title: Effect of MG132 on expression profile of Schistosoma mansoni adult worms

status: Public on Dec 16 2014

city: São Paulo

first: Katia

middle: Cristina Pereira

last: Oliveira

state: O

address: Av Prof lineu prestes 748

department: Centro de Parasitologia e Micologia

country: Brazil

institute: Instituto Adolfo Lutz

summary:
Transcriptional profiling of MG132 treated S. mansoni adult worms (50uM of MG132 in DMSO during 24h) vs. Non-treated S.mansoni adult worms (DMSO during 24h)
Two conditions (treated vs. Non-treated) with four biological samples of treated worms (MG132 1, 2, 3 and 4) and four biological samples of non-treated worms (Control 1, 2, 3 and 4). For each sample (four treated and four non-treated) were performed two technical replicas.

overall_design: Enyara,R,Morais

first: Lizandra

middle: G

last: Magalhães

first: Renato

last: de Paula

first: Alice

first: Érika

last: Moreira

first: Sergio

last: Verjovski-Almeida

first: Vanderlei

last: Rodrigues


title: miRNA transcriptome of Zmpste24-decifient mouse embryonic fibroblasts

status: Public on Dec 30 2014

city: Bronx

first: Hwa Jin

last: Jung

address: 1301 Morris Park Avenue

country: USA

institute: Albert Einstein College of Medicine

type: Expression profiling by high throughput sequencing

summary: In this study, we employed massively parallel sequencing technology to identify miRNAs expressed in Zmpste24 WT MEF and Zmpste24-/- MEF. With data from 19.5 ×106 reads from WT MEFs and 16.5 × 106 reads from Zmpste24-/- MEFs, we discovered a total of 306 known miRNAs expressed in MEFs with a wide dynamic range of read counts ranging from 10 to over 1 million. A total of 8 miRNAs were found to be significantly down-regulated, with only 2 miRNAs upregulated, in Zmpste24-/- MEFs as compared to WT MEFs.

overall_design: Examination of miRNA profile in Zmpste24 WT MEF and Zmpste24-/- MEF

first: Y

last: Suh


title: Lung gene expression analysis of WT, Nlrp3-, Asc-deficient mice in Streptococcus pneumoniae D39 and ATCC6303 infection

status: Public on Dec 15 2014

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

summary: Streptococcus (S.) pneumoniae is the most frequently isolated causative pathogen community-acquired pneumonia, a leading cause of mortality worldwide. We investigated the role of the inflammasome sensor NLRP3 and the inflammasome adapter ASC during S. pneumoniae pneumonia. Detailed analysis of the early inflammatory response in the lung by whole genome transcriptional profiling, we identified several mediators that were differentially expressed between Nlrp3-/- and Asc-/ - mice.

overall_design: WT, Nlrp3- and Asc-deficient mice were intranasally inocculated with Streptococcus pneumoniae D39 and ATCC6303 both at high and low dose. Lung homogenates were harvested and gene expression profiling was performed.

middle: P

first: Tom

last: van der Poll


title: High resolution nulceotide level methylation map of female mouse primary keratinocytes

status: Public on Dec 08 2014

city: Kolkata

first: Raghunath

last: Chatterjee

state: WB

address: 203 BT Road, HGU, Indian Statistical Institute

department: Human Genetics Unit

country: India

institute: Indian Statistical institute

type: Methylation profiling by high throughput sequencing

summary: We determined the high resolution methylation maps of female mouse primary keratinocytes and compared these maps at nucleotide level with the female mouse primary dermal fibroblasts. Single nucleotide level methylation maps led us to identify several additional features of CG methylation. We have detected that differentially methylated regions are epigenetically marked in other cells including embryonic stem cells and neuronal progeniator cells. Different new charecteristics and functions were also discovered with these methylation maps.

overall_design: Determinationof whole genome DNA methylation profiles (BS-seq) of primary mouse keratinocytes

first: Charles

last: Vinson


title: Gene expression profiles during larval development for pearl oyster, Pinctada fucata

status: Public on Dec 04 2014

city: Peking

first: Jun

last: Liu

address: school of lifer science

country: China

institute: Tsinghua University

summary: A microarray analysis has been employed to study the knowledge of different developmental stages and the related gene expression profiles of P.fucata. Our study focused on the global genes expression profiles of the fertilized egg, trochophore, D-shaped stage, umbonal stage, juvenile of P.fucata. Fertilized eggs were harvested immediately after insemination, the trochophore stage, D-shaped stage, umbonal stage larvae and juvenile stage samples were then collected at 24h, 48h, 14days or 35days after a microscopy counting to ensure more than 80% of the individuals had reached the certain growing stages. The collected larvae were snap-frozen in liquid nitrogen, and stored at -80°C.

overall_design: In total, 15 pools of samples from 5 different developmental stages larvae were used for the microarray analysis. Three biological replicates were employed in each developmental stage.

first: Liping

last: Xie

first: Rongqing

last: Zhang


title: Release of Human Cytomegalovirus from latency by a KAP1/TRIM28 phosphorylation switch

status: Public on Mar 18 2015

city: Lausanne

first: Adamandia

last: Kapopoulou

address: Station 15

department: Sciences de la Vie

country: Switzerland

institute: EPFL

type: Genome binding/occupancy profiling by high throughput sequencing

summary: A new actor of HCMV latency is unveiled, where KAP1 protein binds to viral genome to recruit SetDB1 and trigger H3K9 trimethylation. A switch of phosphorylation state mediated by mTOR leads to lytic replication, opening new approaches to curtail CMV infection but also to purge the virus from organ transplants.

overall_design: Analyses of transcriptional profiles and chromatin state in KAP1 WT and KO (or KD)  cells

first: Benjamin

last: Rauwel

first: Suk

middle: M

last: Jang

first: Marco

last: Cassano

first: Isabelle

last: Barde

first: Didier

last: Trono


title: Whole transcriptome of Lewis lung carcinoma cells of Mus musculus

status: Public on Dec 03 2014

city: Novosibirsk

first: Evgeniy

last: Brenner

state: Russia

address: Lavrentiev av., 8

country: Russia

institute: ICBFM SB RAS

summary: Purpose: To study the alteration of whole transcriptome of Lewis lung carcinoma (LLC) cells after the decreasing of malignant properties of tumor by treatment of tumor-bearing mice with RNase A. Methods: Whole transcriptome profile of Lewis lung carcinoma before and after RNase A treatment were generated by deep sequencing using SOLiD 5.5. The sequence reads were mapped by Bioscope 1.3 software, differential expression was evaluated by Cufflinks v.2.0.1 package. Results: Difference in expression was found for 966 genes.  Conclusions: Our study represents the first detailed analysis of alteration of transcriptome of Lewis lung carcinoma after the decrease of malignant prtoperties of the tumor (proliferation and invasion) by RNase A.

first: Nadezhda

middle: L

last: Mironova

first: Olga

middle: A

last: Patutina

first: Evgenyi

middle: V

first: Alexander

last: Kurilshikov

first: Valentin

last: Vlassov

first: Marina

last: Zenkova


title: The effect of REST and its alternatively spliced transcript, REST-003, on breast cancer invasiveness

status: Public on Dec 01 2014

city: Los Angeles

middle: Sook

last: Lee

state: California

address: 1501 San Pablo St.

department: Biomedical Engineering

institute: University of Southern California

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

overall_design: Refer to individual Series


title: Effect of REST-003 downregulation on cancer invasiveness in MDA-MB-231 cells using RNA-sequencing (RNA-seq) analysis .

summary: Fifty six genes from DESeq were differentially expressed in the treated versus control samples.  More than 20% were related to immune, defense, wounding and inflammatory responses

overall_design: Downregulation of  REST-003 using siRNAs in MDA-MB-231 cells; we used siRNA against REST-003, as REST-003 may control invasiveness.  We transfected si-Control (scramble) or si-REST-003 in MDA-MB-231:  duplicate of both (total 4 samples).

middle: S

first: Tade

last: Souaiaia

first: Jennifer

last: Herstein

first: Oleg

last: Evgrafov


title: Effect of REST on cancer invasiveness in MCF-7 and MDA-MB-231 cells using RNA-sequencing (RNA-seq) analysis .

summary:
We report a negative correlation of invasiveness with REST expression. In addition, one alternatively spliced product (ASP) of REST, REST-003, shows a positive correlation with invasiveness.
REST has a well-established role in regulating transcription of genes important for neuronal development.  Its role in cancer, though significant, is less well understood.  We would like to investigate the effect of REST on invasive phenotype.  In order to do so, we downregulate REST by siRNA treatment in weakly invasive MCF-7 breast cancer cells in which REST is expressed highly: 1) si-GAPDH (control), two si-RESTs (2)si-REST_1 and 3) si-REST_2).  Conversely, we  overexpress REST by transfection of wt-REST cDNA in highly invasive MDA-MB-231 cells in which REST is expressed at the low level:  4) EGFP (control), 5) mt-REST (another control) and 6) wt-REST.
REST (repressor element-1 (RE-1) silencing transcription factor) contains a DNA-binding domain that is localized within eight zinc fingers and two repressor domains located at the N-terminal and C-terminal, respectively.   REST suppresses expression of neural-specific genes.  mt-REST lacks two repressor domains, so it can be used as a control for wt-REST.  In contrast, REST-003 is one of alternatively spliced products (ASPs) of REST.

overall_design:
Downregulation of REST using two siRNAs in MCF-7 cells or overexpression of REST with wt- or mt-REST cDNA in MDA-MB-231 cells
REST_ISOFORM_FIG1.pdf was provided to explain *rawRestIsoformCnts.txt files described in the README1.txt file.


title: Affymetrix SNP array data for colon cancer samples

city: Uppsala

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

country: Sweden

institute: Uppsala University

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

summary: DNA from resected colon cancer primary tumour tissue was analyzed for association between tumour dissemination and copy number alterations.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved tissue samples.

first: Markus

last: Mayrhofer

first: Hanna

last: Kultima

first: Helgi

last: Birgisson

first: Magnus

last: Sundström

first: Lucy

last: Mathot

first: Karolina

last: Edlund

first: Björn

last: Viklund

first: Tobias

last: Sjöblom

first: Johan

last: Botling

first: Patrick

last: Micke

first: Lars

last: Påhlman

first: Bengt

last: Glimelius


title: Gene expression patterns in the horned beetles Onthophagus taurus responding to nutritional variation

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

summary: This is a study on genome-wide transcriptional responses to nutritional variation and their dependency on trait and sex in the beetle Onthophagus taurus.

overall_design: This study compares the gene expression level of 16 conditions in Onthophagus taurus. Briefly, we compared two nutritional conditions (optimal and sub-optimal) of male and female animals by using 4 different body regions (2x2x4). Each condition includes pooled RNA samples from 4 animals (64 animals in total). We used the square combining table for the effectiveness of comparisons, which allowed us to generate 48 pairs of comparisons without sacrificing robustness of analyses. These comparisons include biological replicates as well as dye-swaps.

first: Teiya

last: Kijimoto

first: Emilie

last: Snell-Rood

first: Melissa

last: Pespeni

first: Guilherme

last: Rocha

first: Karen

last: Kafadar

first: Armin

last: Moczek


title: Expression data from Regulatory T Cells either exposed to normal salt media or high salt media (+40mM NaCl)

status: Public on Nov 18 2014

city: New Haven

first: Mitja

last: Mitrovic

address: 300 George Street

department: Neurology

institute: Yale School of Medicine

summary:
Sodium Chloride Inhibits Suppressive Function of Foxp3+ Regulatory T Cells
Given the functional changes observed secondary to exposure to high-salt we wanted to know what expression based changes were taking place in the regulatory T cell population that might help to explain the evidenced functional deficits.

overall_design: Regulatory T Cells (Tregs) were incubated either in the presence or absence of an additional 40mM NaCl for 3 days with anti-CD3/anti-CD28 to ascertain phenotypic and expression based changes in the cellular population.

first: Amanda

last: Hernandez

first: David

last: Hafler


title: RNA processing proteins regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA.

status: Public on Nov 20 2014

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: Eukaryotic cells respond to DNA double-strand breaks (DSBs) by activating a checkpoint that depends on the protein kinases Tel1/ATM and Mec1/ATR. Mec1/ATR is activated by RPA-coated single-stranded DNA (ssDNA), which arises upon nucleolytic degradation (resection) of the DSB. Emerging evidences indicate that RNA processing factors play critical, yet poorly understood, roles in genomic stability. Here, we provide evidence that the Saccharomyces cerevisiae RNA decay factors Xrn1, Rrp6 and Trf4 regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA. The lack of Xrn1 inhibits ssDNA generation at the DSB by preventing the loading of the MRX complex. By contrast, DSB resection is not affected in the absence of Rrp6 or Trf4, but their lack impairs the recruitment of RPA, and therefore of Mec1, to the DSB. Rrp6 and Trf4 inactivation affects neither Rad51/Rad52 association nor DSB repair by HR, suggesting that full Mec1 activation requires higher amount of RPA-coated ssDNA than HR-mediated repair. Noteworthy, deep transcriptome analyses do not identify common misregulated gene expression that could explain the observed phenotypes. Our results provide a novel link between RNA processing and genome stability.

overall_design: Strand-specific transcriptome analysis of biological replicates of WT cells (JKM139 strain) at T0, or 60 and 240 minutes after HO induction, and of xrn1∆, rrp6∆ and trf4∆ cells at T0.

first: Nicola

last: Manfrini

first: Camilla

last: Trovesi

first: Marina

last: Martina

first: Daniele

last: Cesena

first: Marc

last: Descrimes

first: Antonin

last: Morillon

first: Fabrizio

last: d’Adda di Fagagna

first: Maria

last: Longhese


title: The influence of reduced oxygen availability on gene expression in Laboratory (H37Rv) and clinical strains (S7 and S10) of Mycobacterium tuberculosis

city: Chennai

first: Alamelu

last: Raja

state: Tamil Nadu

address: No,1 Mayor sathyamoorthy Road, Chetpet

department: Department of Immunology

institute: National Institute for Research in Tuberculosis

summary: Mycobacterium tuberculosis has the ability to persist within the host in a clinically latent stage. One important condition believed to contribute to latency is reduced access to oxygen but the response of M. tuberculosis to hypoxia is partially characterized. Virtually all dormant models against tuberculosis the vaccine tested in animals used laboratory strains H37Rv or Erdman strains. But major outbreaks of TB occur with the strains that have widely different genotypes and phenotypes compare to H37Rv. In this study, we used a commercial oligonucleotide microarray to determine the overall transcriptional response of lab strain (H37Rv) and most prevalent strains of Mycobacterium tuberculosis from South India S7 and S10 to hypoxia. Analysis of microarray results revealed that a total of 1161 genes are differentially regulated in H37Rv, among them 659 genes are upregulated and 502 genes are down regulated when > 1.5 fold change was taken as cut off. Microarray data of clinical isolates showed total of 790 genes are differentially regulated in S7 clinical isolates among which 453 are upregulated and 337 are down regulated. Interestingly numerous genes are differentially regulated in S10 clinical isolates (total of 2805 genes) and 1463 are upregulated and 1342 genes are down regulated during reduced oxygen model (Wayne’s model). Real-time quantitative RT-PCR was performed for few genes to validate the microarray results. To our knowledge, this genome-wide transcriptomics approach has produced the first insights into the response of South Indian prevalent clinical strains of M. tuberculosis when exposed to reduced oxygen stress.

overall_design: Three samples of Mycobacterium tuberculosis namely H37Rv,S7 and S10 were included. All are triplicates. Here control strain is H37Rv.

first: Devasundaram

last: Santhi

first: Imran

last: Khan

first: Neeraj

last: kumar

first: Sulochana

last: Das


title: Analysis of the Fetal and Neonatal Transcriptomic and Neurocognitive Phenotype in the Ts1Cje Mouse Model of Down syndrome

status: Public on Nov 15 2014

city: Medford

first: Heather

middle: C

last: Wick

state: MA

address: 161 College Ave

department: Department of Computer Science

institute: Tufts University

summary:
Down syndrome is characterized by a complex phenotype that includes developmental disabilities and congenital anomalies emerging during fetal life. The molecular origin of these abnormalities is poorly understood. Despite the evidence of prenatal onset of the phenotype, most therapeutic trials have been conducted in affected adults. This study presents evidence for fetal brain molecular and neonatal behavioral abnormalities in the Ts1Cje mouse model of Down syndrome. Gene expression changes were more pronounced in the Ts1Cje fetal brains than adult cerebral cortex and hippocampus. Functional pathway analyses showed that Ts1Cje embryonic brains display significant up-regulation of cell cycle and down-regulation of Solute-carrier amino acid transport pathways.  Several cellular processes, including apoptosis, inflammation, Jak/Stat signaling, G-protein signaling and oxidoreductase activity were consistently dysregulated at both stages. Fetal brain gene expression changes were associated with early behavioral deficits in surface righting, cliff aversion, negative geotaxis, forelimb grasp, ultrasonic vocalization and homing tests. In combination with the human studies, this suggests that the Down syndrome phenotype manifests prenatally and provides a rationale for prenatal therapy to improve perinatal brain development and postnatal neurocognition.
In the present study, we demonstrated that significant gene expression abnormalities were already present in the embryonic day 15 forebrain of the Ts1Cje mouse model of DS. The abnormal Ts1Cje embryonic molecular signature was associated with early postnatal developmental milestones and behavioral changes. These data provide a comprehensive picture of the genotype-phenotype relationship the Ts1Cje model of Down syndrome.

overall_design: We analyzed the forebrain whole transcriptome from embryonic day 15.5 (E15.5) Ts1Cje (n=5) and wild-type (n=5) using Affymetrix mouse gene 1.0 ST array. Data were normalized and analyzed to identify and accurately map genes that are significantly differentially expressed. Functional analyses were performed using GSEA and DAVID and DFLAT to better characterize cellular processes and pathways that are consistently affected in both brain regions. In separate experiments, the Fox scale, ultrasonic vocalization and homing tests were used to investigate postnatal behavioral deficits in Ts1Cje pups (n=29) versus WT littermates (n=64) at days 3 to 21.

first: Faycal

last: Guedj

first: Jeroen

last: Pennings

first: Millie

last: Ferres

first: Lea

last: Graham

first: Klaus

last: Miczek

first: Donna

middle: K

last: Slonim

first: Diana

middle: W

last: Bianchi


title: Temporal gene expression profiling of murine hippocampus with different diet regimens [Hippocampus]

status: Public on Nov 12 2014

city: New Delhi

first: Kanury

middle: VS

last: Rao

state: Delhi

address: Aruna Asaf Ali Marg

institute: ICGEB

summary: In the present study, we used C57BL/6J mouse, as a model for studying diet-induced diabetes and obesity, since this strain accumulates adipose tissue mass, insulin resistance, hyper-insulinemia, and hyper-lipidemia similar to humans fed on an high-fat high-sugar diet (HFHSD).

overall_design: This dataset consists of gene expression changes in hippocampus. It consists of three biological replicates for the low-fat control diet (LFC), high-fat diet (HFC), and three different doses (5 µg, 20µg and 75 µg) of ethano-botanical formulation Kal-1 with HFC diet.

first: Sachin

last: Sharma

first: Parul

last: Tripathi

first: Kamiya

last: Tikoo

first: Shashank

last: Mishra

first: Dhiraj

last: Kumar

last: Sinha

first: Simarjeet

last: Negi

first: Samrat

last: Chatterjee


title: Validation of a genomic classifier that predicts metastasis following radical prostatectomy in at risk patient population

status: Public on Nov 13 2014

city: Vancouver

first: Elai

last: Davicioni

state: British Columbia

address: 1038 Homer st

country: Canada

institute: GenomeDx Biosciences Inc

summary: Purpose: Patients with locally advanced prostate cancer after radical prostatectomy are candidates for secondary therapy. However, this higher risk population is heterogeneous. Many cases do not metastasize even when conservatively managed. Given the limited specificity of pathological features to predict metastasis, newer risk prediction models are needed. We report a validation study of a genomic classifier that predicts metastasis after radical prostatectomy in a high risk population. Method:A case-cohort design was used to sample 1,010 patients after radical prostatectomy at high risk for recurrence who were treated from 2000 to 2006. Patients had preoperative prostate specific antigen greater than 20 ng/ml, Gleason 8 or greater, pT3b or a Mayo Clinic nomogram score of 10 or greater. Patients with metastasis at diagnosis or any prior treatment for prostate cancer were excluded from analysis. A 20% random sampling created a subcohort that included all patients with metastasis. We generated 22-marker genomic classifier scores for 235 patients with available genomic data. ROC and decision curves, competing risk and weighted regression models were used to assess genomic classifier performance.

overall_design: Patients treated with RP between 2000 and 2006 were identified from the Mayo Clinic tumor registry for a case-cohort study design. This involved identification of all patients with metastasis and a representative of the full cohort .Thus, men at high risk of recurrence post-RP (open/robotic) with no prior neoadjuvant/prostate cancer treatment were selected based on any of preoperative PSA >20 ng/mL, pathological Gleason score (GS) ≥8, SVI, or GPSM (GS; preoperative PSA; SVI; margins) score ≥10.The cohort of 1,010 men included 73 cases with metastasis as evidenced by CT or bone scan. A 20% random sample (n=202) was drawn from the cohort. This included 19 of 73 metastatic cases. To increase sampling of metastasis, the remaining 54 metastatic cases were added, resulting in a final study set of 256 patients. 21 samples did not pass QC and were eliminated from this study. Patients not experiencing metastasis regardless of BCR (defined as follow-up PSA ≥0.4 ng/mL >30 days post-RP) were censored at last follow-up. The study was approved by Mayo Clinic Institutional Review Board.

first: R

middle: J

last: Karnes

first: Eric

last: Bergstralh

first: Mercedeh

last: Ghadessi

first: Christine

last: Buerki

first: Anirban

last: Mitra

first: Anamaria

last: Crisan

first: Nicholas

last: Erho

first: Ismael

last: Vergara

first: Lucia

last: Lam

first: Rachel

last: Carlson

first: Darby

last: Thompson

first: Zaid

last: Haddad

first: Benedikt

last: Zimmermann

first: Thomas

last: Sierocinski

first: Timothy

last: Triche

last: Kollmeyer

first: Karla

last: Ballman

first: Peter

last: Black

first: George

last: Klee

first: Robert

middle: B

last: Jenkins


title: Temporal gene expression profiling of murine liver with different diet regimens [liver]

first: Kanury

last: Rao

overall_design: This dataset consists of gene expression changes in liver. It consists of three biological replicates for the low-fat control diet (LFC), high-fat diet (HFC), and three different doses (5 µg, 20µg and 75 µg) of ethano-botanical formulation Kal-1 with HFC diet.

first: Sachin

last: Sharma

first: Parul

last: Tripathi

first: Kamiya

last: Tikoo

first: Shashank

last: Mishra

first: Dhiraj

last: Kumar

first: Neeraj

last: Sinha

first: Simarjeet

last: Negi

first: Samrat

last: Chatterjee


title: Temporal gene expression profiling of murine epididymal adipose with different diet regimens [epididymal adipose]

overall_design: This dataset consists of gene expression changes in epididymal adipose. It consists of three biological replicates for the low-fat control diet (LFC), high-fat diet (HFC), and three different doses (5 µg, 20µg and 75 µg) of ethano-botanical formulation Kal-1 with HFC diet.


title: miRCURY LNATM microRNA Array (7th Gen) profiling of monocyte-derived macrophages and monocyte-derived dendritic cells.

city: Chicago

first: Jezrom

middle: Bokcaerin

last: Self-Fordham

state: IL

address: 801 S Paulina

department: Periodontics

institute: UIC

summary: To examine the miRNA changes that occur during macrophage and dendritic cell differentiation we used the miRCURY LNATM microRNA Array (7th Gen) to profile monocyte-derived macrophages and monocyte-derived dendritic cells. Of the 2046 probes present on the assay, we detected expression of ~400 (20%) miRNAs across all samples.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: CD14+ monocytes were isolated from the peripheral blood of 4 normal, healthy volunteers and differentiated into macrophages and dendritic cells in vitro. Total RNA was isolated from these cells at 0, 1, 4, 12, 24, 72, 120, and 168 hours of culture. RNA was profiled using the Qiagen miRCURY LNATM microRNA Hi-Power Labelling Kit and miRCURY LNATM microRNA Array (7th Gen).

last: Fordham

first: Afsar

middle: R

last: Naqvi

first: Salvador

last: Nares


title: Temporal gene expression profiling of murine epididymal infiltrating macrophages (SVCs) with different diet regimens [epididymal SVCs]

overall_design: This dataset consists of gene expression changes in epididymal infiltrating macrophages(SVCs). It consists of three biological replicates for the low-fat control diet (LFC), high-fat diet (HFC), and three different doses (5 µg, 20µg and 75 µg)  of ethano-botanical formulation Kal-1 with HFC diet.


title: Temporal gene expression profiling of murine subcutaneous adipose with different diet regimens [subcutaneous adipose]

overall_design: This dataset consists of gene expression changes in subcutaneous adipose. It consists of three biological replicates for the low-fat control diet (LFC), high-fat diet (HFC), and three different (5 µg, 20µg and 75 µg) doses of ethano-botanical formulation Kal-1 with HFC diet.


title: Temporal gene expression profiling of murine subcutaneous infiltrating macrophages(SVCs) with different diet regimens

overall_design: This dataset consists of gene expression changes in subcutaneous infiltrating macrophages(SVCs). It consists of three biological replicates for the low-fat control diet (LFC), high-fat diet (HFC), and three different doses (5 µg, 20µg and 75 µg) of ethano-botanical formulation Kal-1 with HFC diet.


title: Temporal gene expression profiling of murine brown infiltrating macrophages (SVCs) with different diet regimens [brown SVCs]

overall_design: This dataset consists of gene expression changes in brown infiltrating macrophages (SVCs). It consists of three biological replicates for the low-fat control diet (LFC), high-fat diet (HFC), and three different doses (5 µg, 20µg and 75 µg) of ethano-botanical formulation Kal-1 with HFC diet.


title: Transcriptome changes associated with apple (Malus domestica) root defense response during Pythium ultimum infection

status: Public on Nov 10 2014

city: Wenatchee

first: Yanmin

last: Zhu

state: WA

address: 1104 N. Western Ave

institute: USDA-ARS

summary: RNA-Seq based transcriptome profiling were performed on these samples with a minimum of 20 million reads per sample; read mapping, transcript discovery and differentially expressed gene (DEG) identification were carried out using CLC Genomics Workbench software suit, followed by Gene Ontology and pathway analyses. The highest defense response occurred at 48 hpi based on the number of the identified DEGs along the infection process. Transcriptomic changes related to oxido-reduction balance, trans-membrane trafficking and metabolic activities indicated the re-direction of cellular activities to combat P. ultimum infection. DEGs functioning in hormone signaling including ethylene, jasmonate, gibberellin, cytokinin and auxin, and those encoding NAC, WRKY, MYB and ERF transcription factors were identified from 24-48 hpi; DEGs encoding enzymes in several biosynthesis pathways of secondary metabolisms and cell wall modification proteins are among the consistently up-regulated in the later stages. DEGs encoding defense and stress related protein such as wall-associated receptor kinase (WAK), endochitinase (PR4), thaumatin (PR5)-like protein, laccase, mandelonitrile lyase and cyanogenic beta-glucosidase were also highly induced.

overall_design: root tissues of apple seedlings inoculated with Pythium ultimum, were sampled at 0, 1, 4, 8, 24, 48, 72 and 96 hour post inoculation (hpi) along with mock inoculated tissue at each time point.

first: Sungbong

last: Shin

first: Ping

last: Zheng

first: Gennaro

last: Fazio

first: Mark

last: Mazzola

first: Dorrie

last: Main


title: Identification of genes differentially expressed during half-head regeneration in Schmidtea mediterranea

city: San Diego

first: Ricardo

last: Zayas

state: CA

address: 5500 Campanile Dr.

institute: San Diego State University

summary: We used Nimblegen arrays with design 2007-11-06_Smed_ESTs_4_exp to measure changes in gene expression during a timecourse of regeneration of one side of the head in Schmidtea mediterranea flatworms.  Following amputation of one side of the head, samples were collected from both the regeneration blastema and non-regenerating side of the head on days 2, 3, and 4 post-amputation.  Gene expression in these samples was compared to that in non-regenerating control samples collected at the time of amputation.

overall_design: Four independent biological replicates for each sample type were collected from non-regenerating control animals and from the blastemas of regenerating animals on days 2, 3, and 4 post-amputation.  Two independent biological replicates were collected from the non-regenerating side of the head on days 2, 3, and 4 post-amputation.  Each probe is spotted in duplicate on the array, providing us with two simultaneously processed technical replicates for each biological sample.

first: Amy

last: Hubert


title: Temporal gene expression profiling of murine brown adipose with different diet regimens [brown adipose]

first: Kanury

last: Rao

overall_design: This dataset consists of gene expression changes in brown adipose. It consists of three biological replicates for the low-fat control diet (LFC), high-fat diet (HFC), and three different doses (5 µg, 20µg and 75 µg) of ethano-botanical formulation Kal-1 with HFC diet.

first: Sachin

last: Sharma

first: Parul

last: Tripathi

first: Kamiya

last: Tikoo

last: Mishra


title: Current DNA motif models can lead to incorrect hypotheses about the genomic recruitment of transcription factors

status: Public on Nov 04 2014

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

summary: The E2F family of transcription factors is typically described as binding the family consensus sequence TTTSSCGC, were S is G or C. Analysis of ChIP-seq experiments, however, reveals that this consensus sequence is found in only 10% of ChIP-seq peaks, suggesting that the mechanism for E2F sequence recognition cannot be explained using previous assumptions.  In order to better understand E2F sequence specificity, we performed high-throughput Universal Protein Binding Microarray experiments to obtain the relative binding affinity for every possible 8-mer, as well a large number of bound and unbound probes intheir native genomic sequence context. Our results show that while the consensus sequence is bound with relatively high affinity, numerous other 8-mers, many distinctly different from the consensus motif, are bound with similar or greater affinity.  These data suggest that the mechanism for E2F sequence specificity is likely complex, and cannot readily be explained through a simple consensus sequence. Because of this, complex regression models were created using the bound and unbound probe binding affinities, and were able to predict binding in vivo, where the consensus sequence and varoius E2F PWMs were not.

overall_design: A protein binding microarray (PBM) experiment of the human transcription factor E2F1 was performed. Briefly, the PBMs involved binding full length GST-tagged transcription factor E2F1 to double-stranded 4x180K Agilent microarrays in order to determine their binding specificity for all possible 8-mer sequences, as well as putative bound and unbound probes in genomic context. Briefly, 4x180K arrays (Agilent Technologies; AmadID 049201) containing the ‘all 10-mer’ universal PBM design were used.  Arrays were incubated with a PBS buffer based protein mixture of 250nM E2F1, 2% milk, 200ng/µL BSA, 50ng/µL Salmon Testes DNA, and 0.02% TX-100.  Bound protein was tagged with 50ng/µL anti-GST antibody conjugated to Alexa 488 (Life Technologies; A11131) in PBS with 2% milk.  Data were analyzed to obtain fluorescence intensities for all 8-mers.  The PBM protocol is described in Berger et al., Nature Biotechnology 2006 (PMID 16998473).

first: Joshua

last: Schipper


title: Influence of RppH on the small RNA transcriptome of Neisseria gonorrhoeae MS11

city: DeKalb

first: Stuart

middle: A.

last: Hill

address: 155 Castle Dr.

department: Department of Biological Sciences

institute: Northern Illinois University

type: Non-coding RNA profiling by high throughput sequencing

summary: We assessed the small RNA transcriptome of Neisseria gonorrhoeae strain MS11 in two genetic backgrounds; using wild type cells as well as cells carrying a rppH insertional mutation.  It was found that the presence of the RppH enzyme affected both the quantity and length of small RNAs in various chromosomal locations.  However, in comparing the two transcriptomes, we found that not all small RNAs were differentially expressed, suggesting that RppH targets only a subset of transcripts.

overall_design: Analysis of the small RNA transcriptome of N. gonorrhoeae in a wild type and ΔrppH mutant background.


title: A genomic classifier improves prediction of metastatic disease within 5 years after surgery in node-negative high-risk prostate cancer patients managed by radical prostatectomy without adjuvant therapy

status: Public on Nov 21 2014

first: Elai

last: Davicioni

summary: To determine whether adding Decipher to standard risk stratification tools (CAPRA-S and Stephenson nomogram) improves accuracy in prediction of metastatic disease within 5 years after surgery in men with adverse pathologic features after RP.

overall_design: The study population consisted of 182 patients selected from 2,641 men who underwent RP at the Cleveland Clinic between 1987-2008 who met the following criteria: 1) preoperative PSA>20 ng/mL, stage pT3 or margin positive, or Gleason score >/8; 2) pathologic node negative; 3) undetectable post-RP PSA; 4) no neoadjuvant or adjuvant therapy; and 5) minimum of 5 years follow-up for the controls.

first: Eric

last: Klein

first: Kasra

last: Yousefi

first: Zaid

last: Haddad

first: Voleak

last: Choeurng

first: Christine

last: Buerki

first: Andrew

last: Stephenson

first: Jianbo

last: Li

first: Michael

last: Kattan

first: Cristina

last: Magi-Galluzzi


title: RNA-sequencing of luminal epithelium and stroma cells isolated by LCM from pseudopregnant day 4 Msx1/Msx2 knockout and control uteri

status: Public on Nov 01 2014

city: Cincinnti

first: SK

last: Dey

address: 3333 Burnet Ave

department: Reproductive Sciences

institute: Cincinnati Children's Hospital

summary: We recently demonstrated that Msx genes, which encode muscle segment homeobox (Msh) transcription factors, regulate the transition of the luminal epithelium from high to low apicobasal polarity that is critical for implantation. In Msx deficient uteri (Msx1d/d/Msx2d/d), apicobasal polarity remains high and implantation fails to occur. However, information on the underlying molecular mechanism of Msx-dependent regulation of epithelial polarity, and the nature of epithelial-mesenchymal interactions that are characteristic of Msx genes, remain limited. In this study, we analyzed gene expression by RNA-sequencing in the luminal epithelium and stroma isolated by laser capture microdissection (LCM) on day 4 of pseudopregnancy in Msx1f/f/Msx2f/f and Msx1d/d/Msx2d/d uteri. We found upregulation of extracellular matrix components in the stroma and downregulation of immunity-related genes in both the luminal epithelium and stroma isolated from Msx1d/d/Msx2d/d mice. In addition, tight junction protein Claudin 1 and small proline-rich protein (Sprr2) were substantially upregulated in Msx1d/d/Msx2d/d epithelia.

overall_design: mRNA profiles of luminal epithelium and stroma from a wildtype Msx1f/f/Msx2f/f and a uterine-specific knockout Msx1d/d/Msx2d/d mouse were asessed by RNA-sequencing with the Illumina HiSeq 1500 system

first: Craig

last: Park

first: Xiaofei

last: Sun

first: S

last: Potter

first: Sudhansu


title: Expression data from fine-needle aspiration biopsies of breast cancer metastases from different anatomical sites

status: Public on Nov 03 2014

city: Stockholm

first: Nicholas

last: Tobin

address: Cancer Center Karolinska

institute: Karolinska Institutet

summary:
To determine whether breast cancer molecular subtypes and tumor characteristics with demonstrated significance in a primary tumor setting can also confer clinically relevant information in breast cancer metastases.
We assessed previously published gene expression modules of seven biological processes and the intrinsic subtypes (PAM50). The translational aspect of the Swedish randomized TEX trial included 112 patients with at least one biopsy from morphologically confirmed loco-regional or distant breast cancer metastasis diagnosed from December 2002 until June 2007. All patients had detailed clinical information, complete follow-up and metastasis gene expression information (Affymetrix array GPL10379).

overall_design: We performed global gene expression profiling on fine-needle aspirates of metastatic lesions from different anatomical sites obtained  from breast cancer patients treated within the Swedish randomized trial (TEX) of first-line chemotherapy for locally advanced or metastatic breast cancer. Samples were collected before commencement of treatment.

first: Linda

last: Lindstrom


title: Gene expression profiling of  oncogenic NRAS driven mouse melanomas that have developed resistance to NRAS withdrawal

status: Public on Oct 31 2014

city: Houston

first: Guo

last: Chen

state: TX

address: 7435 Fannin Street

department: Melanoma Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

summary: Targeted therapies have the potential to revolutionize cancer care by providing personalized treatment strategies that are less toxic and more effective but it is clear that for most solid tumors suppression of a single target is not sufficient to prevent development of resistance. A powerful method to identify mechanisms of resistance and targets for combination therapy is to use an in vivo genetic approach. We have developed a novel retroviral gene delivery mouse model of melanoma that permits control of gene expression post-delivery using the tetracycline (tet)-regulated system. In this study we used this melanoma model to select for resistant tumors following genetic inhibition of mutant NRAS. Analysis of tumors that became resistant to NRAS suppression revealed that the most common mechanism of resistance was overexpression of the Met receptor tyrosine kinase (RTK). Importantly, inhibition of Met overcomes NRAS resistance in this context. Analysis of NRAS mutant human melanoma cells revealed that inhibition of MEK is also associated with adaptive RTK signaling. Furthermore, co-inhibition of RTK signaling and MEK overcomes acquired MEK inhibitor resistance in NRAS mutant melanoma. These data suggest that combined inhibition of RTK and MEK signaling is a rational therapeutic strategy in mutant NRAS driven melanoma.

overall_design: Reversible NRAS Q61R expression in the melanocytes of DCT-TVA;Ink4a/Arf lox/lox mice (FVB/n) was achieved by transducing the animals with Tet-off and TRE-NRASQ61R-IRES-Cre avian leukosis viruses. After tumor initiation, the expression of NRAS Q61R was turned off by administrating doxycycline. Despite initial regression, tumors in 40% of mice developed resistance to NRAS Q61R withdraw. Seven resistant tumors and one control tumor where NRAS Q61R expression was not interrupted were subjected to genome-wide gene expression profiling.

first: Vito

last: Rebecca

first: James

last: Robinson

first: Inna

last: Fedorenko

first: Geoffrey

middle: T

last: Gibney

first: Jane

last: Messina

first: Kristin

last: Lastwika

first: Douglas

last: Grossman

last: Davies

first: Matthew

last: VanBrocklin

first: Keiran

last: Smalley

first: Sheri

last: Holmen


title: Gene expression profiling analysis of murine Villin-Gremlin villi compared to age-matched control mice

status: Public on Oct 24 2014

city: Oxford

first: Ian

last: Tomlinson

state: England

address: WTCHG, Roosevelt Drive

country: United Kingdom

institute: Oxford University

summary: This study was designed to assess the global transcriptional differences between villin-Grem villi compared to normal villi of age-matched mice. We found changes in key gene signatures asscoiated with tumorigenesis.

overall_design: Total RNA obtained from isolated villi from Villin-Gremlin mouse (n=6) and wildtype controls (n=6)

first: Leedham

last: Simon

first: Irshad

last: Shazia


title: Temporal gene expression profiling of murine skeletal muscle tissues with different diet regimens [skeletal muscle]

first: Kanury

last: Rao

overall_design: This dataset consists of gene expression changes in skeletal muscle tissues. It consists of three biological replicates for the low-fat control diet (LFC), high-fat diet (HFC), and three different doses (5 µg, 20 µg and 75 µg) of ethano-botanical formulation Kal-1 with HFC diet.

first: Sachin

last: Sharma

first: Parul

last: Tripathi

first: Kamiya

last: Tikoo

first: Shashank

last: Mishra

first: Dhiraj

last: Kumar

first: Neeraj

last: Sinha

first: Simarjeet

last: Negi

first: Samrat

last: Chatterjee


title: Temporal gene expression profiling of murine spleen with different diet regimens [spleen]

overall_design: This dataset consists of gene expression changes in spleen. It consists of three biological replicates for the low-fat control diet (LFC), high-fat diet (HFC), and three different doses (5 µg, 20µg and 75 µg) of ethano-botanical formulation Kal-1 with HFC diet.


title: Caste-specific RNA editomes in the leaf-cutting ant Acromyrmex echinatior

status: Public on Oct 02 2014

city: Shenzhen

first: Hong

middle: zhi

last: Cao

state: Guangdong

address: F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District

department: Bioinformatics

institute: BGI-SHENZHEN

summary: Eusocial insects have evolved the capacity to generate adults with distinct morphological, reproductive and behavioural phenotypes from the same genome. Recent studies suggest that RNA editing might enhance the diversity of gene products at the post-transcriptional level, particularly to induce functional changes in the nervous system. Using head samples from the leaf-cutting ant Acromyrmex echinatior, we compare RNA editomes across eusocial castes, identifying ca. 11,000 RNA editing sites in gynes, large workers and small workers. Those editing sites map to 800 genes functionally enriched for neurotransmission, circadian rhythm, temperature response, RNA splicing and carboxylic acid biosynthesis. Most A. echinatior editing sites are species specific, but 8–23% are conserved across ant subfamilies and likely to have been important for the evolution of eusociality in ants. The level of editing varies for the same site between castes, suggesting that RNA editing might be a general mechanism that shapes caste behaviour in ants.

overall_design: Analysis of genome-wide RNA editing in three different female castes of the the leaf-cutting ant Acromyrmex echinatior.

first: Qiye

last: Li

first: Zongji

last: Wang

first: Jinmin

last: Lian

first: Morten

last: Schiøtt

first: Lijun

last: Jin

first: Pei

last: Zhang

first: Yanyan

first: Sanne

last: Nygaard

first: Zhiyu

last: Peng

first: Yang

last: Zhou

first: Yuan

last: Deng

first: Wenwei

first: Jacobus

last: Boomsma

first: Guojie


title: Ionizing Radiation Induced micro RNA Expression Alterations in Human Peripheral Blood Mononuclear Cells

status: Public on Sep 26 2014

city: Vienna

first: Lucian

last: Beer

address: Währginer Gürtel 18-20

department: Department of Surgery

country: Austria

institute: Medical University of Vienna

summary: Ionizing Radition is known to cause cell damage. Human peripheral blood mononuclear cells have long been used to study radiation induced gene expression profiling. Whithin this study we evaluated gene and microRNA expression alterations of human PBMC irradiated with 60 Gy g-ray. Cells were cultured for 2, 4 and 20h after irradiation before RNA was isolated and Agilent Human microRNA Microarrays was performed.

overall_design: Radiation induced gene expression in human peripheral blood mononuclear cells were measured at 2, 4 and 20 hours after exposure to doses of 60 Gy g-rays. Non radiated cell of each donor and time point were used as contol cells. Four independent experiments were performed at each time (2, 4, or 20 hours and 0 h - only 1 sample per donor) using 4 different donors.

first: Hendrik

last: Ankermit

first: Michael

last: Mildner


title: Temporal gene expression profiling of Multiple murine tissues with different diet regimens

first: Kanury

last: Rao

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

overall_design: Refer to individual Series


title: Molecular characterisation of the multistep process of lung squamous carcinogenesis by gene expression profiling

city: Marseille

first: Celine

last: Mascaux

address: 27 bvd Lei Roure

department: Centre of research for cancer of Marseille

institute: Aix Marseille University

summary: We comprehensively characterized the gene expression alterations occurring during squamous lung cancer development. Fresh frozen human bronchial biopsies (N=122) at successive morphological stages of lung squamous carcinogenesis were obtained by fluorescence bronchoscopy and analyzed using gene expression microarrays.

overall_design: A total of 122 biopsies from 77 individuals, 35 former and 42 current smokers, were included. The 122 biopsies were distributed according to histology and fluorescence status as follows: 13 biopsies with normal histology and normofluorescent (8/5 biopsies from former/current smokers), 14 with normal histology and hypofluorescent (8/6), 15 hyperplasia (7/8), 15 metaplasia (5/10), 13 mild dysplasia (8/5), 13 moderate dysplasia (7/6), 12 severe dysplasia (2/10), 13 carcinoma in situ (5/8) and 14 squamous cell carcinoma (SCC, 5/9). In addition, normal bronchial biopsies from 16 never-smokers were collected and pooled for use as reference RNA.


title: In vivo disruption of Rb-E2F-Ezh2 signaling loop causes bladder cancer development

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

summary: Bladder cancer (BC) is a highly prevalent human disease in which Rb pathway inactivation and epigenetic alterations are common events. However, the connection between these two processes is still poorly understood. Here we show that the in vivo inactivation of all Rb family genes in the mouse urothelium is sufficient to initiate BC development. The characterization of the mouse tumors revealed multiple molecular features of human BC, including the activation of E2F transcription factor and subsequent Ezh2 expression, and the activation of several signaling pathways previously identified as highly relevant in urothelial tumors. Whole transcriptional characterizations of the mouse bladder tumors revealed a significant overlap with human BC samples, and a predominant role for Ezh2 in the downregulation of gene expression programs. Importantly, we determined that in human superficial BC patients, the increased tumor recurrence and progression in these recurrences is associated with increased E2F and Ezh2 expression and Ezh2-mediated gene expression repression. Collectively, our studies provide a genetically defined model for human high-grade superficial BC and demonstrate the existence of an Rb-E2F-Ezh2 axis in bladder whose disruption can promote tumor development.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Gene expression was analyzed in normal bladder and bladder tumours, both in humans and in transgenic mice.

first: Marta

last: Duenas

first: Monica

last: Martinez-Fernandez

first: Felipe

last: Villacampa

first: Jose

last: Duarte

first: Victor

last: Martinez

first: Maria

last: Gomez-Rodriguez

last: Martin

first: Manoli

last: Fernandez

first: Daniel

last: Castellano

last: Rodriguez-Peralto

first: Federico

last: de la Rosa

first: Julien

last: Sage

first: Mirentxu

last: Santos

first: Begona

last: Alfaya

first: Cristina

last: Saiz-Ladera

first: Clotilde

last: Costa

last: Oteo

first: Patrick

last: Viatour

first: Miguel

last: Morcillo

first: Jesus

middle: M

last: Paramio


title: Radiation response in xenografts of the head and neck cancer UT14 cell line

status: Public on Sep 19 2014

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

summary:
Low passage head and neck squamous cancer cells (UT-14-SCC) were injected into the flanks of female nu/nu mice to generate xenografts. After tumors reached a size of 500mm3, they were treated with either sham RT or 15 Gy in one fraction.
At different time points, days 0, 3, 10 and for controls and days 4, 7, 12, and 21 after irradiation, the tumors were harvested for global gene expression analysis and pathway analysis.

overall_design: Samples from the control time points (n=7) were compared to each of the post-irradiation time points (n=2). The changes in gene expression at each time point were compared to the other time points.

first: George

last: Wilson

first: Laura

last: Fortier

first: Barbara

last: Pruetz

first: Sandra

last: Galoforo

first: Jan

last: Akervall

first: Brian

last: Marples

first: Jiayi

last: Huang


title: Transcript Expression Changes over Time-from-injury in Anterior Cruciate Ligament Tears: Implications for Reconstruction and Repair

status: Public on Sep 13 2014

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

summary: The anterior cruciate ligament (ACL) is an essential stabilizer of the tibiofemoral articulation. ACL tears often lead to functional instability and are associated with an increased risk for osteoarthritis. The healing potential of the injured ACL is poorly understood and is considered to be limited. Transcriptome-wide expression profiles of 24 human ACL remnants recovered at the time of surgical reconstruction were analyzed utilizing the Agilent human 8x60K microarray platform. Gene ontology was performed on differentially expressed transcripts based on time-from-injury (acute, <3 months; intermediate, 3-12 months; chronic, >12 months). A subset of transcripts was validated via microfluidic digital polymerase-chain-reaction. Expression of periostin, a highly differentially expressed transcript, was tested by immunohistochemistry. Numerous transcripts covering important functional classifications were differentially expressed by time-from-injury. In acute tears, processes representing angiogenesis were repressed while those representing stem-cell differentiation were elevated. In intermediate tears, processes representing stem-cell proliferation concomitant with cellular component organization/cellular localization were elevated. In chronic tears, processes denoting myosin filament organization were elevated while those representing cellular component organization/cell localization and extracellular matrix organization were repressed. Expression levels of periostin were down-regulated in chronic tears compared to acute (42-fold) and intermediate (29-fold) tears. Immunohistochemistry confirmed a decline in periostin expression in tissues from chronic tears. These findings suggest an initial attempt of the injured ACL to repair, which declines with time-from-injury. These findings have implications for efforts to repair the ACL and may be relevant for reconstruction of the ACL. The functional role of periostin in ACL injuries, and the potential implication for surgical treatment, warrants further investigation.

overall_design: Total RNA obtained frominjured anterior cruciate ligament (ACL) tissues from pateints undergoing ACL surgery.

first: Muhammad

middle: F

first: Linda

last: Sandell

first: Robert

middle: H

last: Brophy


title: Invertible Elements and their association with Small Non-coding RNAs in Neisseria gonorrhoeae

city: Kingston upon Thames

first: Sabrina

last: Roberts

state: Surrey

address: Penryhn Road

department: Life Sciences

institute: Kingston University

summary: We report for the first time movement of Correia Repeat Enclosed Elements, through inversion of the element at its chromosomal location. Analysis of Ion Torrent generated genome sequence data from Neisseria gonorrhoeae strain NCCP11945 passaged for 8 weeks in the laboratory under standard conditions and stress conditions revealed a total of 37 inversions: 24 were exclusively seen in the stressed sample; 7 in the control sample; and the remaining 3 were seen in both samples. These inversions have the capability to alter gene expression in N. gonorrhoeae through the previously  determined activities of the sequence features of these elements. In addition, the locations of predicted non-coding RNAs were investigated to identify potential associations with CREE. Associations varied between strains, as did the number of each element identified. The analysis indicates a role for CREE in disrupting ancestral regulatory networks, including non-coding RNAs.

overall_design: RNA-Seq was used to examine expression changes related to Correia repeats in the strain

first: Firat

last: Elbeyioglu


title: Dysregulation of genome-wide gene expression and DNA methylation in abnormal cloned piglets

status: Public on Sep 03 2014

city: Wuhan

first: Changchun

last: Li

state: Hu Bei

address: No.1, Shizishan Street · Hongshan District

institute: Huazhong Agriculture University


title: gene expression profiles in KRAS mutant A549 cells after BI-2536 and fasudil combination treatment

status: Public on Aug 29 2014

city: Shanghai

first: Xiufeng

last: Pang

address: 500 Dongchuan Road

department: School of Life Sciences

institute: East China Normal University

summary:
To identify the potential mechanisms of enhanced activity of combined inhibition of PLK1 and ROCK, we conducted a microarray analysis on gene expression profiles in KRAS mutant A549 cells.
We used Affymetrix GeneChip PrimeView Human Gene Expression array to  detail gene expression after indicated treatments and identified  the molecular mechanism during this process to facilitate further studies.

overall_design: A549 cells were treated with vehicle control, BI-2536 (4 nM), fasudil (20 µM), or the combination of BI-2536 and fasudil for 6 h. Samples were obtained from three independent biological replicates.RNA from each sample was labeled and hybridized using Affymetrix GeneChip PrimeView Human Gene Expression array.

first: Jieqiong

last: Wang

first: Kewen

last: Hu

first: Mingyao

last: Liu


title: Dysregulation of genome-wide gene expression and DNA methylation in abnormal cloned piglets (RNA-Seq)

summary:
Backgroud:Epigenetic modifications (especially altered DNA methylation) resulting in altered gene expression may be one reason for development failure or the abnormality of the cloned animals, but the underlying mechanism of the abnormal phenotype in the cloned piglets remains unrevealed. Some cloned piglets in our study showed abnormal phenotypes such as big tongue (longer and thicker), limp, and exomphalos, which is similar to the human BWS syndrome. Here we conducted DNA methylation (DNAm) immunoprecipitation binding high throughput sequencing (MeDIP-seq) and RNA sequencing (RNA-seq) of muscle tissues of cloned piglets to investigate the relationship of abnormal DNAm with gene dysregulation and the unusual phenotypes in cloned piglets.
Results:Analysis of the methylomes revealed that abnormal cloned piglets suffered more hypomethylated differentially methylated regions (DMRs) than hypermethylated DMRs compared to the normal cloned piglets. The DNAm level in the CpG Island was higher in the abnormal cloned piglets. Some repetitive elements, such as SINE/tRNA-Glu Satellite/centr also showed significant differences. Besides we detected 1,711 differentially expressed genes (DEGs) between the two groups, of which 243 genes also changed methylation level in the abnormal cloned piglets. The altered DNA methylation mainly affected the low and silent expression genes. We also found some interesting pathways and genes, such as MAPK signalling pathway, hypertrophic cardiomyopathy pathway, TPM3 gene and the imprinted gene PLAGL1, which may played important roles in the abnormal phenotype development.
Conclusions;The abnormal cloned piglets showed substantial change both in the DNAm and the gene expression levels. Our data may provide new insights into understanding the molecular mechanisms of the reprogramming of genetic information in cloned animals.

overall_design:
We dissected the biceps femoris muscle from the abnormal cloned piglets and the normal cloned piglets, and analyzed the difference of MeDIP-seq and RNA-seq between the two groups.
This represents the RNA-Seq study only

first: G

first: C


title: Genome wide targeting of the epigenetic regulatory protein CTCF to gene promoters by the transcription factor TFII-I [ChIP-Seq]

city: Montreal

first: Michael

last: Witcher

state: QC

address: 3755 Chemin de la Cote Ste-Catherine

institute: Lady Davis Institut

summary: Analysis of CTCF binding in Wehi-231 with TFII-I knockdown compare to Wehi-231 wt.

overall_design: ChIP experiment of CTCF in Wehi-231-CT and Wehi-231-shTFII-I

first: Rodrigo

middle: P

last: Hernandez

first: Maud

last: Marques

first: Khalid

last: Hilmi

first: Teijun

last: Zhao

first: Sonia

middle: V

last: del Rincon

first: Todd

last: Ashworth

first: Ananda

last: Roy

first: Beverly

last: Emerson


title: Genome wide targeting of the epigenetic regulatory protein CTCF to gene promoters by the transcription factor TFII-I [gene expression]

summary: Analysis of the effect of TFII-I depletion on gene expression Wehi-231 cell lines.

overall_design: Total RNA were extract from shCT and shTFII-I Wehi-231 cells.


title: Expression data of age-specific ovaries in rhesus monkey

status: Public on Aug 31 2014

city: guangzhou

first: hengxi

last: wei

address: No. 483, wushan

institute: scau

summary:
The biological function of human ovaries declines with increasing age. Moreover, disorders that cause reproductive failure, such as premature ovarian failure (POF), seriously affect the female health and may be related to abnormal gene expression in the ovaries.
The objective of this study was to generate the gene expression proﬁles of ovaries in rhesus monkeys of different ages, so as to identify age-related changes in the ovaries and understand their significance in various human reproductive problems.

overall_design: Ovaries were obtained from young (Y, 3 to 4 years), middle-age (M, 7 to 8 years) and old (O, 18 to 19 years) monkeys, and each group had 3 monkey replications. Half of ovary from each monkey was isolated mRNA for whole genome gene expression microarray analysis to detect differentially expressed genes, and followed by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses by using a free web-based Molecular Annotation System 3.0 (MAS 3.0).

first: Hengxi

last: Wei

first: Xiangjie

first: Li

first: Xinzheng

last: Guo

first: Lin

first: Shouquan

last: Zhang


title: Redifferentiation of adult human β cells expanded in vitro by inhibition of the WNT pathway

status: Public on Aug 27 2014

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary: In vitro expansion of adult human islet β cells is an attractive solution for the shortage of tissue for cell replacement therapy of type 1 diabetes. Using a lineage tracing approach, we have demonstrated that β-cell-derived (BCD) cells rapidly dedifferentiate in culture and can proliferate for up to 16 population doublings. Dedifferentiation is associated with changes resembling epithelial-mesenchymal transition (EMT). The WNT pathway has been shown to induce EMT and plays key roles in regulating replication and differentiation in many cell types. Here we show that BCD cell dedifferentiation is associated with β-catenin translocation into the nucleus and activation of the WNT pathway. Inhibition of β-catenin expression in expanded BCD cells using short hairpin RNA resulted in growth arrest, mesenchymal-epithelial transition, and redifferentiation, as judged by activation of β-cell gene expression. Furthermore, inhibition of β-catenin expression synergized with redifferentiation induced by a combination of soluble factors, as judged by an increase in the number of C-peptide-positive cells. Simultaneous inhibition of the WNT and NOTCH pathways also resulted in a synergistic effect on redifferentiation. These findings, which were reproducible in cells derived from multiple human donors, suggest that inhibition of the WNT pathway may contribute to a therapeutically applicable way for generation of functional insulin-producing cells following ex-vivo expansion.

overall_design: Gene expression was studied for beta-cells (4 donors). Dedifferentiation was induced by inhibition of β-catenin expression using shRNA. The experiment was performed in 4 batches (see the 'Date' characteristic in the Sample records).

first: Ayelet

last: Lenz

first: Ginat

last: Toren-Hartian

first: Shimon

last: Efrat


title: Transcriptional profiling of shoots and roots in japonica and indica rice seedlings under cold stress and recovery stage

status: Public on Oct 15 2014

city: Taipei

first: Men-Chi

last: Chang

address: No. 1, Section 4, Roosevelt Road

department: Agronomy

country: Taiwan

institute: National Taiwan University

summary: Rice seedlings at 3-leaf stage were used for expression analysis in control and cold stressed (incloudling cold treatment for 3, 24hrs and recovery from cold stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArray＠ v1.

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: Control and treated biological replicates of cold-tolerant cultivar TNG67 (japonica) and cold-sensitive cultivar TCN1 (indica) were analyzed

first: Yun-Wei

last: Yang


title: Differential expression of mRNAs in naïve, effector, and memory CD8 T cells of mir-150 KO and wild-type mice

status: Public on Oct 11 2014

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

country: South Korea

institute: NAR Center, Inc. & Genoplan, Inc.

summary:
microRNA-150 (miR-150) is mainly expressed in the lymph nodes and spleen and is highly up-regulated during the development of mature T and B cells. To understand the signal-transduction network for 'effector or memory T cells' and 'mir-150' in naïve, effector, or memory CD8 T cells of mir-150 knockout and wild-type mice, we analyzed gene expression profiles by microarray. The genetic background of the cells used in this study is CD8 T cells from spleen of the 8 week-old male C57BL/6J mice (for female: WT-memory_2 & KO-memory_2).
Corresponding authors: Inpyo Choi, PhD, Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro,Yuseong, Daejeon 305-806, Republic of Korea. E-mail: ipchoi@kribb.re.kr. Or: Tae-Don Kim, PhD, Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong, Daejeon 305-806, Republic of Korea. E-mail: tdkim@kribb.re.kr.

overall_design: wild-type[WT] vs. mir-150 knockout[KO]; naïve, effector, and memory CD8 T cells.

first: Tae-Don

first: Jung

first: Inpyo

last: Choi


title: Molecular and cellular characterization of Cord Blood derived, IDO expressing human fibrocystic Myeloid Derived Suppressor Cells

status: Public on Aug 26 2014

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary:
By restraining T cell activation and promoting regulatory T cell (Treg) expansion, myeloid-derived suppressor cells (MDSC) and tolerogenic dendritic cells (DC) (tDC) can control self-reactive and anti-graft effector T cells in autoimmunity and transplantation. Their therapeutic use and characterization, however, is limited by their scarce availability in the peripheral blood of tumor-free donors. In the present study we describe and characterize a novel population of myeloid suppressor cells, named fibrocytic MDSC (f-MDSC), that are differentiated from umbilical cord blood (UCB) precursors by a 4 day culture with FDA approved cytokines (rh-GM-CSF and rh-G-CSF). This MDSC subset, characterized by the expression of MDSC-, DC-, and fybrocyte-s associated markers, promotes Treg regulatory cells expansion and promote normoglycemia in a xenogeneic model of Type 1 Diabetes (T1D). In order to exert their pro-tolerogenic function, fibrocytic MDSC require direct contact with activated T cells, which leads to the induction and secretion of indoleamine 2,3 deoxygenase (IDO). This new myeloid subset may represent an important tool for the in vitro and in vivo production of Treg for the treatment of autoimmune diseases, and either prevention or control of allograft rejection.

Keywords: expression profiling by array

overall_design: Human Umbilical cord blood (UCB) samples were cultured for 4 days with GM-CSF and G-CSF after Ficoll-Paque gradient separation and red cell lysis. CD33+/IL-4Rα+ cells were sterilely sorted and part stored in Trizol for RNA extraction (BEFORE CONTACT), and part co-cultured with autologous PHA activated CD3+ T cells either in cell to cell contact (CONTACT) or using a transwell device to separate the two popyulations (TRANSWELL). Three days later, T cells were removed from the co-culture either by repeated washes with PBS or by simply removing the transwell device. Adherent cells were lysed with Trizol and stored at -80’C. RNA extraction was carry on with miRNAeasy mini kit from Quiagen; RNA QC was assessed by Agilent BioAnalyzer 6000 and samples were analyzed with Affymetrix Human 2.0 ST array

first: Alessia

last: Zoso

first: Emilia

last: Mazza

first: Susanna

last: Mandruzzato

first: Vincenzo

last: Bronte

first: Paolo

last: Serafini

first: Luca

last: Inverardi


title: Dynamics of the human skeletal muscle transcriptome in response to exercise training

status: Public on Aug 21 2014

city: Solna

first: Joakim

last: Lundeberg

address: Tomtebodavägen 23A

department: Gene Technology

institute: KTH-Science for Life Laboratory


title: Expression profiles of 186-gene signature in U.S. hepatitis C virus (HCV)-related liver cirrhosis

status: Public on Aug 22 2014

city: Dallas

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

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

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

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

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

overall_design: 145 liver tissue needle biopsy specimens from U.S. HCV cirrhosis cohort patients with histologically proven cirrhosis lacking evidence and a history of hepatic decompensation or HCC.

first: Lindsay

last: King

first: Claudia

last: Canasto-Chibuque

first: Kara

last: Johnson

first: Shun

last: Yip

first: Xintong

last: Chen

first: Kensuke

last: Kojima

first: Manjeet

last: Deshmukh

first: Anu

last: Venkatesh

first: Poh

middle: S

last: Tan

first: Augusto

last: Villanueva

first: Angelo

last: Sangiovanni

first: Venugopalan

last: Nair

first: Milind

last: Mahajan

first: Masahiro

last: Kobayashi

first: Hiromitsu

last: Kumada

first: Massimo

last: Iavarone

last: Colombo

first: Scott

middle: L

last: Friedman

first: Josep

last: Llovet

first: Raymond

last: Chung


title: Ionizing Radiation Induced Gene and micro RNA Expression Alterations in Human Peripheral Blood Mononuclear Cells

first: Lucian

last: Beer

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


title: Ionizing Radiation Induced Gene Expression Alterations in Human Peripheral Blood Mononuclear Cells

summary: Ionizing Radition is known to cause cell damage. Human peripheral blood mononuclear cells have long been used to study radiation induced gene expression profiling. Within this study we evaluated gene and microRNA expression alterations of human PBMC irradiated with 60 Gy g-ray. Cells were cultured for 2, 4 and 20h after irradiation before RNA was isolated and Agilent whole human GenomeOligo Microarray was performed.

overall_design: Radiation induced gene expression in human peripheral blood mononuclear cells were measured at 2, 4 and 20 hours after exposure to doses of 60 Gy g-rays. Non radiated cell of each donor and time point were used as contol cells. Four independent experiments were performed at each time (2, 4, or 20 hours and 0 h - only 1 sample per donor) using 4 different donors.

first: Hendrik

last: Ankermit

first: Michael

last: Mildner


title: A genomic and clinical prognostic index for hepatitis C-related early-stage cirrhosis that predicts clinical deterioration

first: Yujin

last: Hoshida

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

overall_design: Refer to individual Series


title: USU101 gene content determined by array CGH

status: Public on Aug 18 2014

city: Seattle

first: Nina

middle: Reda

last: Salama

address: 1100 Fairview Ave. N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

summary: The monkey infecting Helicobacter pylori strain USU101 used in a long term infection of macaques with and without the dietary carcinogen ENNG was analyzed for gene content compared to the sequenced strains 26695 and J99

overall_design:
We performed array CGH using two microarrays to analyze the gene content of the starting strain (USU101) used for the monkey infection experiment (GSE60405).
The ENNG information is not relevant.

first: Jutta

last: Fero

first: Andre

last: Dubois

first: D

last: Merrell


title: Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors

status: Public on Aug 14 2014

city: RTP

first: Raja

last: Jothi

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health


title: Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors [gene expression]

summary: Cell type-specific master transcription factors (MTFs) play vital roles in defining cell identity and function. However, the roles ubiquitous factors play in the specification of cell identity remain underappreciated. Here we show that all three subunits of the ubiquitous heterotrimeric CCAAT-binding NF-Y complex are required for the maintenance of embryonic stem cell (ESC) identity, and establish NF-Y as a novel component of the core pluripotency network. Genome-wide occupancy and transcriptomic analyses in ESCs and neurons reveal that not only does NF-Y regulate genes with housekeeping functions through cell type-invariant promoter-proximal binding, but also genes required for cell identity by binding to cell type-specific enhancers with MTFs. Mechanistically, NF-Y's distinctive DNA-binding mode promotes MTF binding at enhancers by facilitating a permissive chromatin conformation. Our studies unearth a novel function for NF-Y in promoting chromatin accessibility, and suggest that other proteins with analogous structural and DNA-binding properties may function in similar ways.

overall_design: Genome-wide mapping of NF-YA, NF-YB, and NF-YC subunits of the NF-Y complex in mouse ESCs, and microarray gene expression profiling of control knockdown (KD), NF-YA KD, NF-YB KD, NF-YC KD, and NF-YA/NF-YB/NF-YC triple KD ESCs.

first: Andrew

last: Oldfield

first: Pengyi

last: Yang


title: Chronic Myeloid Leukemia (CML), induced pluripotent stem cell (iPSC)-derived lin-CD34+CD45+ (iCD34) cell population

city: Madison

last: Swanson

state: WI

address: 330 N. Orchard St

institute: Morgridge Institute for Research

summary: Analysis of lin-CD34+CD45+ (iCD34+) cell population from two normal bone marrow-derived (BM1K and BM9) iPSCs  and two CML (CML15 and CML17) iPSCs . CML iCD34+ cells have characteristics similar to primary CML leukemia stem cell in patients. Results provide insight into molecular profile characterized CML iCD34 and mechanism of its maintenance and drug resistance.

overall_design: iCD34+ cell samples obtained from two control BM1K and BM9 iPSCs (both for the same normal donor) and CML15 and CML17 iPSCs (both from the same patient in chronic phase of CML). Each group was treated with DMSO (control) or 5 μM imatinib. The complete phenotype for iCD34+ cells: lin-CD34+CD45+CD90+CD117+CD45RA-. This population also inclyde Rhodaminelow and ALDKhigh cells.

first: Kran

last: Suknuntha

first: Igor

last: Slukvin


title: Genetic diversity of a single Helicobacter pylori strain over a ten year period in a primate model: effect of long term colonization and of a dietary carcinogen


title: Genome wide targeting of the epigenetic regulatory protein CTCF to gene promoters by the transcription factor TFII-I

last: Witcher


title: RUNX1 positively regulates a cell adhesion and migration program in murine hemogenic endothelium prior to blood emergence (DamID-seq)

status: Public on Aug 05 2014

city: manchester

first: michael

last: lie-a-ling

address: The University of Manchester | Wilmslow Road

department: Stem Cell Biology

institute: Cancer Research UK Manchester Institute

summary: During ontogeny the transcription factor RUNX1 governs the emergence of definitive hematopoietic cells from specialized endothelial cells, called hemogenic endothelium (HE). The ultimate consequence of this endothelial-to-hematopoietic transition is the concomitant activation of the hematopoietic program and down-regulation of the endothelial program. However, due to the rare and transient nature of the HE, little is known about the initial role of RUNX1 within this population. We therefore developed and implemented a highly sensitive DamID (DNA adenine methyltransferase identification) based methodology, including a novel data analysis pipeline, to map early RUNX1 transcriptional targets in HE cells. This novel transcription factor binding site identification protocol should be widely applicable to other low abundance cell types and factors. Integration of the RUNX1 binding profile with gene expression data revealed an unexpected early role for RUNX1 as a positive regulator of cell adhesion and migration associated genes within the HE. This suggests that RUNX1 orchestrates HE cell positioning and integration prior to the release of hematopoietic cells. Overall, our genome-wide analysis of the RUNX1 binding and transcriptional profile in the HE provides a novel comprehensive resource of target genes that will facilitate the precise dissection of the role of RUNX1 in early blood development.

overall_design: Runx1b binding profiles of mouse ES derived haemogenonic endothelium were generated by deep sequencing using the SOLiD 3 or 4 System (Applied Biosystems). Three biological duplicates and three technical replicates where sequenced for each of the following lines: iDam_runx1-/- (iDamko) and iRunx1b::Dam_runx1-/- (iRunx1b::Damko)

last: Lie-A-Ling

first: Elli

last: Marinopoulou

first: Yaoyong

last: Li

first: Rahima

last: Patel

first: Monika

last: Stefanska

first: Constanze

last: Bonifer

first: Crispin

last: Miller

first: Valerie

last: Kouskoff

first: Georges

last: Lacaud


title: Gene expression profile of the Cmah gene depletion on mouse liver, lung, kidney and heart

status: Public on Aug 01 2014

first: Deug-Nam

last: Kwon

address: 1 hwayang-dong, Kwangjin-gu

institute: Konkuk University

summary: N-glycolylneuraminic acid (Neu5Gc) is generated by hydroxylation of CMP-Neu5Ac to CMP-Neu5Gc, catalyzed by CMP-Neu5Ac hydroxylase (CMAH). However, humans lack this common mammalian cell surface molecule, Neu5Gc, due to inactivation of the CMAH gene during evolution. CMAH is one of several human-specific genes whose function has been lost by disruption or deletion of the coding frame. It has been suggested that CMAH inactivation has resulted in biochemical or physiological characteristics that have resulted in human-specific diseases. To identify differential gene expression profiles associated with the loss of Neu5Gc expression, we performed microarray analysis using Illumina MouseRef-8 v2 Expression BeadChip, using the main tissues (liver, lung, kidney, and heart) from a control mouse and a Cmah-null mouse.

overall_design: Total RNA was extracted and purified from the liver, lung, kidney, and heart of WT and Cmah-null mice using RNeasy columns (Qiagen; Valencia, CA, USA) according to the manufacturer’s protocol. The RNA quality was verified using an Agilent Bioanalyzer 2100 (Agilent Technologies; Palo Alto, CA, USA) using the RNA 6000 Pico Assay. Generation of double-stranded cDNA, preparation and labeling of cRNA, hybridization to Mouse Ref-8 v2.0 Expression BeadChip (Illumina, Inc.; San Diego, CA, USA), washing, and scanning were all performed according to the standard Illumina protocol. Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner.

first: Jin-Hoi

last: Kim


title: LARP1 mRNP scaffolds mTORC1 to stimulate translation initiation of an essential class of mRNAs

status: Public on Jul 31 2014

city: Baltimore

first: Mallory

middle: Ann

last: Freeberg

state: MD

address: 3400 N Charles St

department: Department of Biology

institute: Johns Hopkins University

summary: The RNA biding protein, LARP1, has been proposed to function downstream of mTORC1 to positively regulate the translation of 5’TOP mRNAs such as ribosome protein (RP) mRNAs. However, its regulatory roles in mTORC1-mediated translation remain unclear. PAR-CLIP of LARP1 revealed its direct and dynamic interactions with RP mRNAs through pyrimidine-enriched sequences in the 5’UTR of RP mRNAs when mTOR activity is inhibited. Importantly, this LARP1 is a direct substrate of mTORC1 and S6K1/Akt, and phosphorylated LARP1 scaffolds mTORC1 on translation-competent mRNAs to facilitate 4EBP1 and S6K1 phosphorylation. Ablation of LARP1 causes multiple defects in the processes of translation including abnormal eIF4G1 interaction with RP mRNAs and inefficient RP mRNA elongation thereby reducing ribosome biogenesis and cell proliferation. These observations illustrate that LARP1 functions both an effector and a regulator for local mTORC1 activity, and acts as a molecular switch for ribosome biogenesis by sensing growth factor/nutrient signaling.

overall_design: LARP1-bound RNA regions were sequenced from HEK293T cells under growing or mTOR-inactive conditions. In parallel, mRNA abundance was quantified, in biological duplicate, from HEK293T cells under the same conditions. Sequencing reads were mapped to human transcriptome reference from hg19 to determine LARP1 binding sites and mRNA abundances.

first: Sungki

last: Hong

middle: A

first: Kamath

last: Avani

first: Han

last: Ting

first: Yao

last: Yao

first: Fukuda

last: Tomoko

first: Kong

last: Andy

first: Suzuki

last: Tsukasa

first: John

middle: K

first: Ken

last: Inoki


title: Gene expression analysis of a double knockout of TCA cycle enzymes IDH and KDH

city: University Park

first: Heather

middle: J

last: Painter

state: Pennsylvania

address: Millennium Science Center

department: Biochemistry and Molecular Biology

institute: Penn State University

summary: New antimalarial drugs are urgently needed to control drug resistant forms of the malaria parasite, Plasmodium falciparum. Although mitochondrial metabolism is the target of both existing drugs and new lead compounds, the role of the mitochondrial tricarboxylic acid (TCA) cycle remains poorly understood. Herein, we describe 11 genetic knockout parasite lines that delete six of the eight TCA cycle enzymes. Although all TCA knockouts grew normally in asexual blood stages, these metabolic deficiencies halted lifecycle progression in later stages. Specifically, aconitase knockout parasites arrested as late gametocytes, whereas α-ketoglutarate dehydrogenase deficient parasites failed to develop oocysts in the mosquitoes. Mass-spectrometry analysis of 13C isotope-labeled TCA mutant parasites showed that P. falciparum has significant flexibility in TCA metabolism. This flexibility manifested itself through changes in pathway fluxes and through altered exchange of substrates between cytosolic and mitochondrial pools. Our findings suggest that mitochondrial metabolic plasticity is essential for parasite development .

overall_design: Two parallel timecourses resulting in a total of 16 samples (8 wildtype, Isocitrate Dehydrogenase/alpha-Ketogluterate Dehydrogenase double knockout) were hybridized against a Cy3-labeled reference pool of 3D7 mixed stage parasites on a two-color array.

first: Hangjun

last: Ke

first: Ian

last: Lewis

first: Joanne

last: Morrisey

first: Kyle

last: McLean

first: Suresh

last: Ganesan

first: Michael

middle: W

last: Mather

first: Marcelo

last: Jacobs-Lorena

first: Manuel

last: Llinás

first: Akhil

middle: B

last: Vaidya


title: Single-Cell Whole-Genome Bisulfite Sequencing for Analysis of Epigenetic Heterogeneity

status: Public on Jul 18 2014

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: We report a single-cell whole-genome bisulfite sequencing method (scBS-Seq) capable of accurately measuring DNA methylation at up to 36% of CpGs. We observed that ESCs grown in serum/LIF or 2i/LIF both display epigenetic heterogeneity, with “2i-like” cells present in serum cultures. In silico integration of 12 individual MII oocytes datasets  recapitulates the whole DNA methylome, making scBS-Seq a versatile tool to explore DNA methylation in rare cells and heterogeneous populations.

overall_design: scBS-Seq has been performed on mouse MII oocytes for technical validation and on mouse ESCs cultured in 2i/LIF and serum/LIF to investage epigenetic heterogeneity

first: Sebastien

last: Smallwood

last: Lee

first: Heba

last: Saadeh

first: Simon

middle: R

last: Andrews

first: Julian

last: Peat

first: Christof

last: Angermueller

first: Oliver

last: Stegle

first: Wolf

last: Reik

first: Gavin

last: Kelsey


title: Circulating miRNA microarray data from breast cancer patients

city: Milano

first: Elena

last: Landoni

address: Via Vanzetti 5

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

summary: Independent studies have reported that circulating miRNAs have the potential as biomarkers; however, no consolidated guidelines for the discovery process are available. We developed a pipeline using innovative applications of existing bioinformatics methods to (1) face the inapplicability of the classical normalization methods, (2) detect global differences of miRNA distributions between the comparison classes and (3) develop a 'robust’ classifier.

overall_design: 78 samples (26 hemolyzed and 52 non hemolyzed) were 1:2 paired with caliper matching according to disease status, age at drawing and drawing year, starting from a total of 208 hybridized samples collected between 1987 and 2004 (including 94 paired samples according to tumor ER status, age at drawing, drawing year, time from surgery, 7 additional samples from 'no evidence of disease' (NED) patients, 10 references, 1 healthy donor and 2 replicated samples)


title: Genome-wide characterization of light-regulated genes in Neurospora crassa

city: Corvallis

first: Kristina

last: Smith

state: OR

department: Biochemisty and Biophysics

institute: Oregon State University

summary: RNA-seq from Neurospora crassa at 5 time points of light induction, with 2 replicates for each, totalling 10 samples

first: Deborah

last: Bell-Pedersen

first: Erin

last: Bredeweg

first: Rigzin

last: Dekhang

first: Jay

middle: C

last: Dunlap

last: Freitag

first: James

last: Galagan

first: Chandrashekara

last: Mallappa

first: Matthew

last: Peterson

last: Sachs

first: Cheng

last: Wu

first: Fei

last: Yang

first: Ying

last: Zhang

first: Jeremy

last: Zucker


title: H. pylori strain content variation after five year infection of macaques measured by array CGH

first: Nina

last: Salama

summary: Helicobacter pylori strains USU101 was infected into macaques, some of which were treated with the dietary carcinogen ENNG. After 5 years, H. pylori isolates were obtained by endoscopy followed by culture. The resulting strains were analyzed for differences in gene content by array CGH.

overall_design: Array CGH was performed by two color microarray. The monkey output strains were labeled with Cy5 (channel 2) and the input strain USU101 was labeled with Cy3 (channel 1). Each output strain was analyzed by 2-3 separate array experiments.

first: Jutta

last: Fero

first: Andre

last: Dubois

first: D

last: Merrell


title: RNA-sequencing of Campylobacter jejuni NCTC 11168 wildtype and fur perR mutant

status: Public on Jul 01 2014

city: Norfolk

first: Arnoud

last: van Vliet

address: Colney Lane

department: Gut Health and Food Safety Programme

institute: Institute of Food Research

summary: We report the use of RNA-seq analysis for the determination of RPKM transcript levels in wildtype and fur perR mutant of Campylobacter jejuni NCTC 11168. This allows for comparison of gene expression levels.

overall_design: Campylobacter jejuni NCTC 11168 wildtype and fur perR mutant were grown to late log phase, RNA was purified and used for RNA-sequencing by Illumina HiSeq sequencing

first: Rebecca

last: Handley

first: Francis

last: Mulholland

first: Mark

last: Reuter

first: Vinoy

last: Ramachandran

first: Heather

last: Musk

first: Leah

last: Clissold

first: Nick

middle: E

last: Le Brun


title: Monitoring Infection-Based Transcriptomic Changes in Staphylococcus aureus using RNA-seq

status: Public on Jul 11 2014

first: Vincent

middle: Michael

last: Bruno

address: 801 West Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

summary: Staphylococcus aureus is a major pathogen of healthcare settings with a high rate of morbidity and mortality. S. aureus has also emerged as a serious threat in healthy individuals in the community. Increasingly, antibiotic resistant S. aureus strains, particularly methicillin resistant S. aureus (MRSA), are causing these community-acquired infections (CA-MRSA). Because of the rising incidence of antibiotic resistance, including resistance to “last resort” antibiotics, development of prophylactic vaccines for S. aureus is considered a high priority. A complete, accurate characterization of the transcriptome of the host during different types of infection would expedite S. aureus vaccine development by identifying antigens that would be optimal vaccine targets. RNA-seq (deep-sequencing of cDNA) provides an unbiased method to comprehensively and systematically define the transcriptome (the complete set of transcribed regions in a genome) of an organism in a manner that is significantly more sensitive than microarray hybridization approaches. We propose a comprehensive characterization of the host transcriptome in two different murine models of infection (systemic infection and skin and soft tissue infection (SSTI)). We believe that this research will provide insight into potential vaccine targets that are expressed at high levels in both types of infection. We also wish to determine what mouse genes are up- or down-regulated during the course of these infections in order to better characterize the host-pathogen interaction. This description of the in vivo transcriptome will give novel insight into how the host senses and responds to infection with S. aureus in different infection types, and how the host tissue responds to bacterial invasion.

overall_design:
S. aureus strain SAP149 was used to infect mice epicutaneously to one ear of immunocompetent mice using an allergy testing needle; the other ear was left alone. RNA was extracted from each at 1, 4 or 7 days post-infection
The transcriptomes were sequenced by Illumina HiSeq of paired end libraries. Reads were mapped against the mouse reference genome and compared through a differential expression analysis.

last: Brady

first: Qi

last: Su

first: Sean

last: Daugherty

last: Creasy

first: Sandra

last: Ott

first: Naomi

last: Sengamalay

first: Claire

last: Fraser

first: Drusilla

last: Burns

middle: M


title: The human skeletal muscle transcriptome assessed with RNA sequencing

status: Public on Jul 15 2014

first: Joakim

last: Lundeberg

summary: The amount of RNA sequencing data on skeletal muscle is very limited. We have analyzed a large set of human muscle biopsy samples and provide extensive information on the baseline skeletal muscle transcriptome, including completely novel protein-coding transcripts.

overall_design: Analyze of transcriptome in 24 skeletal muscle biopsy samples, 12 individuals and one biopsy per leg per individual

first: Maléne

last: Lindholm

first: Mikael

last: Huss

first: Beata

last: Solnestam

first: Sanela

last: Kjellkvist

first: Carl

last: Sundberg


title: Dysregulation of genome-wide gene expression and DNA methylation in abnormal cloned piglets (MeDIP-seq)

status: Public on Sep 03 2014

city: Wuhan

first: Changchun

last: Li

address: No.1, Shizishan Street · Hongshan District

institute: Huazhong Agriculture University

summary:
Backgroud:Epigenetic modifications (especially altered DNA methylation) resulting in altered gene expression may be one reason for development failure or the abnormality of the cloned animals, but the underlying mechanism of the abnormal phenotype in the cloned piglets remains unrevealed. Some cloned piglets in our study showed abnormal phenotypes such as big tongue (longer and thicker), limp, and exomphalos, which is similar to the human BWS syndrome. Here we conducted DNA methylation (DNAm) immunoprecipitation binding high throughput sequencing (MeDIP-seq) and RNA sequencing (RNA-seq) of muscle tissues of cloned piglets to investigate the relationship of abnormal DNAm with gene dysregulation and the unusual phenotypes in cloned piglets.
Results:Analysis of the methylomes revealed that abnormal cloned piglets suffered more hypomethylated differentially methylated regions (DMRs) than hypermethylated DMRs compared to the normal cloned piglets. The DNAm level in the CpG Island was higher in the abnormal cloned piglets. Some repetitive elements, such as SINE/tRNA-Glu Satellite/centr also showed significant differences. Besides we detected 1,711 differentially expressed genes (DEGs) between the two groups, of which 243 genes also changed methylation level in the abnormal cloned piglets. The altered DNA methylation mainly affected the low and silent expression genes. We also found some interesting pathways and genes, such as MAPK signalling pathway, hypertrophic cardiomyopathy pathway, TPM3 gene and the imprinted gene PLAGL1, which may played important roles in the abnormal phenotype development.
Conclusions;The abnormal cloned piglets showed substantial change both in the DNAm and the gene expression levels. Our data may provide new insights into understanding the molecular mechanisms of the reprogramming of genetic information in cloned animals.

overall_design: We dissected the biceps femoris muscle from the abnormal cloned piglets and the normal cloned piglets, and analyzed the difference of MeDIP-seq and RNA-seq between the two groups.

first: Guanglei

first: Chuangchun


title: High intake of dietary sugar enhances bisphenol A (BPA) disruption and reveals ribosome-mediated pathways of toxicity: Acute Exposure

status: Public on Jun 04 2014

city: Boston

first: Alan

last: Branco

address: 665 Huntington Ave.

department: Environmental Health

institute: Harvard School of Public Health

summary: Fly strain y[1]; bw[1]; e[4]; ci[1] ey[R] was obtained from the Bloomington Stock Center. Flies were reared in incubators at 25°C, 65% of relative humidity, and photoperiod of 12 hours. For gene expression analyses flies were exposed to BPA, DEHP, and high sugar for 48 hours (acute exposure). After exposure, they were flash-frozen in liquid nitrogen. Four replicas of each sample were collected and stored at -80°C. Total RNA was extracted from whole flies using TRIzol (Life Technologies). The synthesis of cDNA and its labeling with fluorescent dyes (Cy3 and Cy5) as well as hybridization reactions were carried out using 3DNA protocols and reagents (Genisphere). Slides were scanned using Axon 400B scanner (Axon Instruments) and GenePix Pro 6.0 software. Foreground fluorescence of dye intensities was normalized by the Loess method in Bioconductor / Limma.

overall_design: Dye "swaps," loop design.

middle: T

first: Bernardo

last: Lemos


title: High intake of dietary sugar enhances bisphenol A (BPA) disruption and reveals ribosome-mediated pathways of toxicity: Chronic Exposure

summary: Fly strain y[1]; bw[1]; e[4]; ci[1] ey[R] was obtained from the Bloomington Stock Center. Flies were reared in incubators at 25°C, 65% of relative humidity, and photoperiod of 12 hours. For gene expression analyses flies were reared in media containing BPA, high sugar, and BPA + high sugar (chronic exposure). After development, newly emerged adult male flies were collected, aged for 48 hours, and flash frozen in liquid nitrogen. We collected four replicas of each sample and stored tehm at -80°C. Total RNA was extracted from whole flies using TRIzol (Life Technologies). The synthesis of cDNA and its labeling with fluorescent dyes (Cy3 and Cy5) as well as hybridization reactions were carried out using 3DNA protocols and reagents (Genisphere). Slides were scanned using Axon 400B scanner (Axon Instruments) and GenePix Pro 6.0 software. Foreground fluorescence of dye intensities was normalized by the Loess method in Bioconductor / Limma.