP-chip from MCF-7 cells

status: Public on Apr 24 2014

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

type: Genome binding/occupancy profiling by genome tiling array

summary: Proline-, glutamic acid-, and leucine-rich protein 1 (PELP1) is a transcriptional coactivator that has previously been shown to collaborate with nuclear receptors. Evidence from other groups suggest that PELP1 may stimulate transcription by displacing the linker histone H1 and/or by recruiting the lysine demethylase KDM1 to demethylate H3K9me2. Also known as modulator of the non-genomic activity of estrogen receptor (MNAR), PELP1 has also been implicated promoting estrogen receptor signaling from the plasma membrane. We recently identified PELP1 a factor that interacts with the macro domain of the histone variant macroH2A1. To determine if PELP1 interacts with macroH2A1 in cells, we performed PELP1 ChIP-chip from MCF-7 cells. The pattern of PELP1 bind across the genome strongly correlates with that previously determined for macroH2A1. This data combined with additional experiments allow us to conclude that macroH2A1 regulates target gene expression in part by recruiting the transcriptional coregulator PELP1.

overall_design: Two PELP1 ChIP-chip biological replicates from MCF-7 human breast cancer cells are included.

first: Matthew

last: Gamble

first: Kristine

middle: M

last: Frizzell

first: W


title: High-fat diet-mediated dysbiosis promotes intestinal carcinogenesis independent of obesity

status: Public on Mar 28 2014

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary:
Several aspects common to a Western lifestyle, including obesity and decreased physical activity, are known risks for gastrointestinal cancers. There is an increasing amount of evidence suggesting that diet profoundly affects the composition of the intestinal microbiota. Moreover, there is now unequivocal evidence linking a dysbiotic gut to cancer development. Yet, the mechanisms through which high-fat diet (HFD)-mediated changes in the microbial community impact the severity of tumorigenesis in the gut, remain to be determined.
Here we demonstrate that HFD promotes tumor progression in the small intestine of genetically susceptible K-rasG12Dint mice independent of obesity. HFD consumption in conjunction with K-Ras mutation mediates a shift in the composition of gut microbiota, which is associated with a decrease in Paneth cell antimicrobial host defense that compromises dendritic cell (DC) recruitment and MHC-II presentation in the gut-associated lymphoid tissues (GALTs). DC recruitment in GALTs can be normalized, and tumor progression attenuated completely, when K-rasG12Dint mice are supplemented with the short-chain fatty acid butyrate, a bacterial fermentation endproduct. Importantly, Myd88-deficiency completely blocks tumor progression in K-rasG12Dint mice. Transfer of fecal samples from diseased donors into healthy adult K-rasG12Dint mice is sufficient to transmit disease in the absence of HFD. Furthermore, treatment with antibiotics completely blocks HFD-induced tumor progression, suggesting a pivotal role for distinct microbial shifts in aggravating disease in the small intestine. Collectively, these data underscore the importance of the reciprocal interaction between host and environmental factors in selecting intestinal microbiota that favor carcinogenesis, and suggest tumorigenesis may be transmissible among genetically predisposed individuals.

overall_design: 3 mice each for each treatment.

first: M

last: Arkan

first: Cigdem

last: Atay


title: Plasmodium falciparum assocation study of artemisinin resistance

status: Public on May 28 2014

city: Baltiomore

first: Christopher

last: Jacob

state: MD

address: 685 W. Baltimore St.

department: Center for Vaccine Development

institute: University of Maryland School of Medicine

summary:
A testing association of parasite genotypes with clinical resistance phenotype.
Submission of genotypes from all microarray genotyped samples

overall_design: Comparison of DNA from clinical isolates and generated by next-generation sequencing with prolonged clearance half-life

middle: G

first: Shannon

last: Takala-Harrison

middle: V

last: Plowe


title: Saccharomyces cerevisiae mutant strain with R1158 strain background: Fold change after doxycycline treatment

status: Public on Mar 26 2014

city: Taipei

first: Jun-Yi

last: Leu

address: No. 128, Sec. 2, Academia Rd., Nangang Dist.

country: Taiwan

institute: Institute of Molecular Biology

summary: To understand the extent that Heat shock protein 90 (Hsp90) regulated its target proteins at the transcription level, transcriptomic change was profiled in yeast cells upon Hsp90 compromising. We genetically modified the R1158 strain (resulting genotype of mutant strain: TETp-HSC82 hsp82Δ arg4Δ lys5Δ car2Δ::URA3) and then reduced the Hsp90 amount with doxycycline treatment. Fold change of mRNA from untreated to treated cells indicated the transcriptomic change. Totally, we identified 1104 genes mis-regulated with a fold change of no less than 1.5 (P <0.05) upon Hsp90 compromising.

overall_design: Two-condition experiment, treated vs. untreated cells. Biological duplicates, independently grown and harvested. Technical triplicates for RNA isolation.

first: Jun

middle: Y


title: Expression profiling of EpH4 mouse mammary epithelial cells overexpressing the AP-1 transcription factor component Fra1

status: Public on Mar 22 2014

city: MADRID

first: Erwin

middle: F

last: Wagner

address: C/ Melchor Fernández Almagro, 3

department: F-BBVA CCBP

institute: CNIO

summary: RNA of control mouse mammary epithelial cells (EpH4 control) and corresponding fra1 overexpressing cells (EpH4fra1 cl1 and EpH4fra1 cl2) was hybridized onto an 53MM chip and differentially expressed targets were further analysed. For each sample hybridization was performed in technical triplicate

overall_design: By comparison of the gene expression profiles of these samples, genes with significantly altered expression levels will be selected and further characterized.

first: Latifa

last: Bakiri

first: Sabine

last: Macho-Maschler

first: Ivana

last: Custic


title: Comparative Genomic Hybridization (CGH) reveals sex chromosome location and gene movement in stalk-eyed flies (family Diopsidae)

status: Public on Mar 06 2014

city: College Park

first: Gerald

last: Wilkinson

address: Bldg 144, 4094 Campus Dr

department: Biology

institute: University of Maryland

type: Genome binding/occupancy profiling by array

summary:
We utilized Comparative Genomic Hybridization (CGH), using probes designed from de novo assembly of 10 tissues into a grand transcriptome to identify genes located on the X and Y chromosomes of a stalk-eyed fly, Teleopsis dalmanni.
We use next generation sequencing of RNA to identify over 500 genes that are differentially expressed in the testes due to the effects of a driving X chromosome (XSR) in T. dalmanni.   Most of these genes were X-linked, evolving more rapidly than control genes, and exhibit elevated expression in the gonads.  Finally, XSR has become genetically differentiated from standard X chromosomes – using the RNA sequence data, we found nearly 1000 sites in X-linked genes and only a handful in autosomal genes where there was a fixed nucleotide difference.  We conclude that XSR has led to widespread sequence and expression divergence on the X chromosome in T. dalmanni.

overall_design: Two-condition experiment, female vs. male DNA, for one species with 4 biological replicates

first: Josephine

last: Reinhardt

first: Richard

last: Baker


title: Effects of equol on gene expression in female cynomolgus monkey iliac arteries

status: Public on Mar 11 2014

city: Vermillion

first: Kathleen

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

institute: University of South Dakota

summary:
Objective:  To examine the effects of the phytoestrogen metabolite, equol, on gene expression in the monkey iliac artery.
Design:  Eight ovariectomized cynomolgus monkeys were on a high fat diet for 6.5 years.  The left iliac artery was biopsied prior to randomization to equol (0.0237 g/100 g chow, n=4) or vehicle (n=4) for 8 months.  The right iliac artery was obtained at necropsy.  Gene expression in the iliac arteries in response to equol was determined by DNA microarray and confirmed by real time RT-PCR.
Results:  Atherosclerotic lesions in the iliac arteries ranged in size from 0.113-1.003 mm2 in equol-treated animals and from 0-0.873 mm2 in control animals.  59 genes were down-regulated and 279 were up-regulated in response to equol.  Comparison of these data to previous work identified 10 genes regulated in opposite directions by equol compared to presence of atherosclerosis plaque.  55 genes were differentially expressed in the same direction in response to both equol and estradiol.
Conclusions:  Similar responses of genes to both equol and estradiol may reflect the extent to which equol serves as a natural selective estrogen receptor modulator in the arteries.  Opposite responses of 10 genes to equol versus the presence of atherosclerosis implicates those genes in the potential protective effects of equol in the vasculature.

overall_design:
Experiment Design:
Goal of the experiment:  To examine differential gene expression in the iliac arteries of ovariectomized cynomolgous monkeys on a high fat diet in response to treatment with equol.

Brief description of the experiment:
Objective:  To examine the effects of the phytoestrogen metabolite, equol, on gene expression in the monkey iliac artery.
Design:  Four ovariectomized cynomolgous monkeys were on a high fat diet for 6.5 years.  The left iliac artery was biopsied prior to randomization to equol (0.0237 g/100 g chow, n=4 or vehicle (n=4) for 8 months.  The right iliac artery was obtained at necropsy.  Gene expression in response to equol was determined by CodeLink Whole Human Genome DNA microarrays and confirmed by real time RT-PCR.
Results:  Atherosclerotic lesions in the iliac arteries ranged in size from 0.113-1.003 mm2 (mean 0.512 ± 0.19 mm2) in pretreatment arteries and 0.025-1.217 mm2 (mean 0.748 ± 0.22 mm2) post-equol treatment.  59 genes were down-regulated and 279 were up-regulated in response to equol.  Comparison of these data to previous work identified 10 genes regulated in opposite directions by equol compared to presence of atherosclerosis plaque.  55 genes were differentially expressed in the same direction in response to both equol and estradiol.
Conclusions:  Similar responses of genes to both equol and estradiol may reflect the extent to which equol serves as a natural selective estrogen receptor modulator in the arteries.  Opposite responses of 10 genes to equol versus the presence of atherosclerosis implicates those genes in the potential protective effects of equol in the vasculature.

Keywords:  nonhuman primate, equol treatment, soy isoflavones

Experimental factors:  equol treatment

Experimental design:  Female cynomolgous monkeys (n=4) had been ovariectomized for 4 years and on a high fat diet for 6.5 years. The left iliac artery was removed at surgical biopsy.  Animals were treated with equol for 8 months, then necropsied.  The right iliac artery was obtained at necropsy.  The presence and size of atherosclerotic plaque was quantified in the iliac arteries.  Arterial tissue from the iliac arteries was used for DNA microarray analysis of gene expression.

Quality control steps:  The cRNA that was synthesized from each iliac artery was used for hybridization to a single CodeLink (Applied Microarrays, Tempe, AZ) whole human microarray.  Only one sample was hybridized with each slide and only one dye (Alexa 647) was used so no dye swaps were necessary.  Bacterial control spikes were used as per manufacturer's instructions.

Samples used, extract preparation and labeling:
The origin of each biological sample:  The samples were iliac arterial tissue from cynomolgous monkeys.

Manipulations of biological samples and protocols used:  Cynomolgous monkeys were placed on a high fat diet 6.5 years before the experiment and ovariectomized 4 years prior to the experiment to induce a surgical menopause.  The left iliac artery was surgically removed from each animal in the study before treatment with equol, the the right iliac artery was removed after the treatment period at necropsy.  The presence and size of atherosclerotic plaque was quantified in the iliac arteries

Experimental factor:  hormone treatment

Technical protocols:  The iliac arteries were homogenized in TRI reagent, bromochloropropane and sodium acetate were added, and the samples were centrifuged to separate the phases.  The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity of RNA were evaluated by an Agilent Bioanalyzer using the RNA 6000 Nanoassay LabChip.

Labeled cRNA was prepared using the MessageAmp II-Biotin enhanced kit (Ambion).  0.275 microgram of total iliac artery RNA was mixed with bacterial control RNA spikes and primed with T7 oligo(dT) primer for 10 min at 70C.  (The bacterial control spikes included araB, entF, fixB, gnd, hisB, and leuB.)  The first strand of cDNA was synthesized with first strand buffer, dNTP mix, RNase inhibitor, and reverse transcriptase for 2 h at 42C.  The second strand cDNA synthesis reaction was prepared using second strand buffer, dNTP mix, DNA polymerase mix, and RNase H; the reaction was carried out for 2h at 16C.  The double-stranded cDNA was purified on QIAquick columns (Qiagen) and the eluent was dried down in a SpeedVac concentrator.  The double-stranded cDNA was resuspended in a mixture containing T7 reaction buffer, T7 ATP, T7 GTP, T7 UTP, T7 CTP, biotin-11-UTP, and T7 enzyme mix for the synthesis of cRNA.  The cRNA synthesis reaction was terminated after 14h at 37C by purifying the cRNA on RNeasy columns (Qiagen).  The concentration of cRNA was determined by spectrophotometry.

Hybridization procedures and parameters:  10 micrograms of cRNA was mixed with fragmentation buffer and heated to 94C for 20 min.  The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides, and hybridized for 18 hours at 37C.
The slides were washed in 0.75x TNT (Tris-HCl, NaCl, Tween-20) at 46C for 1h then incubated with streptavidin-Alexa 647 fluorescent dye for 30 min at room temperature.  The Alexa fluor was prepared in TNB blocking buffer (0.1M Tris-HCl, 0.15M NaCL, 0.5% NEN Blocking Reagent-PerkinElmer)  The slides were then washed 4 times for 5 min each in 1x TNT and twice in 0.05% Tween 20 for 5 sec each.  The slides were dried by centrifugation and scanned in an Axon GenePix 4000B scanner.

first: Susan

last: Appt

first: Abha

last: Chalpe

first: Thomas

middle: C

last: Register

last: Clarkson