title: Coxsackievirus B3 (CVB3) infection of 129S1 and 129X1 (heart tissue day 6)

status: Public on Apr 01 2013

city: Montreal

first: Jennifer

last: Marton

state: Quebec

address: 3649 Prom. Sir William Osler

department: Human Genetics

institute: McGill University

summary: We infected two strains of mice, 129S1/SvImJ and 129X1/SvJ, with coxsackievirus type b3 (CVB3) at a dose of 500 pfu/g.  129S1 mice developed increased cardiopathology despite equal viral replication.  We hypothesized that the increased cardiopathology might result from an ongoing pathologic host response that we could characterize by global expression profiling.  Gene expression was assessed in hearts from 129S1 and 129X1 mice that were uninfected or infected for 6 days.

overall_design: Total RNA obtained from hearts of 3 129S1 and 3 129X1 that were infected or uninfected with CVB3(H3) at 500pfu/g and collected at day 6 post infection

first: Silvia

middle: M

last: Vidal


title: Global genomic profiling of p53-regulated genes

status: Public on Apr 21 2013

city: Stanford

first: Stephano

last: Spano Mello

state: CA

address: 269 Campus Drive

country: USA

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: p53 is a critical tumor suppressor and works as a stress-induced transcription factor to induce target genes mediating apoptosis, cell cycle arrest and senescence or other responses. To gain new insights into p53 biology, we used high-throughput sequencing to analyze global p53 transcriptional networks in primary mouse embryo fibroblasts in response to DNA damage. ChIP-sequencing reveals 4785 p53-bound sites in the genome located near 3193 genes involved in diverse biological processes. RNA-sequencing analysis shows that only a subset of p53-bound genes is transcriptionally regulated, yielding a list of 432 p53-bound and regulated genes. Furthermore, we define a list of 1269 basal-p53 regulated genes, of which 253 are p53-bound and basal-p53 regulated.

overall_design: ChIP-seq was performed to determine the genome-wide p53 binding sites in doxorubicin-treated primary MEFs. RNA-seq was used to define differentially expressed genes in response to DNA damage in wild-type and p53-/- MEFs, and basal p53 regulated genes by deriving differentially expressed genes between untreated wild-type and p53-/- MEFs.

first: Daniela

last: Kenzelmann Broz

first: Laura

middle: D

last: Attardi


title: RNAseq analysis of the human neutrophil transcriptome, with and without in vitro cytokine stimulation

status: Public on Mar 06 2013

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

country: United Kingdom

institute: University of Liverpool

summary: We report cytokine specific changes in gene expression in the human neutrophil transcriptome using TNF-alpha and GM-CSF stimulation of healthy neutrophils

overall_design: Healthy human neutrophils were stimulated with TNF-alpha or GM-CSF for 1h in vitro. RNA was analysed by SOLiD and Illumina sequencing.  RNA from one biological donor was sequenced on both platforms, and two different biological donors were sequenced by Illumina.

middle: L

first: Huw

middle: B

last: Thomas

first: Robert

middle: J

last: Moots

first: Steven

middle: W

last: Edwards


title: Temporal gene expression across osteoblastogenesis.

status: Public on Jun 23 2014

city: Bar Harbor

first: Cheryl

last: Ackert-Bicknell

state: ME

address: 600 Main Street

institute: The Jakcson Laboratory

summary:
Purpose: Osteoblast cells mature from a mesenchymal stem cell pool to become cells capable of forming bone matrix and mineralizing this matrix.  The goal of this study was to characterize temporal changes in the transcriptome across osteoblast maturation, starting with committed mesenchymal stem cell/ early pre-osteoblast stage through to mature osteoblasts capable of matrix mineralization.
Methods:  Enriched populations of pre-osteoblast like cells were obtained from neonatal calvaria from C57BL/6J mice expressing CFP under the control of the Col3.6 promoter.  These cells were placed into culture for 4 days, removed from culture and subjected FACS sorting based on the presence/absence of CFP expression.  Cells expressing CFP were returned to culture, subjected to an osteoblast differentiation cocktail and RNA was collected at 2, 4, 6, 8, 10, 12, 14, 16 and 18 days post differentiation.
Methods II:  mRNA profiles for each time point were generated by next generation RNA sequencing, using an Illumina HiSeq 2000.  Three technical replicates per samples were sequenced. The alignments for abundance estimation of transcripts was conducted using Bowtie version 0.12.9, using the NCBIm37 reference genome. Expression level per gene was calculated using RSEM version 1.2.0 with the parameters of --fragment-length-mean 280 and --fragment-length-sd 50, and the expression level for each sample was normalized relative to the per sample upper quartile.

overall_design: Gene expression in calvarial osteoblasts from neonatal C57BL/6J-Col3.6 CFP mice at 9 time points post differentiation

first: Matthew

middle: A

last: Hibbs

first: Kwangbom

last: Choi


title: Discovery and validation of a prostate cancer genomic classifier that predicts early metastasis following radical prostatectomy

status: Public on Jul 01 2013

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

institute: Veracyte, Inc

summary:
Purpose: Clinicopathologic features and biochemical recurrence are sensitive, but not specific, predictors of metastatic disease and lethal prostate cancer.  We hypothesize that a genomic expression signature detected in the primary tumor represents true biological potential of aggressive disease and provides improved prediction of early prostate cancer metastasis.

Methods: A nested case-control design was used to select 639 patients from the Mayo Clinic tumor registry that underwent radical prostatectomy between 1987 and 2001. A genomic classifier (GC) was developed by modeling differential RNA expression using 1.4 million feature high-density expression arrays of men enriched for rising PSA after prostatectomy, including 213 that experienced early clinical metastasis after biochemical recurrence. A training set was used to develop a random forest classifier of 22 markers to predict for cases - men with early clinical metastasis after rising PSA. Performance of GC was compared to prognostic factors such as Gleason score and previous gene expression signatures in a withheld validation set.

Results: Expression profiles were generated from 545 unique patient samples, with median follow-up of 16.9 years.  GC achieved an area under the receiver operating characteristic curve of 0.75 (0.67 - 0.83) in validation, outperforming clinical variables and gene signatures. GC was the only significant prognostic factor in multivariable analyses. Within Gleason score groups, cases with high GC scores experienced earlier death from prostate cancer and reduced overall survival. The markers in the classifier were found to be associated with a number of key biological processes in prostate cancer metastatic disease progression.

Conclusion: A genomic classifier was developed and validated in a large patient cohort enriched with prostate cancer metastasis patients and a rising PSA that went on to experience metastatic disease. This early metastasis prediction model based on genomic expression in the primary tumor may be useful for identification of aggressive prostate cancer.

overall_design: 545 formalin-fixed paraffin-embedded (FFPE) tissue samples from primary prostate cancer obtained from Radical Prostatectomy.

first: Nicholas

last: Erho

first: Anamaria

last: Crisan

first: Ismael

last: Vergara

first: Anirban

middle: P

last: Mitra

first: Mercedeh

last: Ghadessi

first: Christine

last: Buerki

first: Eric

last: Bergstralh

first: Thomas

last: Kollmeyer

first: Stephanie

last: Fink

first: Zaid

last: Haddad

first: Benedikt

last: Zimmermann

last: Sierocinski

first: Karla

middle: V

last: Ballman

first: Timothy

last: Triche

first: Peter

middle: C

last: Black

first: R

last: Karnes

first: George

last: Klee

last: Jenkins


title: FS001: Aberrant gene expression in dogs with portosystemic shunts

status: Public on Mar 01 2013

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: Background: Congenital portosystemic shunts are developmental anomalies of the vascular system that cause portal blood to bypass the liver. Large-breed dogs are reported to have a predisposition for intrahepatic portosystemic shunts (IHPSS) and small-breed dogs a predisposition for extrahepatic portosystemic shunts (EHPSS). While the physiological consequences of the two types of shunt are identical, the metabolic pathways involved are probably different. The aim of this study was to gain insight into the metabolic pathways involved in the different types of portosystemic shunting. Results: Microarray analysis of mRNA expression in liver tissue from dogs with EHPSS and IHPSS revealed that the expression of 26 genes was altered in either IHPSS or EHPSS samples compared with that in liver samples from control dogs. Quantitative real-time PCR of these genes in 14 IHPSS, 17 EHPSS, and 8 control liver samples revealed a significantly different expression of ACBP, CCBL1, GPC3, HAMP, PALLD, VCAM1, and WEE1. Immunohistochemistry studies revealed that the pattern of VCAM1 and WEE1 protein expression supports the involvement of these proteins in the development of EHPSS and IHPSS, respectively. Conclusions: We identified a small list of genes possibly involved in two genetically different types of portosystemic shunt with identical pathophysiological consequences. WEE1 was found to be aberrantly expressed at an RNA and protein level in dogs with IHPSS. A decreased VCAM1 expression may play a role in the development of intrahepatic portal vascularization in dogs with EHPSS.

overall_design: Total RNA was isolated from liver tissue from 2 healthy dogs, 32 dogs with EHPSS, and 14 dogs with IHPSS. Pooled RNA isolated from healthy liver tissue was used as reference. Dye swap of Cy3 and Cy5 was performed to reduce dye bias.

first: Frank

middle: G

last: van Steenbeek

first: Lindsay

last: van den Bossche

first: Guy

last: Grinwis

first: Anne

last: Kummeling

first: Ingrid

middle: H

last: van Gils

first: Dik

last: van Leenen

last: Holstege

first: Louis

last: Penning

first: Jan

last: Rothuizen

last: Leegwater

first: Bart

last: Spee


title: Transcriptome profile of subcutaneous adipocytes isolated from obese vs. lean postmenopausal women

status: Public on Feb 02 2013

city: Houston

first: Zheng

last: Yin

state: TX

address: 6670 Bertner Street R6-414

department: Systems Medicine and Bioengineering

institute: The Methodist Hospital Research Institute

summary: Adipocytes isolated from lean and obese postmenopausal women with no significant differences in metabolic syndrome parameters demonstrate changes in multiple inflammatory, metabolic and structural gene families.

overall_design: Purified adipocyte samples were isolated from subcutaneous adipose tissue surgical biopsies of 7 obese (BMI>30) and 7 lean (BMI<25) postmenoposal women and gene expression was quantified with Agilent-014850, 4X44K human whole genome platform arrays (GPL6480)

first: Willa

last: Hsueh

first: Christopher

last: Lyon

first: Tuo

last: Deng


title: Gene Expression Profiling of Tuberculous Meningitis coinfected with HIV

status: Public on Dec 31 2012

city: Bangalore

first: Akhilesh

last: Pandey

email: pandey@jhmi.edu, arivusudar@ibioinformatics.org, sameerkumar.iob@gmail.com, microarray@ibioinformatics.org

state: Karnataka

address: UnitI, Discoverer building, ITPL

country: India

institute: Institute of Bioinformatics

summary: Tuberculosis co-infected with HIV may increase the risk of causing meningitis. Tuberculous meningitis co-infected with HIV associated with high mortality and severe neurological abnormalities in affected individuals. We have carried out TBM co-infected with HIV gene expression study using whole human genome microarrays. We identified 796 differentially expressed genes with fold change cut off of 2 or more than 2. Out of 796 differentially expressed genes, 398 were upregulated and 396 were downregulated. We have validated two molecules from microarray data using immunohistochemistry.

overall_design: The proposed study carried out mRNA expression profiling of five samples from patients diagnosed with tuberculous meningitis coinfected with HIV and four head injury cases were used as controls. We have used 4X44K arrays from agilent platform. To validate our microarray results, we have done immunohistochemistry on 10 TBM+HIV cases and 10 control groups.


title: Expression data from 2-amino acetophenone (2-AA) treated mouse Skeletal muscle

status: Public on Jan 28 2013

city: Boston

first: Laurence

last: Rahme

state: MA

address: 50 Blosson St, Thier 340

department: Surgery

institute: Massachusetts General Hospital

summary:
Metabolic responses begin promptly upon the initiation of infection, and progress as a series of coordinated events. Mitochondria may play a key role in the development of insulin resistance. Reduced energy production and mitochondrial dysfunctional may further favor infection, and be an important step in the establishment of chronic and persistent infections.
We have used mouse skeletal muscle transcriptome data which have led to the hypothesis that 2-AA causes harm to the host by triggering mitochondrial dysfunction in skeletal muscle.

overall_design: The gastrocnemius muscles were isolated from control and 4days 2-AA treated mouse for RNA extraction and hybridization on Affymetrix microarrays.

first: A

last: Tzika

first: Arunava

last: Bandyopadhaya


title: Ovary transcriptome profiling via application of artificial intelligence predicts egg quality in striped bass

status: Public on Dec 10 2012

city: Charleston

first: Marion

last: Neely

state: SC

address: 331 Ft. Johnson Rd

department: NCCOS

institute: National Ocean Services

summary: We modeled profiles of ovary gene expression and their relationship to egg quality, evaluated as production of viable mid-blastula stage embryos, in striped bass (Morone saxatilis) using artificial neural networks and supervised machine learning. Collective changes in expression of a limited suite of genes (233) representing only 2% of the queried ovary transcriptome explained >90% of the eventual variance in embryo survival. Egg quality related to minor changes in expression (≤0.2-fold), with most gene transcripts making minor contribution (<1%) to the overall prediction of egg quality. Correlation analyses of this suite of candidate genes indicated that collective dysfunction of the ubiquitin-26S proteasome, COP9 signalosome, and subsequent control of the cell cycle engenders embryonic developmental incompetence in striped bass. Our results show that the transcriptomic signature evidencing this dysfunction is of, and therefore likely to influence, egg quality, a biologically complex trait that is crucial to reproductive fitness.

overall_design: Female striped bass were sorted into groups (N=8 each) producing ‘high quality’ or ‘low quality’ eggs (spawns) based upon the percentage of eggs bearing viable 4 h embryos. Spawns with >50% of eggs producing 4 h embryos were considered to be of high quality and spawns with <30% of eggs producing 4 h embryos were considered to be of low quality.

first: Benjamin

last: Reading

first: Robert

last: Chapman

first: Valerie

middle: N

last: Williams

first: Brad

last: Ring

first: Michael

last: Hopper

first: Andy

middle: S

last: McGinty

first: Craig

last: Sullivan


title: A macrophage autonomous α4β1integrin-Syk-Rac2 signaling axis controls macrophage differentiation, tumor growth and metastasis

status: Public on Nov 15 2012

first: Lei

last: Bao

address: 3855 Health Sciences Drive

department: Cancer Center

institute: UCSD

summary: Macrophages, play an essential role in promoting tumor growth by affecting angiogenesis, immune suppression, invasion and metastasis. The signal transduction events within macrophages which encode the complex cascade of events required for tumor growth and polarization of macrophages are poorly understood. We have discovered an ECM dependent signaling pathway in macrophages that regulates M2 macrophage differentiation, tumor growth, invasion and metastasis. We provide direct evidence that a macrophage autonomous, α4β1 integrin dependent Syk-Rac2 signaling axis acts in concert with the p110 isoform (PTEN-PI-3 kinase pathway) to control metastasis.

overall_design: SmoA1 Tg MB tumor cells were sorted into CD15+ and CD15- populations. RNA from these samples were hybridized to Affymetrix Mouse Genome 1.0 ST array.

first: Shweta

last: Joshi

first: Alok

middle: R

last: Singh

first: Muamera

last: Zulcic

first: Karen

last: Messer

first: Donald

last: Durden


title: Nascent-Seq Reveals Novel Features of Mouse Circadian Transcriptional Regulation [RNA-Seq]

status: Public on Nov 10 2012

city: College Station

first: Jerome

last: Menet

address: 301 Old Main Drive, Building 1530, ILSB

department: Dept of Biology

institute: Texas A&M University

summary: Over the past decade, genome-wide assays have underscored the broad sweep of circadian gene expression. A substantial fraction of the transcriptome undergoes oscillations in many organisms and tissues, which governs the many biochemical, physiological and behavioral functions under circadian control.  Based predominantly on the transcription feedback loops important for core circadian timekeeping, it is commonly assumed that this widespread mRNA cycling reflects circadian transcriptional cycling. To address this issue, we directly measured dynamic changes in mouse liver transcription using Nascent-Seq. Many genes are rhythmically transcribed over the 24h day, which include precursors of several non-coding RNAs as well as the expected set of core clock genes. Surprisingly however, nascent RNA rhythms overlap poorly with mRNA abundance rhythms assayed by RNA-seq. This is because most mouse liver genes with rhythmic mRNA expression manifest poor transcriptional rhythms, indicating a prominent role of post-transcriptional regulation in setting mRNA cycling amplitude. To gain further insight into circadian transcriptional regulation, we also characterized the rhythmic transcription of liver genes targeted by the transcription factors CLOCK and BMAL1; they directly target other core clock genes and sit at the top of the molecular circadian clock hierarchy in mammals. CLK:BMAL1 rhythmically bind at the same discrete phase of the circadian cycle to all target genes, which not surprisingly have a much higher percentage of rhythmic transcription than the genome as a whole. However, there is a surprisingly heterogeneous set of cycling transcription phases of direct target genes, which even include core clock genes. This indicates a disconnect between rhythmic DNA binding and the peak of transcription, which is likely due to other transcription factors that collaborate with CLK:BMAL1. In summary, the application of Nascent-Seq to a mammalian tissue provides surprising insights into the rhythmic control of gene expression and should have broad applications beyond the analysis of circadian rhythms.

overall_design:
Mouse liver nascent RNA profile over 6 time points of the 24h light:dark cycle, in duplicate, sequenced using Ilumina GAII (Nascent-Seq); Mouse liver mRNA profile over 6 time points of the 24h light:dark cycle, in duplicate, sequenced using Ilumina HiSeq2000 (RNA-Seq); CLK and BMAL1 DNA binding profile in the mouse liver at ZT8, sequenced along an Input sample using GAII (ChIP-Seq); Mouse liver strand-specific nascent RNA profile over 6 time points of the 24h light:dark cycle, in duplicate, sequenced using Ilumina HiSeq2000 (Strand-specific Nascent-Seq);
Supplementary file RNASeq_Mouse_Liver_NormalizedGeneSignal.txt represents mRNA abundance (reads per base pair) for each sample.

first: Joe

last: Rodriguez

last: Rosbash


title: Nascent-Seq Reveals Novel Features of Mouse Circadian Transcriptional Regulation [Nascent-Seq]

overall_design:
Mouse liver nascent RNA profile over 6 time points of the 24h light:dark cycle, in duplicate, sequenced using Ilumina GAII (Nascent-Seq); Mouse liver mRNA profile over 6 time points of the 24h light:dark cycle, in duplicate, sequenced using Ilumina HiSeq2000 (RNA-Seq); CLK and BMAL1 DNA binding profile in the mouse liver at ZT8, sequenced along an Input sample using GAII (ChIP-Seq); Mouse liver strand-specific nascent RNA profile over 6 time points of the 24h light:dark cycle, in duplicate, sequenced using Ilumina HiSeq2000 (Strand-specific Nascent-Seq);
Supplementary file NascentSeq_Mouse_Liver_NormalizedGeneSignal.txt represents Nascent RNA abundance (reads per base pair) for each sample.


title: Genome-wide gene expression profiling of mesenchymal stem cells, osteosarcoma cells, and osteosarcoma cell lines.

status: Public on Dec 19 2012

city: Oslo

first: Marieke

middle: Lydia

last: Kuijjer

address: Gaustadalléen 21

country: Norway

institute: Centre for Molecular Medicine Norway

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

overall_design: Refer to individual Series


title: Epithelial Expression of Toll-like Receptor 5 is Modulated in Healthy Smokers and Smokers with Chronic Obstructive Lung Disease

status: Public on Oct 03 2012

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: The toll-like receptors (TLRs) are important components of the respiratory epithelium host innate defense, enabling the airway surface to recognize and respond to a variety of insults in inhaled air. Based on the knowledge that smokers are more susceptible to pulmonary infection and the airway epithelium of smokers with chronic obstructive pulmonary disease (COPD) is characterized by bacterial colonization and acute exacerbation of airway infections, we assessed whether smoking alters the expression of TLRs in human small airway epithelium, the primary site of smoking-induced disease. Microarrays were used to survey the TLR family gene expression in small airway (10th-12th order) epithelium from healthy nonsmokers (n=60), healthy smokers (n=73) and smokers with COPD (n=36). Using the criteria of detection call of present in ≥50%, 6 of 10 TLRs (1, 2, 3, 4, 5 and 8) were expressed. Compared to nonsmokers, the most strikingly changed gene is TLR5, which down-regulated in healthy smokers (1.4-fold decrease, p<10-13) and in smokers with COPD (1.6-fold, p<10-14). TaqMan RT-PCR confirmed these observations. Bronchial biopsies immunofluorescence showed that TLR5 protein was expressed mainly on the apical side of the human airway epithelium and decreased in healthy smokers and smokers with COPD. In vitro studies showed that the level of TLR5 downstream genes, IL-6 and IL-8 were highly induced in TLR5 high-expressing cells compared to TLR5 low-expressing cells after flagellin exposure. In the context that TLR5 functions to recognize pathogens and activate innate immune responses, the smoking-induced down-regulation of TLR5 likely contributes to smoking-related susceptibility to airway infection.

overall_design:
The toll-like receptors (TLRs) are important components of the respiratory epithelium host innate defense. Microarrays were used to survey the TLR family gene expression in small airway (10th-12th order) epithelium from healthy nonsmokers (n=60), healthy smokers (n=73) and smokers with COPD (n=36). Using the criteria of detection call of present in ≥50%, 6 of 10 TLRs (1, 2, 3, 4, 5 and 8) were expressed. Compared to nonsmokers, the most strikingly changed gene is TLR5, which down-regulated in healthy smokers (1.4-fold decrease, p<10-13) and in smokers with COPD (1.6-fold, p<10-14). In the context that TLR5 functions to recognize pathogens and activate innate immune responses, the smoking-induced down-regulation of TLR5 likely contributes to smoking-related susceptibility to airway infection.
*** Processed data not provided for all gene expression records. ***

first: Joumana

last: Ahmed

first: Rui

last: Wang

first: Guoqing

first: Ibrahim

last: Hassan

first: Jacqueline

last: Salit

first: Ronald

last: Crystal


title: Transcriptome study in rhesus monkey

status: Public on Oct 10 2012

city: Beijing

first: Jia-Yu

last: Chen

address: No.5 Yiheyuan Road Haidian District

department: Institute of Molecular Medicine

country: China

institute: Peking University

summary: RNA-Seq technology was widely used to study gene expression, splicing structure and RNA editing. To facilitate transcriptome study in rhesus macaque, and provide an evolutionary context to understand human biology, we performed 90bp × 2, paired-end, strand-specific, polyA-postive RNA-Seq in 10 tissues of the same macaque animals. The data were deposited under accession number GSE42857 and GSE34426.

overall_design: 5 tissue samples examined: prefrontal cortex, liver, skeletal muscle, adipose, testis

first: Chuan-Yun

last: Li


title: Open chromatin maps of genetically different yeast strains

status: Public on Nov 02 2012

city: Daejeon, Seoul

first: kwoneel

last: kim

address: Gwahangno, Yuseong gu

country: South Korea

institute: KAIST

summary: Open chromatin provides access to a wide spectrum of DNA binding proteins for DNA metabolism processes such as transcription, repair, recombination, and replication. In this regard, open chromatin profiling has been widely used to identify the location of regulatory regions, including promoters, enhancers, insulators, silencers, replication origins, and recombination hotspots. For a quantitative getic analysis of chromatin regulation, we generated open chromatin maps of 100 yeast samples including the parental strains (BY and RM, and two replicates for each) and their descendants by using the FAIRE-seq technique

overall_design: Open chromatin in two parental strains and 94 segregants of their crossing

first: KiBaick

last: Lee

first: Kwoneel

last: Kim

first: Jung-Kyoon

last: Choi


title: Purified human leukocyte subtype DNA methylation profiles

status: Public on Nov 05 2012

first: William

last: Accomando

address: Kresge Bldg 911, 677 Huntington Ave

department: Epidemiology

institute: Harvard School of Public Health

summary: The objective of the study was to identify differentially methylated regions of DNA (DMRs) that distinguish human leukocyte subtypes, and hence serve as biomarkers for those immune cell types. This file contains Illumina Infinium HumanMethylation27 BeadChip data for human leukocyte subtypes that were purified from whole blood samples via magnetic activated cell sorting (MACS) and purity confirmed by flourescence activated cell sorting (FACS).

overall_design: Bisulfite converted DNA from the 73 samples were hybridized to the Illumina Infinium HumanMethylation27 Beadchip v1.2

first: John

middle: K

last: Wiencke

first: Karl

middle: T

last: Kelsey


title: Genome-wide analysis of human and mouse macrophages, resting and activated

status: Public on Sep 29 2012

city: Guildford

first: Fernando

middle: O

last: Martinez Estrada

state: Surrey

address: Stag Hill

department: Faculty of Health & Medical Sciences

institute: University of Surrey

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Genome-wide Transcriptional Responses of the Filamentous Fungus Aspergillus niger to Lignocellulose (Wheat straw) using RNA-sequencing

status: Public on Aug 27 2012

city: Nottingham

first: David

last: Archer

address: University Park

department: School of Biology

institute: University of Nottingham

summary: We have studied the physiological response of the fungus Aspergillus niger when exposed to wheat straw as a model lignocellulosic substrate. Using RNA-sequencing we showed that, 24 hours after exposure to straw, gene expression of known plant cell wall degrading enzymes represents a huge investment for the cells (about 20 % of the total mRNA). Our results also uncovered new esterases and surface interacting proteins that might form part of the fungal degradative arsenal. We also show that antisense transcripts are abundant and that their expression can be regulated by conditions.

overall_design: Triplicate samples of A. niger N402 taken at each of three timepoints: After  48 h growth in minimal media with Glucose as sole carbon source, After transfer to Wheat Straw media for 24 h and  5 h after after the exogenous addition of glucose to the wheat starw media.

first: Stéphane

last: Delmas

first: Steven

last: Pullan

first: Sanyasi

last: Gaddipati

first: Matthew

last: Kokolski

first: Sunir

last: Malla

first: Martin

last: Blythe

first: Roger

last: Ibbet

first: Maria

last: Campbell

first: Susan

last: Liddell

first: Aziz

last: Aboobaker

first: Gregory

last: Tucker


title: Differentially expressed miRNAs in TGF-β1-knock down rhabdmyosarcoma cell lines vs controls

status: Public on Sep 13 2012

city: suzhou

first: shouli

last: wang

address: renai road 199, suzhou industrial park

department: pathology

institute: soochow university school of medicine

summary: To investigate the role of TGF-β1-regulated miRNAs in the progression of RMS,we performed comprehensive miRMA microarray analysis on RNA derived from typical RMS cell lines and TGF-β1 knock-down cell lines. We identified a novel set of TGF-β1-related miRNAs.

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

overall_design: Total RNA was isolated from TGF-β1-knock down rhabdmyosarcoma cell lines and controls. Three-condition experiment: shRNA-TGF-β1/RD cells vs. shRNA-Control/RD cells, shRNA-TGF-β1/SMS-CTR cells vs. shRNA-Control/ SMS-CTR cells, and shRNA-TGF-β1/RH28 cells vs. shRNA-Control/RH28 cells. Biological replicates: 1 RD cells stably transfected with shRNA-TGF-β1- pSUPER gfp-neo, 1SMS-CTR cells stably transfected with shRNA-TGF-β1- pSUPER gfp-neo, 1RH28 cells stably transfected with shRNA-TGF-β1- pSUPER gfp-neo, 1RD cells stably transfected with shRNA-Control- pSUPER gfp-neo, 1SMS-CTR cells stably transfected with shRNA-Control- pSUPER gfp-neo, and 1RH28 cells stably transfected with shRNA-Control- pSUPER gfp-neo, independently grown and harvested. One replicate per array.

first: Shouli

last: Wang


title: Expression profiling of TGF-beta-induced and hnRNP E1-mediated epithelial-mesenchymal transition

status: Public on Aug 30 2012

first: Philip

last: Howe

address: howelab

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

summary:
Regulation of gene expression at the post-transcriptional level plays an indispensable role during TGFbeta-induced EMT and metastasis. This regulation involves a transcript-selective translational regulatory pathway in which a ribonucleoprotein (mRNP) complex, consisting of heterogeneous nuclear ribonucleoprotein E1 (hnRNP E1) and eukaryotic elongation factor 1A1 (eEF1A1), binds to a 3’-UTR regulatory BAT (TGFβ activated translation) element and silences translation of Dab2 and ILEI mRNAs, two transcripts which are involved in mediating EMT. TGFbeta activates a kinase cascade terminating in the phosphorylation of hnRNP E1, by isoform-specific stimulation of protein kinase B/Akt2, inducing the release of the mRNP complex from the 3’-UTR element, resulting in the reversal of translational silencing and increased expression of Dab2 and ILEI transcripts.
We adopted a combinatorial approach involving polysome profiling and RIP-Chip analyses using hnRNP E1 and filtered the array data based on the regulatory mechanism of Dab2 and ILEI. This led to the identification and validation of a cohort of target mRNAs that follow the same pattern of regulation as Dab2 and ILEI.

overall_design: To identify potential target mRNA transcripts that are translationally regulated by hnRNP E1 in a TGF-beta-dependent manner, we adopted a combinatorial approach involving expression profiling analyses and RNA immunoprecipitation analysis (RIP-Chip). We performed a screen using: 1) total mRNA and 2) RNA isolated from monosomal (non-translating) versus polysomal (translating) fractions from TGF-beta-treated (24 h) and non-treated NMuMG cells and from the hnRNP E1 knockdown derivative (E1KD), that undergo constitutive EMT even in the absence of TGF-beta. In addition, we screened for transcripts that selectively interact with hnRNP E1 in NMuMG cells under unstimulated conditions and subsequently lose their temporal association following TGF-beta stimulation. The samples were individually hybridized to Affymetrix GeneChip® Mouse Genome 430 2.0 arrays.

first: George

last: Hussey


title: Molecular Characterization of 126 Intermediate Risk Prostate Cancer Patient Samples

status: Public on Sep 28 2012

city: Toronto

first: Igor

last: Jurisica

state: ON

address: 101 College St.

country: Canada

institute: Princess Margaret Cancer Center

type: Genome variation profiling by genome tiling array

summary: The primary objective of this study was to correlate genetic alterations from Hh pathway genes with biochemical free relapse rate.

overall_design:
aCGH data of 126 intermediate risk men with histologically confirmed adenocarcinoma of the prostate who had chosen radical radiotherapy as their primary treatment between 1996-2006.

Please note that the '2014-11-11_IGRT_aCGH_gene_matrix_GEO.csv' was generated as following;
The gene matrix is a gene by sample matrix, where -1 corresponds to deletion, 0 to copy neutral, and 1 to gain. The normalized data on GEO was converted from hg18 to hg19 using the liftOver tool from UCSC (version dated 2011-11-27). Fragments overlapping centromeres, telomeres, or other gaps in the hg18 build were trimmed conservatively (regions were shortened rather than elongated). To generate contiguous CNA regions, probe-based CNA calls were collapsed with neighbouring probes within the same chromosome with the same copy number. CNA regions with only one supporting probe were removed. In addition, any CNAs found entirely within centromeres or telomeres, as defined by the UCSC ~Qgap~R table, were removed. CNA regions were intersected with a merged and collapsed version of the RefSeq gene annotation (GRCh37/hg19) to generate gene-based CNA calls. This gene list was further filtered to match the published gene list from the MSKCC radical prostatectomy cohort

The 'IGRT_full_clinical_info.txt' file contanis additional/updated clinical data (including survival).

first: Chad

middle: M

last: McKee

first: Ruth

last: Muschel


title: piRNAs initiate an epigenetic memory of non-self RNA in the C. elegans germline.

status: Public on Jul 17 2012

city: Worcester

first: Craig

last: Mello

address: 368 Plantatoin Street, Suite AS5-2047

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

type: Non-coding RNA profiling by high throughput sequencing

summary: Organisms exhibit a fascinating array of gene-silencing pathways, which have evolved in part, to confront invasive nucleic acids such as transposons and viruses. A key question raised by the existence of these pathways is how do they distinguish “self” from “non-self” nucleic acids?  Evidence exists for a number of mechanisms that might facilitate detection of foreign sequences including mechanisms that sense copy-number, unpaired DNA, or aberrant RNA (e.g.dsRNA). Here we describe an RNA-induced epigenetic silencing pathway, RNAe, that permanently silences single-copy transgenes. We show that the Piwi Argonaute PRG-1 and its genomically encoded piRNA cofactors initiate RNAe, while maintenance depends on chromatin factors and the WAGO Argonaute pathway. Our findings support a model in which PRG-1 scans for foreign sequences, while two other Argonaute pathways serve as epigenetic memories of "self" and "non-self" RNAs. These findings suggest how organisms may utilize RNAi-related mechanisms not only to recognize and silence foreign genes, but also to keep inventory of all genes expressed in the germ-line.

overall_design: Examine small RNA population changes in different transgene lines. FLAG::WAGO-9 was immunoprecipitated from 20 mg of lysate essentially as described (Gu et al., 2009). Small RNAs were extracted from WAGO-9 immune complexes as well as a portion of the input lysate, gel-purified, pre-treated with TAP, cloned and sequenced as described (Gu et al., 2009).

first: Masaki

last: Shirayama

first: Meetu

last: Seth

first: Heng-Chi

last: Lee

first: Weifeng

last: Gu

first: Takao

last: Ishidate

first: Darryl

last: Conte


title: Comparison of gene expression profile of naive versus arsenic trioxide resistant acute promyelocytic leukemia cell line NB4

status: Public on Aug 02 2013

first: Genotypic

last: technology

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

institute: Genotypic Technology

summary: The aim of this study was to gain insight into the potential mechanism of resistance to arsenic trioxide (ATO). The gene expression profile of naive (NB4) (Acute promyelocytic leukemia (APL) cell line and one of its in house generated ATO resistant sub clone (NB4-VM-AsR1) was done using whole genome microarray and compared to generate the differential expression profile which will give insight into the mechanisms of ATO resistance in APL.

overall_design:
Agilent one-color experiment,Organism: Human ,Agilent Whole Genome Human 4x44k (AMADID: 014850)  , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)
naive versus arsenic trioxide resistant acute promyelocytic leukemia cell line NB4

first: Vikram

last: Mathews

first: Ezhilarasi

last: Chendamarai


title: The Expression of MicroRNA and microRNA Clusters in the Aging Heart

status: Public on Aug 20 2012

city: Little Rock

first: Jeanne

last: Wei

address: 4301 West Markham Street

department: Geriatrics

institute: University of Arkansas for Medical Sciences

summary: Adult aging is a complex biological process associated with altered gene expression and a decline in physiological performance. The microRNAs have been implicated in cardiac development, cardiac hypertrophy and heart failure. However, the impact of adult aging on cardiac expression of both miRNA guide strand (miR) and passenger strand (miR*), as well as miRNA clusters have not been well established.    We explored the expression profile of both miR and miR* in the heart. We found that 65 miRNAs were differentially expressed in old versus young adult heart; approximately half of them were clustered miRNAs that were distributed in 11 miRNA clusters. Each miRNA cluster contains from 2 to as many as 71 miRNA genes. The majority of the clusters displayed unified expression, with most cluster members within a cluster being either increased or decreased together, suggesting that most clusters are regulated by a common signaling mechanism and that the combined expression of multiple miRNA genes in a cluster could pose an impact on a broad range of targets during aging. We also found age-related changes in the expression of miR*s. Bioinformatic analysis revealed that miR-21 and miR-21* had their own silencing targets. The expression of both miR and miR* correlated with that of pri-miRNA transcript over the time course from development and maturation through adult aging. Age-related changes in the expression of Ago1 and Ago2 proteins in the heart were also observed.    Our data suggest that a concert of effects, including transcriptional regulation of pri-miRNA transcript and altered expression of Argonaut proteins, contribute to age-related changes in the expression of both miR and miR* strands during adult aging. The major changes occurred later in life, from middle to old age. It is likely that the expression of both miR and miR* is regulated by transcription and Ago1 and Ago2 proteins.

overall_design: Six healthy C57BL/6 mice were used in this study. Three of them were 4 months old (young adult mice: YA), and the other three were 24 months old (old mice). Total RNA samples were isolated from mouse hearts and then shipped to Exiqon Inc., where microRNA array analysis was performed. Three array slides were used for the hybridization. Each array slide hybridized with two samples labeld with either Hy3 or Hy5, with array #1 being hybridized with samples YA-1 (Hy3) and Old-1 (Hy5), array #2 with samples YA-2 (Hy3) and Old-2 (Hy5) and array #3 with samples YA-3 (Hy5) and Old-3 (Hy3). In our publication, we reveal the detail of the experiment and statistical analysis that were provided by Exiqon Inc.

first: Xiaomin

last: Zhang

first: Gohar

last: Azhar

middle: Y


title: The Peripheral Blood Transcriptome Predicts the Presence and Extent of Disease in Idiopathic Pulmonary Fibrosis

status: Public on Jul 01 2012

city: Aurora

first: David

last: Schwartz

state: CO

address: Anschutz Medical Campus

department: Medicine

institute: University of Colorado, Anschutz Medical Campus

summary: Peripheral blood biomarkers are needed to identify and determine the extent of idiopathic pulmonary fibrosis (IPF). Current physiologic and radiographic prognostic indicators diagnose IPF too late in the course of disease. These results demonstrate that the peripheral blood transcriptome can distinguish normal individuals from patients with IPF, as well as extent of disease when samples were classified by percent predicted DLCO, but not FVC.

overall_design: Gene expression profiles of peripheral blood RNA from 93 IPF patients were collected on Agilent microarrays. Blood was collected in PAXRNA tubes.  30 healthy controls are compared to IPF patients classified by disease severity when categorized by DLCO or FVC.

first: Ivana

last: Yang

first: Mark

last: Steele


title: Time Series of gene expression during the course of myogenic differentiation in mouse skeletal muscle cells

status: Public on Jul 05 2012

city: Ottawa

first: Theodore

last: Perkins

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary: In skeletal myogenesis, the transcription factor MyoD activates distinct transcriptional programs in progenitors compared to terminally differentiated cells. Using ChIP-seq and gene expression analyses, we show that in primary myoblasts, Snail-HDAC1/2 repressive complex bind and exclude MyoD from its targets. Notably, Snail binds E-box motifs that are G/C-rich in their central dinucleotides, and such sites are almost exclusively associated with genes expressed during differentiation. By contrast, Snail does not bind the A/T-rich E-boxes associated with MyoD targets in myoblasts. Thus, Snai1-HDAC1/2 prevents MyoD occupancy on differentiation-specific regulatory elements and the change from Snail- to MyoD-binding often results in enhancer switching during differentiation. Furthermore, we show that a regulatory network involving Myogenic Regulatory Factors (MRFs), Snail/2, miR-30a and miR-206 acts as a molecular switch that controls entry into myogenic differentiation. Together, these results reveal a regulatory paradigm that directs distinct gene expression programs in progenitors versus terminally differentiated cells.

overall_design: This data set contains 3 replicates of a myotube growth time series (0h, 2d, 5d). The data was RMA normalized per replicate set.

first: Vahab

middle: D

last: Soleimani

first: Michael

last: Rudnicki


title: Portrait of early-onset breast cancer in Brazilian patients: germline mutation screening of BRCA1, BRCA2 and TP53 genes and tumor expression profiling

status: Public on Apr 09 2013

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

summary: Differentially expressed genes between BRCA1/BRCA2 negative and positive mutation driven-tumors.

overall_design: Screening for germline mutations was performed in a cohort of 55 patients under the age of 35 years in the BRCA1, BRCA2, CHEK2 (c.del1,100C) and TP53 genes, and the respective tumors were investigated regarding hormonal receptors status, HER2 expression. Transcriptional profiles were performed using Agilent one color hybridizations in a G4112F platform.

first: Dirce

last: Carraro

first: Maria

last: Brentani


title: Gene expression changes in IPF

status: Public on Jun 30 2012

city: Birmingham

first: Yan

last: Sanders

state: AL

address: 901 19th Street S

institute: University of Alabama at Birmingham

summary: To compare the gene expression changes in IPF and normal lung tissues.

overall_design: 4 IPF and 4 Normal samples


title: C. elegans piRNAs mediate the genome-wide surveillance of germline transcripts

status: Public on Sep 01 2012

first: Craig

last: Mello

summary: Piwi Argonautes and Piwi-interacting RNAs (piRNAs) mediate genome defense by targeting transposons. However, many piRNA species lack obvious sequence complementarity to transposons or other loci. For example, only one C. elegans transposon is a known piRNA target. Here we show that, in mutants lacking the Piwi Argonaute PRG-1 and associated piRNAs (21U-RNAs), many silent loci in the germline exhibit increased levels of mRNA expression and depletion of an amplified RNAdependent RNA polymerase (RdRP)-derived species of small RNA termed 22G-RNAs. Sequences depleted of 22G-RNAs are enriched nearby potential target sites that base pair imperfectly but extensively to 21U-RNAs. We show that PRG-1 is required to initiate, but not to maintain, silencing of transgenes engineered to contain complementarity to endogenous 21U-RNAs. Our findings support a model in which C. elegans piRNAs utilize their enormous repertoire of targeting capacity to scan the germline transcriptome for foreign sequences, while endogenous germline-expressed genes are actively protected from piRNA-induced silencing.

overall_design: Examine small RNA population changes in prg-1 and rescued strains

first: Heng-Chi

last: Lee

first: Weifeng

last: Gu


title: CG methylated microarrays identify novel methylated sequence bound by the CEBPB|ATF4 heterodimer that are active in vivo

status: Public on Mar 08 2013

city: Kolkata

first: Raghunath

last: Chatterjee

state: WB

address: 203 BT Road, HGU, Indian Statistical Institute

department: Human Genetics Unit

institute: Indian Statistical institute

type: Methylation profiling by high throughput sequencing

summary: To evaluate the effect of CG methylation on DNA binding of sequence-specific B-ZIP transcription factors (TFs) in a high-throughput manner, we enzymatically methylated the cytosine in the CG dinucleotide on protein binding microarrays.  Using this novel technology, we show that CG methylation enhanced binding for CEBPA and CEBPB and inhibited binding for CREB, ATF4, JUN, JUND, CEBPD and CEBPG.  The CEBPB|ATF4 heterodimer bound a novel motif CGAT|GCAA 10-fold better when methylated.  EMSA confirmed these results.  CEBPB ChIP-seq data using primary female mouse dermal fibroblasts with 50X methylome coverage for each strand indicate that the methylated sequences well-bound on the arrays are also bound in vivo.  CEBPB bound 39% of the methylated canonical 10-mers ATTGC|GCAAT in the mouse genome.  After ATF4 protein induction by thapsigargin which results in ER stress, CEBPB binds methylated CGAT|GCAA in vivo, recapitulating what was observed on the arrays.  mRNA-seq of primary female mouse dermal fibroblasts with and without thapsigargin identified differentially expressed genes.  Genes that are commonly bound by CEBPB and ATF4 to TGAT|GCAA (the best-bound 8-mer in the array) at the promoters were highly expressed and up-regulated or remained unchanged in the thapsigargin treated primary female mouse dermal fibroblasts.

overall_design:
RNA-Seq: Examination of whole genome transcriptome profiles (RNA-seq) of primary mouse dermal fibroblasts with and without Thapsigargin treatment
ChIP-Seq: Examination of transcription factor binding in dermal fibroblasts with and without Thapsigargin teratment
BS-Seq: Determination of whole genome DNA methylation profiles (BS-seq) of primary mouse dermal fibroblasts

first: Charles

last: Vinson


title: Snail regulates MyoD binding-site occupancy to direct enhancer switching and differentiation-specific transcription in myogenesis

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

overall_design: Refer to individual Series

middle: A


title: Modulation of Cystatin A Expression in Human Airway Epithelium Related to Genotype, Smoking COPD and Lung Cancer

status: Public on Jun 20 2012

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

institute: Weill Cornell Medical College

type:
Expression profiling by array
SNP genotyping by SNP array

summary: Cystatin A (gene: CSTA), is up-regulated in non-small-cell lung cancer (NSCLC) and dysplastic vs normal human bronchial epithelium. In the context that chronic obstructive pulmonary disease (COPD), a small airway epithelium (SAE) disorder, is independently associated with NSCLC (especially squamous cell carcinoma, SCC), but only occurs in a subset of smokers, we hypothesized that genetic variation, smoking and COPD modulate CSTA gene expression levels in SAE, with further up-regulation in SCC. Gene expression was assessed by microarray in SAE of 178 individuals [healthy nonsmokers (n=60), healthy smokers (n=82), and COPD smokers (n=36)], with corresponding large airway epithelium (LAE) data in a subset (n=52). Blood DNA was genotyped by SNP microarray. Twelve SNPs upstream of the CSTA gene were all significantly associated with CSTA SAE gene expression (p<0.04 to 5 x 10-4). CSTA gene expression levels in SAE were higher in COPD smokers (28.4 ± 2.0) than healthy smokers (19.9 ± 1.4, p<10-3), who in turn had higher levels than nonsmokers (16.1 ± 1.1, p<0.04). CSTA LAE gene expression was also smoking-responsive (p<10-3). Using comparable publicly available NSCLC expression data, CSTA was up-regulated in SCC vs LAE (p<10-2) and down-regulated in adenocarcinoma vs SAE (p<10-7). All phenotypes were associated with significantly different proportional gene expression of CSTA to cathepsins. The data demonstrate that regulation of CSTA expression in human airway epithelium is influenced by genetic variability, smoking, and COPD, and is further up-regulated in SCC, all of which should be taken into account when considering the role of CSTA in NSCLC pathogenesis.

overall_design:
CSTA gene expression was assessed in the small airway epithelium obtained by bronchoscopy from 178 individuals, including healthy nonsmokers (n= 60) and healthy smokers (n= 118) and the large airway epithelium from healthy nonsmokers (n=21) and healthy smokers(n=31).
*** Processed data not provided for all gene expression records. ***

Blood DNA from the majority of these individuals was genotyped and an association analysis of gene expression with genotypes of all 48 SNPs within 100 kb of CSTA was performed in PLINK, and tested for significance following 103 permutations within ancestral clusters.
Supplementary file (linked below) reports genotypes of all 48 SNPs within 100 kb of the CSTA gene for the 112 genotyping Samples.

first: Marcus

middle: W

last: Butler

first: Tomoya

last: Fukui

first: Jacqueline

last: Salit

first: Renat

last: Shaykhiev

first: Jason

last: Mezey

first: Neil

last: Hackett

first: Ronald

last: Crystal


title: DNA Copy-Number Alterations in clear-cell Renal Cell Carcinoma (ccRCC) Tumors and Tumorgrafts for samples deficient in BAP1 or PBRM1

status: Public on Jun 10 2012

city: Dallas

first: Samuel

last: Peña-Llopis

address: 6000 Harry Hines Blvd., NB5.102

department: Internal Medicine - Oncology Division

institute: UT Southwestern Medical Center

summary: Renal cell carcinoma (RCC) exhibits some unusual features and genes commonly mutated in cancer are rarely mutated in clear-cell RCC (ccRCC), the most common type. The most prevalent genetic alteration in ccRCC is the inactivation of the tumor suppressor gene VHL. Using whole-genome and exome sequencing we discovered BAP1 as a novel tumor suppressor in ccRCC that shows little overlap with mutations in PBRM1, another recent tumor suppressor. Whereas VHL was mutated in 81% of the patients (142/176), PBRM1 was lost in 58% and BAP1 in 15% of the patients analyzed. All these tumor suppressor genes are located in chromosome 3p, which is partially or completely lost in most ccRCC patients. However, BAP1 but not PBRM1 loss was associated with higher Fuhrman grade and, therefore, poorer outcome. Xenograft tumors (tumorgrafts) implanted orthotopically in mice retained >92% of mutations and exhibited similar DNA copy number alterations to corresponding primary tumors. Thus, after inactivation of VHL, the acquisition of a mutation in BAP1 or PBRM1 defines a different program that might alter the fate of the patient. Our results establish the foundation for an integrated pathological and molecular genetic classification of about 70% of ccRCC patients, paving the way for subtype-specific treatments exploiting genetic vulnerabilities.

overall_design: The genomic DNA of clear-cell renal cell carcinoma (ccRCC) primary tumors, tumors growing in immunodeficient mice (tumorgrafts), and normal samples were labeled and hybridized to Affymetrix SNP arrays 6.0.

first: James

last: Brugarolas


title: Bovine Peyer's Patch Infected with Mycobacterium avium ssp. paratuberculosis and Mycobacterium avium ssp. avium

status: Public on Oct 03 2012

city: College Station

first: Leslie

middle: Garry

last: Adams

address: 402 Raymond Stotzer Blvd.

department: Veterinary Pathobiology

institute: Texas A&M University

summary:
Mycobacterium avium subspecies paratuberculosis (MAP) infection is established following the ingestion of bacteria, their penetration of the intestinal mucosa and subsequent events of the host-parasite interaction. These bacteria invade M cells, macrophages and are capable of resisting host defenses and multiply to reach very high numbers intracellular. Mycobactrium avium subsp. avium (MAA) is an antigenically and genetically similar organisms but is relatively nonpathogenic for cattle.  MAA organisms appear to infect cattle, but unlike cattle infected with MAP, cattle infected with MAA typically mount an effective systemic immune response, form caseous granuloma, and eliminate the infection. This study was designed to understand the similarities and differences in the host responses during MAP and MAA infection.  Neonatal calves were infected (ligated ileal loops) with PBS, MAP, or avirulent MAA following which samples were collected at 30 min, 1h, 2h, 4h, 8h, or 12h. Post-infection, RNA was collected, processed, and then hybridized to custom bovine gene expression arrays, each of which represented 13,258 transcripts spotted in duplicate.  Arrays were normalized by scaling against the average reference intensity value (i.e., average across all arrays), normalized by global mean, and then log transformed before statistical analyses were performed. Pairwise comparisons of averaged signal values and Student’s t test were performed using GeneSifter software (VizX Labs, Seattle, WA). A fold-change of at least 1.5-fold and a p value of 0.05 or less was required for a difference in signal to be considered statistically significant.   When comparing the transcriptional responses of calves infected with the MAA versus MAP, unique patterns of expression were clearly visible. In general, numbers of transcripts altered in response to infection were much greater for MAA-infected animals than for those infected with the MAP.  No genes were significantly up-regulated in MAP-infected animals at the earliest time point tested (30 min), and only modest numbers of genes were increased in expression over the experimental time course. On the other hand, up-regulated transcripts were detected by 30 min in MAA-infected animals and peaked by 2 hr. Differences in the numbers of down-regulated genes between MAP-infected and MAA-infected animals (compared to PBS-infected controls) were less pronounced. At the earliest time points, MAP-infected calves had a greater number of down-regulated genes than did animals infected with MAA. This trend was reversed at 8 and 12 hr post-infection.

Keywords: Gene expression profiling by microarray

overall_design: Microarrays were used to examine the transcriptional profiles of bovine intestinal mucosa inoculated with PBS, MAP or MAA and  across six time points (30 min, 1, 2, 4, 8, and 12 hours).  Experiments were performed in quadruplicate for PBS, MAP, and MAA (bovine ligated ileal loops surgeries were performed with four calves).  For one surgery, MAA was used for 4 time ponts only, thus generateing a total of 70 arrays.

first: Sangeeta

last: Khare

first: Sara

last: Lawhon

first: Carlos

last: Rossetti

first: Robin

middle: E

last: Everts

first: Cristi

middle: L

last: Galindo

first: Josely

middle: F

last: Figueiredo

first: Jairo

last: Nunes

first: Tamara

last: Gull

first: Kenneth

last: Drake

first: Harold

last: Garner

first: Harris

last: Lewin

first: L


title: Transcriptome of 4 developmental stages of Colletotrichum higginsianum during infection of Arabidopsis thaliana

status: Public on Jun 04 2012

city: Cologne

first: Emiel

last: Ver Loren van Themaat

address: Carl von linneweg

country: Germany

institute: Max Planck Institute

overall_design: 3 biological replicates per stage. The four stages are : in vitro apressoria (VA), penetrating apressoria (AP), Biotrophic hyphea from the biotrophic phase (BH) and the switch from biotrophic hyphea to necrotrophic phase(SW). Each biological replicate of the last three stages, the in planta stages, was two fold deeper due to plant contamination (Arabidopsis thaliana)


title: Altered DNA Methylation Profile in Idiopathic Pulmonary Fibrosis

first: Yan

last: Sanders

type:
Methylation profiling by array
Expression profiling by array


title: T Cell Activation in Microgravity Compared to 1g (Earth's) Gravity

status: Public on Jun 21 2012

city: San Francisco

first: Tammy

last: Chang

address: 513 Parnassus Ave., HSW 1601

department: Surgery

institute: University of California, San Francisco

summary: This study tested the hypothesis that transcription of immediate early genes is inhibited in T cells activated in microgravity (mg).  Immunosuppression during spaceflight is a major barrier to safe long-term human space habitation and travel.  The goals of these experiments were to prove that mg was the cause of impaired T cell activation during spaceflight as well as understand the mechanisms controlling early T cell activation.  T cells from 4 human donors were stimulated with concanavalin A (ConA) and anti-CD28 onboard the International Space Station (ISS).  An onboard centrifuge was used to generate a 1g simultaneous control to isolate the effects of mg from other variables of spaceflight.  Microarray expression analysis after 1.5 hours of activation demonstrated that mg- and 1g-activated T cells had distinct patterns of global gene expression and identified 47 genes that were significantly differentially down-regulated in mg.  Importantly, several key immediate early genes were inhibited in mg.

overall_design: T cells were isolated from human volunteers.  T cells from each donor were kept separate and loaded into individual chambers in separate cassettes for the following treatments: mg non-activated, mg activated, and 1g activated.  Therefore, samples represent biological triplicates.  Experimental units were launched into space and placed into the KUBIK facility onboard the International Space Station.   The 1g units were placed in the central centrifuge positions and centrifuged with an applied 1g force.  The mg units were place in the static positions for continued mg exposure.  After 30 minutes of pre-incubation, mg non-activated units were fixed by addition of RNALater (QIAGEN, Valencia, CA), removed from the incubator, and stored in 4°C.  The mg and 1g activated units were injected with final concentration 10mg/ml Con A and 4mg/ml anti-CD28.  These cassettes were replaced into KUBIK on either the centrifuge or static positions and activated for 1.5 hours.  Activation was stopped with the addition of RNALater and the units were then moved to 4°C storage.  All units were returned to Earth for analysis.

first: Millie

last: Hughes-Fulford


title: Molecular Genetic Classification of clear-cell Renal Cell Carcinoma (ccRCC) based on the Gene Expression Profiling of Tumors and Tumorgrafts deficient for BAP1 or PBRM1

first: Samuel

last: Peña-Llopis

summary: Renal cell carcinoma (RCC) exhibits some unusual features and genes commonly mutated in cancer are rarely mutated in clear-cell RCC (ccRCC), the most common type. The most prevalent genetic alteration in ccRCC is the inactivation of the tumor suppressor gene VHL. Using whole-genome and exome sequencing we discovered BAP1 as a novel tumor suppressor in ccRCC that shows little overlap with mutations in PBRM1, another recent tumor suppressor. Whereas VHL was mutated in 81% of the patients (142/176), PBRM1 was lost in 58% and BAP1 in 15% of the patients analyzed. All these tumor suppressor genes are located in chromosome 3p, which is partially or completely lost in most ccRCC patients. However, BAP1 but not PBRM1 loss was associated with higher Fuhrman grade and, therefore, poorer outcome. Xenograft tumors (tumorgrafts) implanted orthotopically in mice exhibited similar gene expression profiling to corresponding primary tumors. Gene expression profiling of tumors and tumorgrafts displayed different signatures for BAP1- and PBRM1-deficient samples. Thus, after inactivation of VHL, the acquisition of a mutation in BAP1 or PBRM1 defines a different program that might alter the fate of the patient. Our results establish the foundation for an integrated pathological and molecular genetic classification of about 70% of ccRCC patients, paving the way for subtype-specific treatments exploiting genetic vulnerabilities.

overall_design: The RNA of clear-cell renal cell carcinoma (ccRCC) primary tumors, tumors growing in immunodeficient mice (tumorgrafts), and normal kidney cortices were labeled and hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays.

first: James

last: Brugarolas


title: Role of class III HD‐ZIP transcription factors in shade signaling

status: Public on Jun 01 2012

city: Frederiksberg C

first: Stephan

last: Wenkel

address: Thorvaldsensvej 40

country: Denmark

institute: University of Copenhagen

summary: Unlike the situation in animals, the final morphology of the plant body is highly modulated by the environment. During Arabidopsis development, intrinsic factors provide the framework for basic patterning processes. CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD‐ZIPIII) transcription factors are involved in embryo, shoot and root patterning and during vegetative growth regulate several polarity set‐up processes such as in leaves and the vascular system. Here we show that besides being involved in basic patterning, HD‐ZIPIII transcription factors also have a critical role in controlling elongation growth that is induced when plants experience shade. By using a ChIP‐Seq approach, we have identified several direct target genes of the HD‐ZIPIII transcription factor REVOLUTA (REV). We show that REV acts upstream of auxin biosynthesis and directly regulates several HAT transcription factors that control shade avoidance responses in Arabidopsis. Plants in which HD‐ZIPIII genes are mutated show altered responses to shade revealing that the basic patterning machinery also regulates adaptive development. Thus, HD-ZIPIII transcription factors contribute to shade signaling and act upstream of both auxin and HAT activation.

overall_design: A. thaliana REVOLUTA ChIP-seq w control

first: Ronny

last: Brandt

first: Thomas

last: Musielak

first: Christa

last: Lanz

first: Felix

last: Ott

first: Markus

last: Schmid

last: Greb


title: Planarian stem cell transcriptome

city: Portland

first: Bret

middle: J

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

summary: Many long-lived species of animals require the function of adult stem cells throughout their lives.  However, the transcriptomes of stem cells in invertebrates and vertebrates have not been compared, and consequently ancestral regulatory circuits that control stem cell populations remain poorly defined.  In this study, we have used data from high-throughput RNA sequencing (RNA-Seq) to compare the transcriptomes of pluripotent adult stem cells from planarians with the transcriptomes of human and mouse pluripotent embryonic stem cells.  From a stringently-defined set of 4,432 orthologs shared between planarians, mice and humans, we identified 123 conserved genes that are ≥ 5-fold differentially expressed in stem cells from all three species.  Guided by this gene set, we used RNAi screening in adult planarians to discover novel stem cell regulators, which we found to affect the stem cell-associated functions of tissue homeostasis, regeneration, and stem cell maintenance.  Examples of genes that disrupted these processes included the orthologs of TBL3, PSD12, TTC27, and RACK1.  From these analyses, we concluded that by comparing stem cell transcriptomes from diverse species, it is possible to uncover conserved factors that function in stem cell biology.  These results provide insights into which genes composed the ancestral circuitry underlying the control of stem cell self-renewal and pluripotency.

overall_design: Three planarian tissues were analyzed:  stem cells, stem cell progeny, and differentiated tissues.  For the manuscript:  Labbe, RM, et. al., 2012, Stem Cells

first: B


title: Peripheral blood DNA methylation profiles are predictive of head and neck squamous cell carcinoma

status: Public on Jun 24 2012

city: Cincinnati

first: Scott

last: Langevin

state: OH

address: 160 Panzeca Way, ML0056

department: Department of Environmental Health

institute: University of Cincinnati College of Medicine

summary: Genome wide DNA methylation profiling and semi-supervised classification of blood samples from a case-control study of head and neck squamous cell carcinoma (HNSCC). The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in peripheral blood. Samples included peripheral blood samples from 92 incident cases of HNSCC and 92 control subjects.

overall_design: Bisulphite converted DNA from the 184 samples were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: S

first: K

last: Kelsey


title: Global microRNAs profile and signaling pathways in the development of hypertrophy

status: Public on Jun 09 2012

city: Guangzhou

first: Wei

last: Ouyang

state: Guangdong

address: 253 Gongyedadao Road, Guangzhou, People's Republic of China

department: Department of Nuclear Medicine,Zhujiang Hospital, Southern Medical University,Guangzhou,  People's Republic of China

summary: The aberrantly expressed differences of microRNAs in the cardiac hypertrophy model between sham surgery and TAC surgery methods were successfully detected. The global miR expression profile, comprehensive prediction of miR targets and signaling pathway analysis during cardiac hypertrophy were conducted in depth.

overall_design: In this study, the aberrantly expressed situation of microRNAs in the cardiac hypertrophy model with TAC surgery was compared with the one in the sham surgery model, which was used with MicroRNA microarray assay. Besides, related bioinformatics analyses including miR targets and signaling pathway were finished.

first: Huijuan

last: Feng

first: Jinhua

last: Liu

first: Yungang

last: Sun

first: Rui

last: Hu

first: Liuhua

last: Huang

first: Jialiang

last: Xian

first: Chenfeng

last: Jing

first: Maojun

last: Zhou


title: Methylation Changes in Soybean Early Maturation Seed Parts

status: Public on May 11 2012

city: Los Angeles

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary: Seeds are comprised of three majors parts of distinct parental origin: the seed coat, embryo, and endosperm.  The maternally-derived seed coat is important for nurturing and protecting the seeds during development.  By contrast, the embryo and the endosperm are derived from a double fertilization event, where one sperm fertilizes the egg to form the diploid zygote and the other sperm fertilizes the central cell to form the triploid endosperm.  Each seed parts undergo distinct developmental programs during seed development.  What methylation changes occurring in the different seed parts, if any, remains unknown. To uncover the possible role of DNA methylation in different parts of the seed, we characterized the methylome of three major parts of an early maturation stage seed: seed coat, embryonic cotyledons, and embryonic axis using Illumina sequencing.

overall_design: Illumina sequencing of bisulfite-converted genomic DNA, transcripts, and small RNAs from three parts of an early maturation stage seed: seed coat (EM-SC), embryonic cotyledons (EM-COT), and embryonic axis (EM-AX).

first: Robert

middle: B

first: Min

last: Chen

first: Jer-Young

last: Lin

first: Brandon

middle: H

last: Le


title: Methylation Changes in Soybean Early Maturation Seed Compartments Using Laser Capture Microdissection (LCM)

summary: What methylation changes are occurring in different compartments of early maturation stage seed largely remains unknown. To uncover the possible role of DNA methylation in different compartments of early maturation stage seed, we characterized the methylome of two major compartments (abaxial parenchyma and adaxial parenchyma) in embryonic cotyledon, four major compartments (parenchyma, plumule, root tip, and vascular) in embryonic axis, and seed coat layers (parenchyma and palisade) using Illumina sequencing. The whole seed coat and embryonic cotyledons were captured using LCM to serve as controls.

overall_design: Illumina sequencing of bisulfite-converted genomic DNA from cotyledon abaxial parenchyma (EM-COT-ABPY), cotyledon adaxial parenchyma (EM-COT-ADPY), seed coat parenchyma (EM-SC-PY), seed coat palisade (EM-SC-PA), axis parenchyma (EM-AX-PY), axis plumule (EM-AX-PL), axis root tip (EM-AX-RT), axis vascular (EM-AX-VS), whole seed coat (EM-SC), and whole embryonic cotyledons (EX-COT)

first: Jer

first: Jungim

last: Hur


title: Real-time quantitative PCR analysis of miRNA expression in human melanoma MMRU cell line after Sox4 knockdown

city: Vancouver

first: Seyed Mehdi

last: Jafarnejad

state: BC

address: Room 436A, 2660 Oak St.

department: Dermatology and Skin Science

institute: The University of British Columbia

summary: We used Applied Biological Materials (ABM)’s miRNA profiling platform to quantitate expression of miRNAs in a human melanoma cell line (MMRU) in Sox4 siRNA treated cells (siSox4) compared with the control siRNA treated cells (siCTR) or after overexpression of Flag-Dicer in Sox4 knockdown cells (siSox4=F-Dicer) compared with control cells.

overall_design: 72 hours after transfection, Total RNA from siCTR, siCTR+empty Flag-vector (CTR), siSox4 or siSox4+-F-Dicer transfected MMRU cells was prepared with Qiazol extraction followed by Poly-A Tailing reactions and miRNA cDNA synthesis (ABM C204). Real-time qPCR reactions and instrumental analysis was performed using Roche LightCycler480.

first: Mehdi

first: Gholamreza

middle: S

last: Ardekani

first: Mazyar

last: Ghaffari

first: Magdalena

last: Martinka

first: Gang

last: Li


title: Characterization of gene expression profiles of gastric cancer in MD Anderson Cancer Center cohort

status: Public on Apr 30 2012

city: Houston

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: Clinical heterogeneity of gastric cancer reflected in unequal outcome of treatment is poorly defined in molecular level, and molecular subtypes and their associated biomarkers have not been established to improve prognostification and treatment of gastric cancer. Using microarray technologies, we analyzed gene expression profiling data from patients with advanced gastric cancer and uncovered potential prognostic subtypes and identify gene expression signature associated with prognosis.

first: Ju-Seog

last: Lee


title: Microarray analysis of gene expression differences in prostate specific antigen negative (PSA-ve) cells versus PSA+ve cells in LAPC9 and LNCaP prostate cancer (PCa) cells

status: Public on May 10 2012

city: Smithville

first: Dean

middle: G

last: Tang

address: 1808 Park road 1C

department: Carcinogenesis

institute: U.T M. D. Anderson Cancer Center

summary: Prostate cancer (PCa) is heterogeneous containing both phenotypically differentiated and undifferentiated tumor cells. An important unanswered question is whether these two populations of PCa cells are functionally different. Here we report the distinct molecular, cellular, and tumor-propagating properties of PCa cells that express high (i.e., PSA+) and low (PSA-/lo) levels of the differentiation marker PSA (prostatespecific antigen). PSA-/lo PCa cells are quiescent and resistant to multiple stresses including androgen deprivation, exhibit high clonogenic potential, and possess long-term tumor-propagating capacity in male mice. They preferentially express stem cell-associated genes and can undergo asymmetric cell division generating PSA+ cells. Importantly, PSA-/lo PCa cells can initiate robust tumor development in castrated hosts, survive androgen deprivation, and harbor highly tumorigenic castration-resistant PCa cells that can be further enriched using the ALDH+CD44+α2β1+ phenotype. In contrast, PSA+ PCa cells possess more limited tumor-propagating capacity, mainly undergo symmetric division, and are sensitive to castration. Together, our study suggests that PSA-/lo and PSA+ PCa cells are functionally distinct and PSA-/lo cells may represent one critical source of castration-resistant PCa cells.

overall_design: There are two sets of samples in this study corresponding to two different prostate cancer cell lines LNCaP and LAPC9. Both LNCaP and LAPC9 sets include 3 technical triplicates each that were performed onvdual color arrays and each individual array includes comparison between PSA- (Cy5) and PSA+ (Cy3) cells of the respective cell line.

first: Jichao

last: Qin

first: Xin

last: Liu

first: Brian

last: Laffin

first: Grace

last: Choy

first: Collene

last: Jeter

first: Tammy

last: Calhoun-Davis

first: Hangwen

first: Ganesh

last: Palapattu

first: Shen

last: Pang

first: Kevin

first: Jiaoti

first: Ivan

last: Ivanov

first: Mahipal

middle: V

last: Suraneni


title: Genome-wide gene expression analysis of high-grade osteosarcoma

status: Public on Mar 28 2012

city: Oslo

first: Marieke

middle: Lydia

last: Kuijjer

address: Gaustadalléen 21

institute: Centre for Molecular Medicine Norway

summary: We performed genome-wide gene expression data of high-grade osteosarcoma samples. In order to detect osteosarcoma drivers, we integrated these data with copy number data. We performed two different methods - a non-paired and a paired integrative analysis.

overall_design: Genome-wide gene expression analysis was performed on 84 pre-treatment high-grade osteosarcoma diagnostic biopsies, of which 29 overlapped with the 32 samples used for copy number analysis. Two different sets of control samples were used for comparison: osteoblasts (n=3) and mesenchymal stem cells (n=12, GEO accession number GSE28974).

first: Halfdan

last: Rydbeck

first: Stine

last: Kresse

first: Emilie

middle: P

last: Buddingh

first: Ola

last: Myklebost

first: Horst

last: Bürger

first: Pancras

middle: C

last: Hogendoorn

first: Leonardo

last: Meza-Zepeda

first: Anne-Marie

last: Cleton-Jansen


summary: Genome-wide gene expression profiling of mesenchymal stem cells (MSCs).

overall_design: 12 MSC samples were hybridized on Illumina Human-6 v2.0 BeadChips.


title: Gene expression profiles uncover molecular classifiers for the prediction of progression-free survival in diffuse large B-cell lymphoma: results of a DASL assay from formalin fixed paraffin embedded tissue

status: Public on May 25 2012

city: Seoul

first: Insuk

last: Sohn

address: 50, Irwon-Dong, Gangnam-Gu

institute: samsung cancer research Institute

summary:
Diffuse large B-cell lymphoma (DLBCL) exhibits heterogeneous clinical outcomes even in tumors of the same stage and with similar pathological characteristics. A substantial number of patients with DLBCL still fail to be cured despite recent improvements in therapy.
In this study, we used formalin fixed paraffin embedded (FFPE) tumor samples for microarray gene expression profiling to develop robust prognostic profiles for DLBCL.

overall_design: We performed a retrospective microarray gene expression profiling study of FFPE from a cohort of DLBCL patients using the whole genome cDNA mediated Annealing, Selection and Ligation (WG-DASL) assay. After removing poor-quality samples, data from 164 patients were used for statistical analyses to develop and validate a prognostic gene expression signature using a gradient lasso and leave-one-out cross-validation process.


title: RNA-Seq Quantification of the Transcriptome of Genes Expressed in the Small Airway Epithelium of Nonsmokers and Smokers

status: Public on Mar 05 2012

city: New York

first: Yael

last: Strulovici-Barel

department: Department of Genetic Medicine

summary: The small airway epithelium (SAE) the pseudostratified epithelium that covers the majority of the human airway surface from the 6th generation to the alveoli, is the major site of lung disease caused by smoking, and the cell population that exhibits the earliest manifestations of smoking-induced disease. The focus of this study is to use RNA-Seq (massive parallel sequencing technology) to sequence all polyA+ mRNAs expressed by the SAE of healthy nonsmokers to gain new insights into the biology of the SAE, and how these cells respond to cigarette smoke. Taking advantage of RNA-Seq providing quantitative mRNA levels, that data demonstrates that while the SAE shares its transcriptome with many cell types, it has unique characteristics that are enriched in this cell population, with the mostly highly expressed genes (SCGB1A1) characteristics of Clara cells, an airway epithelial cell unique to the human small airways. Among other genes expressed by the SAE are those characteristic of ciliated and mucin-producing cells, basal cells and neuroendocrine cells. The RNA-Seq data includes identification of the highly expressed SAE transcription factors, transmembrane receptors, signaling ligands and growth factors. RNA-Seq permitted quantification of expression of highly homologous gene families, the absolute smoking-induced changes in SAE gene expression, including genes expressed at low levels, and assessment of the effect of smoking on SAE gene splicing. Together, these observations can serve as the baseline for assessment of the dysregulation of SAE gene expression in human airway disease.

overall_design: The small airway epithelium (SAE) is the major site of lung disease caused by smoking, and the cell population that exhibits the earliest manifestations of smoking-induced disease. This study used RNA-Seq  to sequence all polyA+ mRNAs expressed by the SAE of 5 healthy nonsmokers to gain new insights into the biology of the SAE, and evaluate how these cells respond to cigarette smoke using 6 healthy smoker samples (SRA029282.1). Taking advantage of RNA-Seq providing quantitative mRNA levels, that data demonstrates that while the SAE shares its transcriptome with many cell types, it has unique characteristics that are enriched in this cell population.  Coverage of RNA-Seq expression was also compared to the HG-U133 Plus 2.0 microarray expression of 27 previously published healthy nonsmoker samples presented here.

first: Neil

middle: R

last: Hackett

first: Marcus

last: Butler

first: Jacqueline

last: Salit

first: Larsson

last: Omberg

first: Juan

last: Rofriguez-Florez

first: Jason

last: Mezey

first: Ronald

last: Crystal


title: The PSA-/lo prostate cancer cells harbor self-renewing long-term tumor-propagating cells that resist castration

first: Dean

last: Tang

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

overall_design: Refer to individual Series

first: Jichao

last: Qin

first: Xin

last: Liu

first: Brian

last: Laffin

last: Chen

first: Grace

last: Choy

first: Collene

last: Jeter

first: Tammy

last: Calhoun-Davis

first: Hangwen

last: Li

first: Ganesh

last: Palapattu

first: Shen

last: Pang

first: Kevin

last: Lin

first: Jiaoti

last: Huang

first: Ivan

last: Ivanov

first: Wei

first: Mahipal

last: Suraneni


title: Plac8-dependent and iNOS-dependent T cell-mediate mechanisms clear Chlamydia muridarum infections from the genital tract

status: Public on Mar 14 2012

city: New Haven

first: Raymond

middle: Morris

last: Johnson

state: CT

department: Med/Infectious Diseases

institute: Yale University

summary: Comparison of two Chlamydia-specific CD4 T cells that are dependent on iNOS to terminate Chlamydia replication in epithelial cells to two Chlamydia-specific CD4 T cells that are iNOS-independent:  Chlamydia trachomatis urogenital serovars replicate predominately in epithelial cells lining the reproductive tract.  This tissue tropism poses a unique challenge for the host immune system and vaccine development.  Studies utilizing the Chlamydia muridarum mouse model have shown that CD4 T cells are critical and sufficient to clear primary genital tract infections.  In vitro studies have shown that CD4 T cells terminate the infection in epithelial cells by up regulating epithelial iNOS transcription and nitric oxide production via IFN-gamma and T cell-epithelial cell interactions mediated by LFA-1-ICAM-1.  This mechanism however is not critical as iNOS-deficient mice clear infections normally, and IFN-gamma deficient mice clear 99.9% of the infection with near normal kinetics.  We recently showed that a subset of Chlamydia-specific CD4 T cell clones were able to terminate replication in epithelial cells using a mechanism that was independent of iNOS and IFN-gamma.  That mechanism did not require physical lysis of infected cells, but instead required T cell degranulation.  In this study we advanced that work using gene expression microarrays to compare CD4 T cell clones that are able to terminate epithelial replication via an iNOS-independent mechanism to iNOS-dependent CD4 T cell clones.  Micro array experiments showed that Plac8 was differentially expressed by the T cell clones having the iNOS-independent mechanism.  Plac8-deficient mice had significantly delayed clearance of C. muridarum genital tract infections, and that the large majority of Plac8-deficient mice treated with the iNOS-inhibitor N-monomethyl-L-arginine (MLA) were unable to resolve a C. muridarum genital tract infection over 8 weeks.  These results demonstrate that there are two independent and redundant T cell mechanisms for clearing C. muridarum genital tract infections; one mechanism dependent on iNOS, the other mechanism dependent on Plac8.  While T cells subsets have been defined by cytokine profiles, there are important subdivisions by effector functions, in this case CD4Plac8.

overall_design: Gene expression study using 4 experimental groups with 4 replicates each.

middle: M

first: Micah

last: Kerr

first: James

last: Slaven


title: Type I and II Interferon-Stimulated Genes in Murine Primary Bone Marrow Macrophages

status: Public on Feb 15 2012

first: Su-Yang

address: 615 Charles E. Young Dr. South Rm 246

department: Microbiology, Immunology, and Molecular Genetics

summary: We used microarrays to compare interferon-alpha (IFNa)- and interferon-gamma (IFNg)-stimulated genes under an equivalent biological input. The goal was to compare IFNa- and IFNg-stimulated genes, as well as to identify common and distinct sets of type I and II ISGs.

overall_design: Bone marrow macrophages derived from mouse bone marrow in M-CSF for 7 days. The cells were stimulated with 62U/mL IFNa and 1U/mL of IFNg for 2.5 hrs in culture. These concentrations induced equivalent STAT1 phosphorylation in BMMs.

first: Su

middle: Y

first: Genhong

last: Cheng


title: Human colon cancer HT-29 and LS174T cells: stably transfected with shRNA-Ascl2/EGFP vs. stably transfected with shRNA-Control/EGFP

status: Public on Jan 07 2012

city: Chongqing

first: Rongquan

last: Wang

state: Chongqing

address: Gaotanyan Main Street 30#

department: Department of Gastroenterology

institute: Southwest Hospital

summary: Achaete scute-like 2 (Ascl2), a basic helix-loop-helix (bHLH) transcription factor, controls the fate of intestinal stem cells. However, the role of Ascl2 in colon cancer progenitor cells remains unknown. The cell lines HT-29 (47.5-95% of CD133+ population) and LS174T (0.45% of CD133+ population) were chosen for functional evaluation of Ascl2 in colon cancer progenitor cells after gene knockdown by RNA interference.  The microRNA (miRNA) microarrays identified 26 two-fold up-regulated miRNAs and 58 two-fold down-regulated miRNAs in shRNA-Ascl2/HT-29 cells and 178 two-fold up-regulated miRNAs and 172 two-fold down-regulated miRNAs in shRNA-Ascl2/LS174T cells.

overall_design: Two-condition experiment: shRNA-Ascl2/HT-29 cells vs. shRNA-Ctr/HT-29 cells, and shRNA-Ascl2/LS174T cells vs. shRNA-Ctr/LS174T cells. Biological replicates: 1 HT-29 cells stably transfected with shRNA-Ascl2/EGFP, 1 LS174T cells stably transfected with shRNA-Ascl2/EGFP, 1 HT-29 cells stably transfected with shRNA-Control/EGFP, and 1 LS174T cells stably transfected with shRNA-Control/EGFP, independently grown and harvested. One replicate per array.

first: Rong

last: Zhu


title: ArrayCGH of human hepatocellular carcinoma (HCC)

status: Public on Jan 20 2012

city: Bethesda

first: Xin

middle: Wei

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

summary: We used array-based comparative genomic hybridization (arrayCGH) of 76 hepatocellular carcinomas (HCCs) to search for genetically disrupted genes.

overall_design: Seventy-six HCC clinical specimens were analyzed. Genomic DNA of the tumor sample was labeled with Cy5 and reference normal DNA (Promega) was labeled with Cy3.

first: Stephanie

last: Roessler


title: Identification of osteosarcoma driver genes by integrative analysis of copy number and gene expression data

first: Marieke

last: Kuijjer

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

summary:
High-grade osteosarcoma is a tumor with a complex genomic profile, occurring primarily in adolescents with a second peak at middle age. The extensive genomic alterations obscure the identification of genes driving tumorigenesis during osteosarcoma development. In order to identify such driver genes, we integrated DNA copy number profiles (Affymetrix SNP 6.0) of 32 diagnostic biopsies with 84 expression profiles (Illumina Human-6 v2.0) of high-grade osteosarcoma as compared with its putative progenitor cells, i.e. mesenchymal stem cells (n=12) or osteoblasts (n=3). In addition, we performed paired analyses between copy number and expression profiles of a subset of 29 patients for which both DNA and mRNA profiles were available. Integrative analyses were performed in Nexus Copy Number software and statistical language R. Paired analyses were performed on all probes detecting significantly differentially expressed genes in corresponding LIMMA analyses. For both non-paired and paired analyses, copy number aberration frequency was set to >35%. Non-paired and paired integrative analyses resulted in 45 and 101 genes, respectively, which were present in both analyses using different control sets. Paired analyses detected >90% of all genes found with the corresponding non-paired analyses. Remarkably, approximately twice as many genes as found in the corresponding non-paired analyses were detected. Affected genes were intersected with differentially expressed genes in osteosarcoma cell lines, resulting in 31 new osteosarcoma driver genes. Cell division related genes, such as MCM4 and LATS2, were overrepresented and genomic-instability was predictive for metastasis-free survival, suggesting that deregulation of the cell cycle is a driver of osteosarcomagenesis.

This SuperSeries is composed of the SubSeries listed below.

overall_design: For data processing, we refer to the individual series. We performed both non-paired and paired integrative analyses on SNP and gene expression data. Non-paired integrative analysis was performed by importing lists of differentially expressed genes into the Copy Number module of Nexus software version 5 (BioDiscovery, CA). Based on the length of the gene list, Nexus software performs a Fisher's exact test in order to determine whether the number of differentially expressed genes in a specific region with a significant copy number alteration is larger than expected by chance. Genes present in such regions of copy number alteration with FDR-adjusted P-values (Q-bounds in Nexus software) < 0.05 were returned from this integrative analysis. Nexus software only reports genes which are both gained and overexpressed, or both deleted and downregulated. For the paired integrative analysis, copy number data of all autosomal overlapping genes between the copy number and gene expression arrays were exported from Nexus software, and converted into a binary file containing all genes with a gain (1) and no gain (0), and a similar binary file for losses. As in the non-paired integrative analysis, we did not apply any restrictions on the size of copy number alterations. Gene expression data of each probe for each sample were normalized against average gene expression of the corresponding probes over all control samples (either expression data from 12 MSCs, or from 3 osteoblasts). This was performed by subtracting the average expression of the control samples from the expression levels of the sample of interest, since these are log-transformed expression values. For both analyses, only genes that were significantly differentially expressed between the 84 osteosarcoma samples and the specific control set were analyzed, in order to make sure that no genes returned from the integrative analysis were not significantly differentially expressed. Subse quently, genes that overlapped between the copy number binary files and that matched the fold change of expression (upregulation for genes with gains, and downregulation for genes with losses) were returned.


title: Expression data from mouse pancreatic cell lines treated with chromatin-targeting small molecules

status: Public on Mar 09 2012

city: Cambridge

first: Paul

middle: A

last: Clemons

state: MA

address: 7 Cambridge Center

department: Chemical Biology Program

institute: Broad Institute of Harvard and MIT

summary:
We measured the genome-wide expression changes induced by 29 compounds targeting HDACs, DNMTs, histone lysine methyltransferases (HKMTs), and protein arginine methyltransferases (PRMTs) in pancreatic α- and β-cell lines.
We used microarrays to detail the global programme of gene-expression changes induced by chromatin-targeting compounds at 1, 6, and 24 hours.

overall_design: To identify a comprehensive list of target genes that can be regulated by modulating the activities of chromatin-modifying enzymes, we measured the genome-wide transcriptional effects of 29 compounds in pancreatic alpha and beta cell lines at three time points. The results indicate that compounds cause similar effects independent of the cell line in which they were profiled. All clinical HDAC inhibitors fell into the structural classes of hydroxamic acids and ortho-amino anilides, respectively and up- and down-regulated hundreds of transcripts. In contrast, more selective compounds like the HKMT inhibitor BIX-01294 have specific effects.

first: Stefan

last: Kubicek

first: Joshua

last: Gilbert

first: Dina

last: Fomina-Yadlin

first: Alexander

middle: D

last: Gitlin

first: Yuan

last: Yuan

first: Florence

last: Wagner

first: Edward

last: Holson

first: Tuoping

last: Luo

first: Timothy

last: Lewis

first: Bradley

last: Taylor

first: Supriya

last: Gupta

first: Alykhan

last: Shamji

first: Bridget

middle: K

first: Stuart

last: Schreiber


title: Gene expression profiles in human kidney cancer cells in response to FoxO1 or FoxO3 activation

status: Public on Oct 21 2011

first: Sujun

last: Hua

state: Tx

address: 1901 East Rd

institute: MD Anderson Cancer Center

summary: The mammalian FoxO transcription factors - FoxO1, FoxO3, FoxO4 - function in the nucleus to direct transcription of specific gene targets governing cellular survival, proliferation, metabolism, differentiation and oxidative defense. Activation of PI3K by extracellular growth factors leads to AKT-mediated phosphorylation of FoxO1, FoxO3 and FoxO4, resulting in their sequestration in the cytoplasm such that they are unable to regulate their gene targets. Our study identified FoxOs as novel tumor suppressors in kidney cancer (Gan et al, 2010, Cancer Cell). To understand the tumor suppression function of FoxOs in kidney cancer cells, we performed gene expression profiling in human kidney cancer cells upon FoxO1 or FoxO3 reactivation in order to identify the key transcriptomic alterations mediating FoxO tumor suppression function in kidney cancer cells.

overall_design: We generated RCC4 and UMRC2 cell lines (two human kidney cancer cells with low endogenous FoxO1 and FoxO3 expression) with stable expression of FoxO1(TA)ERT2 or FoxO3(TA)ERT2 construct, which expressed a fusion protein consisting of FoxO(TA) (containing three Ser/Thr AKT phosphorylation sites mutated to alanine) fused to the T2-modified estrogen receptor (ERT2) moiety. We documented that the FoxO(TA)ERT2 fusion protein sequestered FoxO(TA) in the cytoplasm and that 4OHT treatment resulted in rapid translocation of FoxO(TA)ERT2 into the nucleus. We also established stable cell lines with ERT2 expression as control cell lines. (For simplicity, ERT2, FoxO1(TA)ERT2 and FoxO3(TA)ERT2 cell lines will be referred to as EV (empty vector), FoxO1 and FoxO3, respectively, hereafter). We then conducted comparative transcriptome analysis (using the Human Genome U133 Plus 2.0 Array) of EV, FoxO1, or FoxO3-expressing RCC4 and UMRC2 cells at 12 hours with or without 100 nm 4OHT treatment (cultured in DMEM+10% FBS with puromycin selection). To enrich for more proximal actions of FoxO, we selected the 12 hour time point as time course studies revealed dramatic transcriptional changes of known FoxO targets (such as Cyclin D1), yet no discernable cellular phenotypes (apoptosis and cell cycle arrest). We generated 4 transcriptome datasets: FoxO1 RCC4, FoxO3 RCC4, FoxO1 UMRC2, and FoxO3 UMRC2 (by comparing transcriptome data with or without 4OHT treatment), and normalized these transcriptome data against 4OHT-treated EV cells, which show modest 4OHT-induced transcriptional changes.

first: Boyi

last: Gan

first: Ronald

last: DePinho


title: Expression data from Adriamycin-treated Emu-myc; Suv39h1-/- B-cell lymphoma

status: Public on Jul 04 2013

city: Berlin

first: Maja

last: Milanovic

address: Augustenburgerplatz 1

department: Hematology and Oncology

institute: Charite University Medicine, Berlin

summary: Oncogene-induced senescence (OIS), a terminal cell cycle block countering (pre)neoplastic lesions, is characterised on the molecular level by trimethylated histone H3 lysine 9 (h3K9me3), a transcriptionally repressive chromatin mark linked to silencing of S-phase-promoting genes. Whether H3K9-governed chromatin remodelling influences anticancer treatment-induced senescence (TIS) and whether functional control of this mark impacts on treatment outcome is not known. We used global gene expression profiling by microarrays to gain insight into the molecular responses of Emu-myc; Suv39h1-/- B-cell lymphoma cells to senescence-inducing anticancer agent Adriamycin (ADR).

overall_design: Primary lymphoma cells isolated from lymph nodes of Emu-Myc; Suv39h1-/- mice were used. In this model, the c-Myc oncogene is constitutively expressed in the cells of the B-cell lineage, leading to spontaneous development of aggressive B-cell lymphomas. Adriamycin (ADR), a cytostatic drug used as a standard part of several lymphoma treatment regimens, is known to massively induce TIS in Suv39h1-proficient lymphomas, protected from apoptosis by Bcl-2 over expression (Myc;Bcl2). In order to discern the impact of Suv39h1 to TIS induction under these conditions, we analysed here transcriptional profiles of matched pairs of Emu-myc;Suv39h1-/-;Bcl2 lymphomas, untreated or treated for 5 days with ADR.

first: Clemens

last: Schmitt

first: Michael

last: Hummel

first: Dido

last: Lenze

first: Jan

last: Dörr