title: The activation of the NF-κB-JNK pathway is independent of the PI3K-Rac1-JNK pathway involved in the bFGF-regulated human fibroblast cell migration

status: Public on Jan 22 2018

city: Wenzhou

first: Yuanhu

last: Xuan

address: Chashan High School District

department: Medical School

institute: wenzhou medical university

summary: Wound healing is a complex process that repairs organ-tissues including skin after injury. Cell migration is an important process of wound healing and fibroblast growth factor bFGF has been reported to accelerate cell migration. However, knowledge of how bFGF regulates cell migration is limited. Here, we used human foreskin fibroblast primary cells and RNA-Seq based transcriptome analysis to isolate bFGF-regulating signal pathways that regulate cell migration. Among the many pathways identified, an inflammatory response pathway was further examined for its role in fibroblast cell migration through analysis of function by the key regulator NF-κB. Application of Bay11-7082 and LPS, a typical inhibitor and inducer of inflammatory response, promoted and inhibited cell migration, respectively. Biochemical data showed that Bay11-7082 treatment induces the phosphorylation level of JNK，but PI3K inhibitor LY294002 application did not alter the IκBα phosphorylation level. In addition, Bay11-7082 and JNK inhibitor SP600125 together inhibit while LY294002 together with Bay11-7082 maintains normal cell migration, indicating that NF-κB is independent of the PI3K pathway for regulation of JNK activity during cell migration. Taken together, the present study broadens our understanding of the bFGF-regulation mechanism and further identifies a new bFGF-regulating mechanism by which NF-κB regulates JNK during human fibroblast cell migration.

overall_design: In this study, we utilized a RNA-Seq approach to isolate bFGF-regulating gene pools and to further identify target molecules that regulate human fibroblast cell migration.

first: Litai

last: Jin

first: Lisha

last: Chi

first: Haishan

last: Tian

first: Yuting

last: Zhu

first: Wanhui

last: Cai

first: Chao

last: Niu

first: Minglong

last: Shao

first: Yusheng

last: Sun

first: Weitao

last: Cong

first: Zhongxin

first: Zhaoyu

last: Li

first: Yang

last: Wang


title: Expression data from thymic endothelial cells after damage

status: Public on Feb 01 2018

city: Seattle

first: Kirsten

last: Cooper

state: WA

address: 1100 Fairview Ave. N, Rm S3-208

country: USA

institute: Fred Hutchinson Cancer Research Center

summary:
The thymus is extremely sensitive to damage but also has a remarkable ability to repair itself. However, the mechanisms underlying this endogenous regeneration remain poorly understood and this capacity diminishes considerably with age. To identify alternate regeneration pathways in the thymus, we performed an unbiased transcriptome analysis of the non-hematopoietic (CD45-) stromal cell compartment of the thymus, which is less sensitive to thymic damage compared to the CD45+ hematopoietic compartment.
Recent work has suggested that ECs can contribute towards thymic regeneration via their production of so-called angiocrine factors. Using a technique to constitutively activate the Akt pathway in ECs using the pro-survival adenoviral gene E4ORF1, ECs can be propagated and expanded ex vivo (exEC) while maintaining their phenotype and vascular tube formation capacity. We compared the gene expression of freshly isolated thymic ECs and exEC-derived from the thymus.

overall_design: Thymic non-hematopoietic stromal cells were isolated using CD45 MACS cell depletion. Endothelial cells were then FACS purified (CD45- EpCAM- VE-Cad+). exEC were generated by lentiviral transduction with the E4ORF1 gene. Microarray analysis was performed on an Affymetrix MOE 430 A 2.0 platform in triplicate for freshly isolated ECs from untreated mice, and for exECs transduced with the pro-survival adenoviral gene E4ORF1.

first: Tobias

last: Wertheimer

first: Enrico

last: Velardi

first: Jennifer

last: Tsai

first: Jarrod

middle: A

last: Dudakov

first: Marcel

middle: R

last: van den Brink


title: PAX3-FOXO1 establishes myogenic super enhancers and recruits BRD4 de novo [7250 ChIP-seq]

status: Public on Apr 27 2017

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The fusion transcription factor PAX3-FOXO1 drives oncogenesis in a subset of rhabdomyosarcomas, however the mechanisms by which it remodels chromatin are unknown.  We find PAX3-FOXO1 reprograms the cis-regulatory landscape by inducing super enhancers (SEs), in collaboration with master transcription factors MYOG, MYOD and MYCN.  This myogenic SE circuitry is consistent across cell lines and primary tumors. Deregulation of PAX3-FOXO1 itself occurs by translocation-induced chromatin loops bringing the PAX3 promoter under the control of FOXO1 enhancers.   Protein targets induced by, or bound to, PAX3-FOXO1 occupied SEs, were selectively sensitive to small molecule inhibition. PAX3-FOXO1 co-binds BRD4 at SEs, and BET bromodomains are required for PAX3-FOXO1-dependent transcription and cancer cell growth.

overall_design: Genome-wide profiles for histone mark H3K27ac, DNase hypersensitivity, PAX3-FOXO1 and coactivator BRD4 in fibroblast cells stably transduced with either empty vector or PAX3-FOXO1 vector.

first: Berkley

middle: E

last: Gryder

first: Xinyu

last: Wen


title: Epigenetic Lanscape and BRD4 Transcriptional Dependency of PAX3-FOXO1 Driven Rhabdomyosarcoma

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Old Human Serum Increases Apoptosis and Molecular Ageing Markers In Human Hippocampal Progenitor Cells

status: Public on Nov 02 2017

city: London

first: Timothy

middle: Robert

last: Powell

address: 16 De Crespigny Park

department: SGDP Centre

country: United Kingdom

institute: King's College London

summary: The aim of this study was to compare the effects of old versus young serum on genome-wide expression in human hippocampal progenitor cells (HPC0A07/03C) as they differentiate into neurons/glial cells.

overall_design: We compared the differential impact serum obtained from old versus young individuals had on genome-wide expression in human hippocampal progenitor cells as they differentiate (5 time points), whilst correcting for gender and batch effects.

first: Tytus

last: Murphy

first: Aleksandra

last: Maruszak

first: Chiara

last: de Lucia

first: Simone

last: de Jong

first: Gerome

last: Breen

first: Jack

last: Price

first: Simon

last: Lovestone

first: Sandrine

last: Thuret


title: Critical role of pDC in regulating gene expression and innate immune responses to human rhinovirus

status: Public on Jun 10 2017

city: North Coogee

first: Denise

last: Anderson

address: 71 Caledonia Loop

country: Australia

institute: INSiGENe Pty Ltd

summary: Human rhinoviruses (HRV) are usually innocuous viruses; however, they can trigger serious consequences in certain individuals, especially in the setting of deficient interferon (IFN) synthesis. Plasmacytoid dendritic cells (pDC) are key IFN producing cells, though we know little about the mechanisms by which pDC regulate HRV-induced immune responses. Herein we used gene expression microarrays to examine HRV-induced mRNA in blood mononuclear cells from healthy people, in combination with pDC depletion to assess whether observed expression patterns were pDC dependent. As expected, pDC depletion led to a major reduction in HRV-induced IFN-α release, and this was associated with profound differences in gene expression between intact PBMC and pDC depleted PBMC. pDC depletion led to major changes in upstream regulators, with 70-80% of the HRV activated genes appearing to be pDC dependent. PCR validation experiments confirmed changes seen in the microarrays, specifically the extent to which the following differentially expressed genes were highly pDC dependent: the transcription factor IRF7, both IL-27 chains (IL-27 and EBI3), the alpha chain of the IL-15 receptor (IL-15RA) and the IFN stimulated gene IFI27. IL-6, IFN-γ and IL-27 protein synthesis were also highly pDC dependent. Supplementing pDC-depleted cultures with either recombinant IFN-γ, IL-15, IL-27 or IL-6 was able to restore the IFN-α response, thereby compensating for the absence of pDC. Though pDC comprise only a minority population of migratory leukocytes, our findings highlight the extent to which these cells are able to exert a profound effect on the immune response to HRV.

overall_design: PBMC samples from healthy people (n=11) were cultured in the presence (RV16) or absence (CTRL) of rhinovirus type 16. To investigate the role of plasmacytoid dendritic cells (pDC) in the response, pDC were depleted from cultures of these PBMC samples. Hence, each individual has four samples (PBMC-CTRL, PBMC-RV16, pDCdepleted-CTRL, pDCdepleted-RV16) for a total of 44 samples.

first: John

middle: W

last: Upham


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyW familly).

status: Public on Mar 01 2017

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

country: Japan

institute: Institute for Environmental Science

type: Genome variation profiling by genome tiling array

summary:
Transgenerational effects of continuous low dose-rate (LDR) gamma-ray irradiation have not been well studied.
C57BL/6JNrs male mice were maintained in non-irradiated room for 400 days from 8 weeks of age.
This study  investigated the De novo mutation by comparing the parents and children.
This is secondary screening.
This study was performed under contract with the Aomori Prefectural Government, Japan.

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyWM), female (20mGyWF) and their progenies (20mGyW1 to 20mGyW6) vs. reference male mouse.

first: Ogura

last: Keiji


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyU familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyUM), female (20mGyUF) and their progenies (20mGyU1 to 20mGyU8) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyZ familly).

status: Public on Feb 25 2017

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyZM), female (20mGyZF) and their progenies (20mGyZ1 to 20mGyZ5) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyY familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyYM), female (20mGyYF) and their progenies (20mGyY1 to 20mGyY6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyS familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGySM), female (20mGySF) and their progenies (20mGyS1 to 20mGyS3) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyAA familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyAAM), female (20mGyAAF) and their progenies (20mGyAA1 to 20mGyAA5) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyT familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyTM), female (20mGyTF) and their progenies (20mGyT1 and 20mGyT2) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyV familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyVM), female (20mGyVF) and their progenies (20mGyV1 to 20mGyV6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyR familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyRM), female (20mGyRF) and their progenies (20mGyR1 to 20mGyR4) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyO familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyOM), female (20mGyOF) and their progenies (20mGyO1 to 20mGyO6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyN familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyNM), female (20mGyNF) and their progenies (20mGyN1 to 20mGyN6) vs. reference male mouse.


title: Structural basis for human respiratory syncytial virus NS1-mediated modulation of host responses

status: Public on Jun 15 2017

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: Human respiratory syncytial virus (hRSV) is a major cause of morbidity and mortality in the pediatric, elderly, and immune compromised populations. A gap in our understanding of hRSVdisease pathology is the interplay between virally encoded immune antagonists and host components that limit hRSV replication. hRSV encodes for non-structural (NS) proteins that are important immune antagonists; however, the role of these proteins in viral pathogenesis is incompletely understood. Here we report the crystal structure of hRSV NS1 protein, which suggests that NS1 is a structural paralog of hRSV matrix (M) protein. Comparative analysis of the shared structural fold with M revealed regions unique to NS1. Studies on NS1 WT or mutant alone or in recombinant RSVs demonstrate that structural regions unique to NS1 contribute to modulation of host responses, including inhibition of type I IFN responses, suppression of dendritic cell maturation, and promotion of inflammatory responses. Transcriptional profiles of A549 cells infected with recombinant RSVs show significant differences in multiple host pathways, suggesting that NS1 may have a greater role in regulating host responses than previously appreciated. These results provide a framework to target NS1 for therapeutic development to limit hRSV associated morbidity and mortality.

overall_design: 12 samples where analysed. A549 cell line was infected with mock, hRSV or mutated hRSV virus. Samples are: control mock-infected (2 replicas), hRSV wild-type NS1 infected (3 replicas), hRSV NS1 1-118 infected (3 replicas), hRSV NS1 L132A/L133A infected (2 replicas) and hRSV NS1 Y125A infected (2 replicas). Libraries was prepared for 96 h.p.i.

first: Srirupa

last: Chatterjee

first: Priya

last: Luthra

first: Ekaterina

last: Esaulova

first: Eugene

last: Agapov

first: Benjamin

middle: C

last: Yen

first: Dominika

middle: M

last: Borek

first: Megan

last: Edwards

first: Anuradha

last: Mittal

first: David

middle: S

last: Jordan

first: Parameshwar

last: Ramanan

first: Martin

middle: L

last: Moore

first: Rohit

middle: V

last: Pappu

first: Michael

middle: J

last: Holtzman

first: Max

first: Christopher

middle: F

last: Basler

first: Gaya

middle: K

last: Amarasinghe

first: Daisy

last: Leung


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyM familly).

first: Keiji

last: OGURA

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyMM), female (20mGyMF) and their progenies (20mGyM1 to 20mGyM8) vs. reference male mouse.

first: Ogura

last: Keiji


title: Transcriptome analysis of neuroblastoma

status: Public on Mar 15 2017

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

summary: Present material was analyzed for activation of intracellular pathways in neuroblastoma compared to normal tissues (neural crest cells, healthy adrenal gland).

overall_design: Neuroblastoma samples were obtained from pediatric patients who had undergone surgery. Samples were formain fixed and embedded in paraffin. Tumors were evaluated by a pathologist to confirm the diagnosis and estimate the tumor cell numbers. All tumor samples used in this study contained at least 80% of tumor cells.

first: Elena

last: Ilnitskaya

first: Dmitry

last: Konovalov

first: Maksim

last: Sorokin

first: Ivan

last: Petrov

first: Daria

last: Allina

first: Anton

last: Buzdin


title: Transcriptome analysis of healthy adrenal glands, mbryonic neural crest cells, and neuroblastoma

overall_design: Refer to individual Series


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyL familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyLM), female (20mGyLF) and their progenies (20mGyL1 to 20mGyL8) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyQ familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyQM), female (20mGyQF) and their progenies (20mGyQ1 to 20mGyQ4) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyI familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyIM), female (20mGyIF) and their progenies (20mGyI1 to 20mGyI7) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyH familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyHM), female (20mGyHF) and their progenies (20mGyH1 to 20mGyH6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyX familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyXM), female (20mGyXF) and their progenies (20mGyX1 to 20mGyX7) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyJ familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyJM), female (20mGyJF) and their progenies (20mGyJ1 to 20mGyJ6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyX familly).

status: Public on Feb 24 2017

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyXM), female (0GyXF) and their progenies (0GyX1 to 0GyX6) vs. reference male mouse.

last: Ogura


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyW familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyWM), female (0GyWF) and their progenies (0GyW1 to 0GyW6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyF familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyFM), female (20mGyFF) and their progenies (20mGyF1 to 20mGyF6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyQ familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyQM), female (0GyQF) and their progenies (0GyQ1 to 0GyQ8) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyG familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyGM), female (20mGyGF) and their progenies (20mGyG1 to 20mGyG7) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyC familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyCM), female (20mGyCF) and their progenies (20mGyC1 to 20mGyC5) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyV familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyVM), female (0GyVF) and their progenies (0GyV1 to 0GyV7) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyA familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyAM), female (20mGyAF) and their progenies (20mGyA1 to 20mGyA6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyR familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyRM), female (0GyRF) and their progenies (0GyR1 to 0GyR6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyZ familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyZM), female (0GyZF) and their progenies (0GyZ1 to 0GyZ5) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyO familly).

status: Public on Feb 22 2017

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyOM), female (0GyOF) and their progenies (0GyO1 to 0GyO8) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyU family)

status: Public on Feb 21 2017

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyUM), female (0GyUF) and their progenies (0GyU1 to 0GyU5) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyE familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyEM), female (20mGyEF) and their progenies (20mGyE1 to 20mGyE5) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyB familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyBM), female (20mGyBF) and their progenies (20mGyB1 to 20mGyB5) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyS family)

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GySM), female (0GySF) and their progenies (0GyS1 to 0GyS6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyL family)

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyLM), female (0GyLF) and their progenies (0GyL1 to 0GyL6) vs. reference male mouse.


title: Genomic Profiling of Neuroblastoma Cell Lines

status: Public on Feb 07 2017

city: Philadelphia

first: Jo Lynne

last: Rokita

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

overall_design: Refer to individual Series


title: Transcriptomic Profiling of 39 Neuroblastoma Cell Lines

summary: Neuroblastoma cell lines are an important and cost-effective model used to study oncogenic drivers of the disease. While many of these cell lines have been previously characterized with SNP, methylation, and/or expression microarrays, there has not been an effort to comprehensively sequence these cell lines. Here, we present raw whole transcriptome data generated by RNA sequencing of 39 commonly-used neuroblastoma cell lines. This data can be used to perform differential expression analysis based on a genetic aberration or phenotype in neuroblastoma (eg: MYCN amplification status, ALK mutation status, 11q status, sensitivity to pharmacological pertubation). Additionally, we designed this experiment to enable structural variant and/or long-noncoding RNA analysis across these cell lines. Finally, as more DNase/ATAC and histone/transcription factor ChIP sequencing is performed in these cell lines, our RNA-Seq data will be an important complement to inform transcriptional targets as well as regulatory (enhancer or repressor) elements in neuroblastoma.

overall_design: We sequenced neuroblastoma cell lines (N=39) with varying genomic characteristics, disease stages, and phases of therapy. We also sequenced the hTERT-immortalized retinal pigmented epithelial cell line, RPE-1 (N=1), which is commonly used as a non-neuroblastoma control, as well as RNA from the fetal brain (N=1), which can serve as a non-neuroblastoma neural-cell derived control.

first: JoLynne

last: Harenza

first: Maura

last: Diamond

first: Rebecca

middle: N

last: Adams

last: Song

first: Heather

last: Davidson

first: Maish

middle: H

last: Dent

first: Paolo

last: Fortina

first: C

middle: P

last: Reynolds

first: John

last: Maris


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyH family)

status: Public on Jan 27 2017

first: Keiji

last: OGURA

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyHM), female (0GyHF) and their progenies (0GyH1 to 0GyH8) vs. reference male mouse.

first: Ogura

last: Keiji


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyD family1)

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyDM), female (0GyDF) and their progenies (0GyD1 to 0GyD4) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyN familly).

status: Public on Jan 31 2017

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyNM), female (0GyNF) and their progenies (0GyN1 to 0GyN6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyM familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyMM), female (0GyMF) and their progenies (0GyM1 to 0GyM7) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyJ familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyJM), female (0GyJF) and their progenies (0GyJ1 to 0GyJ5) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyC family)

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyCM), female (0GyCF) and their progenies (0GyC1 to 0GyC6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyK familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyKM), female (0GyKF) and their progenies (0GyK1 to 0GyK7) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyI family)

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyIM), female (0GyIF) and their progenies (0GyI1 to 0GyI6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyT family)

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyTM), female (0GyTF) and their progenies (0GyT1 to 0GyT5) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyP familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyPM), female (0GyPF) and their progenies (0GyP1 to 0GyP7) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyG family)

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyGM), female (0GyGF) and their progenies (0GyG1 to 0GyG6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyD family2)

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyDM), female (0GyDF) and their progenies (0GyD5 to 0GyD8) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyE family)

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyEM), female (0GyEF) and their progenies (0GyE1 to 0GyE6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 20mGyD familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyDM), female (20mGyDF) and their progenies (20mGyD1 to 20mGyD5) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyF family)

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyFM), female (0GyFF) and their progenies (0GyF1 to 0GyF7) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyX familly).

status: Public on Jan 12 2017

summary:
Transgenerational effects of continuous low dose-rate (LDR) gamma-ray irradiation have not been well studied.
C57BL/6JNrs male mice were maintained in non-irradiated room for 400 days from 8 weeks of age.
This study  investigated the De novo mutation by comparing the parents and children.
This is primary screening.
This study was performed under contract with the Aomori Prefectural Government, Japan.

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyXM), female (20mGyXF) and their progenies (20mGyX1 to 20mGyX7) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyW familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyWM), female (20mGyWF) and their progenies (20mGyW1 to 20mGyW6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyAA familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyAAM), female (20mGyAAF) and their progenies (20mGyAA1 to 20mGyAA5) vs. reference male mouse.


title: Genomic hallmarks of localized, non-indolent prostate cancer

status: Public on Jan 10 2017

city: Toronto

first: Yu-Jia

last: Shiah

state: Ontario

address: MaRS Centre 661 University Avenue Suite 510

department: Informatics and Bio-computing

country: Canada

institute: Ontario Institute for Cancer Research

summary: Prostate tumours are highly variable in their response to therapies, but clinically available prognostic factors can explain only a fraction of this heterogeneity. Here we analysed 200 whole-genome sequences and 277 additional whole-exome sequences from localized, non-indolent prostate tumours with similar clinical risk profiles, and carried out RNA and methylation analyses in a subset. These tumours had a paucity of clinically actionable single nucleotide variants, unlike those seen in metastatic disease. Rather, a significant proportion of tumours harboured recurrent non-coding aberrations, large-scale genomic rearrangements, and alterations in which an inversion repressed transcription within its boundaries. Local hypermutation events were frequent, and correlated with specific genomic profiles. Numerous molecular aberrations were prognostic for disease recurrence, including several DNA methylation events, and a signature comprised of these aberrations outperformed well-described prognostic biomarkers. We suggest that intensified treatment of genomically aggressive localized prostate cancer may improve cure rates.

overall_design: In total we have 73 samples across 3 different batches. Batch 1 and 3 are based on HuGene2.0 platform whereas batch 2 is based on HTA2.0 platform

first: Paul

last: Boutros

first: Robert

middle: G

last: Bristow

first: Michael

last: Fraser


type:
Expression profiling by array
Methylation profiling by array

overall_design: Refer to individual Series


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyA family)

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyAM), female (0GyAF) and their progenies (0GyA1 to 0GyA3) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Secondary screening for 0GyB family)

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0GyBM), female (0GyBF) and their progenies (0GyB1 to 0GyB6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyY familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyYM), female (20mGyYF) and their progenies (20mGyY1 to 20mGyY6) vs. reference male mouse.

last: Ogura


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyZ familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyZM), female (20mGyZF) and their progenies (20mGyZ1 to 20mGyZ5) vs. reference male mouse.


overall_design: In total, we have methylation profiles for 160 samples (corresponding to 104 unique samples). Out of the 104 unique samples, 34 samples were repeated twice, 8 samples repeated three times, 2 samples repeated four times.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyV family)

status: Public on Dec 27 2016

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyVM), female (20mGyVF) and their progenies (20mGyV1 to 20mGyV6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyU family)

status: Public on Dec 28 2016

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyUM), female (20mGyUF) and their progenies (20mGyU1 to 20mGyU8) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyR familly).

status: Public on Dec 23 2016

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyRM), female (20mGyRF) and their progenies (20mGyR1 to 20mGyR4) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyT familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyTM), female (20mGyTF) and their progenies (20mGyT1 and 20mGyT2) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyS familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGySM), female (20mGySF) and their progenies (20mGyS1 to 20mGyS3) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyQ familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyQM), female (20mGyQF) and their progenies (20mGyQ1 to 20mGyQ4) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyN familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyNM), female (20mGyNF) and their progenies (20mGyN1 to 20mGyN6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyI familly).

status: Public on Dec 22 2016

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyIM), female (20mGyIF) and their progenies (20mGyI1 to 20mGyI7) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyO familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyOM), female (20mGyOF) and their progenies (20mGyO1 to 20mGyO6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyH familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyGM), female (20mGyGF) and their progenies (20mGyG1 to 20mGyG6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyJ familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyJM), female (20mGyJF) and their progenies (20mGyJ1 to 20mGyJ6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyF familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyFM), female (20mGyFF) and their progenies (20mGyF1 to 20mGyF6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyL familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyLM), female (20mGyLF) and their progenies (20mGyL1 to 20mGyL8) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyC familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyCM), female (20mGyCF) and their progenies (20mGyC1 to 20mGyC5) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyG familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyGM), female (20mGyGF) and their progenies (20mGyG1 to 20mGyG7) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyD familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyDM), female (20mGyDF) and their progenies (20mGyD1 to 20mGyD5) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyE familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyEM), female (20mGyEF) and their progenies (20mGyE1 to 20mGyE5) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyB familly).

status: Public on Dec 20 2016

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyBM), female (20mGyBF) and their progenies (20mGyB1 to 20mGyB5) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyZ familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0mGyZM), female (0mGyZF) and their progenies (0mGyZ1 to 0mGyZ5) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyA familly)

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyAM), female (20mGyAF) and their progenies (20mGyA1 to 20mGyA6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyT familly).

status: Public on Dec 18 2016

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0mGyTM), female (0mGyTF) and their progenies (0mGyT1 to 0mGyT5) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyW familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0mGyWM), female (0mGyWF) and their progenies (0mGyW1 to 0mGyW6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyU familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0mGyUM), female (0mGyUF) and their progenies (0mGyU1 to 0mGyU5) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyV familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0mGyVM), female (0mGyVF) and their progenies (0mGyV1 to 0mGyV7) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyR familly).

status: Public on Dec 15 2016

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0mGyRM), female (0mGyRF) and their progenies (0mGyR1 to 0mGyR6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyP familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0mGyPM), female (0mGyPF) and their progenies (0mGyP1 to 0mGyP7) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyX familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0mGyXM), female (0mGyXF) and their progenies (0mGyX1 to 0mGyX6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyQ familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0mGyQM), female (0mGyQF) and their progenies (0mGyQ1 to 0mGyQ8) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 20mGyM familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (20mGyMM), female (20mGyMF) and their progenies (20mGyM1 to 20mGyM8) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyO familly).

status: Public on Dec 14 2016

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0mGyOM), female (0mGyOF) and their progenies (0mGyO1 to 0mGyO8) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyM familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0mGyMM), female (0mGyMF) and their progenies (0mGyM1 to 0mGyM7) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyN familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0mGyNM), female (0mGyNF) and their progenies (0mGyN1 to 0mGyN6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyK familly).

status: Public on Nov 29 2016

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0mGyKM), female (0mGyKF) and their progenies (0mGyK1 to 0mGyK7) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyL familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0mGyLM), female (0mGyLF) and their progenies (0mGyL1 to 0mGyL6) vs. reference male mouse.


title: Inner ear supporting cells are organized tissue-resident macrophages arranged like cobblestones.

status: Public on Dec 10 2016

city: Nakahara-ku, Kawasaki-shi

first: Nobuyuki

last: Tanaka

state: Kanagawa

address: 1-356, Kosugi-cho

department: Department of Molecular Oncology

institute: Institute for Advanced Medical Sciences, Nippon Medical School

summary: Sensorineural hearing loss (SHL) is a relatively common disease, and studies have suggested viral infection as a major cause. In the inner ear, the blood-labyrinthine barrier prevents access of the peripheral immune system; therefore, the immune system remains poorly understood. Here we found that cochlear accessory supporting cells (SCs), which are anchored by tight junctions, are organized tissue-resident macrophages. Virus-infected supporting cells change into activated macrophages and protect audiosensory receptor hair cells (HCs) against virus infection by producing interferon (IFN)-α/β. Moreover, we also observed bacterial phagocytosis by SCs. However, tumour necrosis factor-related apoptosis-inducing ligand (Trail), produced by virus-infected SCs, induced sensory hair loss and HC death by necroptosis. Notably, corticosteroid, the only effective drug for SHL, inhibited the virus-induced macrophage change of SCs. These results revealed an inner ear immune system, and suggest a possible mechanism for virus-induced SHL.

overall_design: To understand the mechanism of virus- and LPS-induced macrophage change of cochlear supporting cells, we analysed the mRNA expression profiles of inner ear sensory epithelium in the absence of and presence of these stimulations. The RNeasy Micro Kit (Qiagen) was used to extract total RNA from three cochlear sensory epithelia. For microarray, total RNA was extracted from nine mock explants, nine explants treated with 1000 ng/ml LPS for 16 h, or fourteen explants infected with TMEV (Theiler’s murine encephalomyelitis virus) for 16 h using the RNeasy Micro Kit. TMEV infection for 16 h induced cochlear cell death in hair cells and supporting cells, so a greater number of TMEV-infected cochleae were needed compared with mock and LPS-treated cochleae to equalize the amount of total RNA. Filgen (the company for biological technical service) performed the microarray analysis using GeneChip Mouse Gene 2.0 ST Array (Affymetrix).

first: Yushi

last: Hayashi

first: Hidenori

last: Suzuki

first: Wataru

last: Nakajima

first: Ikuno

last: Uehara

first: Atsuko

last: Tanimura

first: Toshiki

last: Himeda

first: Satoshi

last: Koike

first: Tatsuya

last: Katsuno

first: hin-ichiro

last: Kitajiri

first: Naoto

last: Koyanagi

first: Yasushi

last: Kawaguchi

first: Koji

last: Onomoto

first: Hiroki

last: Kato

first: Mitsutoshi

last: Yoneyama

first: Takashi

last: Fujita


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyJ familly).

first: Keiji

last: OGURA

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0mGyJM), female (0mGyJF) and their progenies (0mGyJ1 to 0mGyJ5) vs. reference male mouse.

last: Ogura


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyS familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0mGySM), female (0mGySF) and their progenies (0mGyS1 to 0mGyS6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyC family)

status: Public on Nov 03 2016

summary:
Transgenerational effects of continuous low dose-rate (LDR) gamma-ray irradiation have not been well studied.  Recent advances in DNA technology enabled us to examine a whole genome at molecular level.  Here we adopted one of these techniques called oligo-microarray comparative genome hybridization (CGH) and studied trans-generational effects on DNA copy number aberrations (CNAs).
C57BL/6JNrs male mice were exposed to LDR gamma-rays (20 mGy/day) for 400 days (total dose: 8000 mGy) from 8 weeks of age.  Progeny from 20 mGy/day irradiated mice had significantly higher frequencies of genomic aberrations than the progeny of non-irradiated mice.
This study investigated the De novo mutation by comparing the parents and children using 25 irradiated male family and 25 non irradiated male family.
This study was performed under contract with the Aomori Prefectural Government, Japan.

overall_design:
Two-condition experiment, C57BL/6JNrs tail tissue non-irradiated male (0mGyCM), female (0mGyCF) and their progenies (0mGyC1 to 0mGyC6) vs. reference male mouse.

We irradiated and non irradiated male mice (C57BL/6JNrs) for 400 days and cross to non irradiated female mice (C57BL/6JNrs) and got F1 mice.  After they dead the DNA were prepared from their tails.
At first, primary screening using １M oligo-microarray was performed.  The array was mounted autosomal fragment at intervals of an average about 3kb.
Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse.  This reference male mouse was from the same colony used in this experiment.  Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.
Identification the chromosomal location of the probe.  Probes adjacent to the probe with aberration were set at high density.  The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening.  Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.
Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyI familly).

overall_design: Two-condition experiment, C57 BL/6JNrs tail tissue non-irradiated male (0mGyDM), female (0mGyDF) and their progenies (0mGyI1 to 0mGyI6) vs. reference male mouse.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyF family)

status: Public on Nov 16 2016

summary:
Transgenerational effects of continuous low dose-rate (LDR) gamma-ray irradiation have not been well studied. Recent advances in DNA technology enabled us to examine a whole genome at molecular level. Here we adopted one of these techniques called oligo-microarray comparative genome hybridization (CGH) and studied trans-generational effects on DNA copy number aberrations (CNAs).
C57BL/6JNrs male mice were exposed to LDR gamma-rays (20 mGy/day) for 400 days (total dose: 8000 mGy) from 8 weeks of age. Progeny from 20 mGy/day irradiated mice had significantly higher frequencies of genomic aberrations than the progeny of non-irradiated mice.
This study investigated the de novo mutation by comparing the parents and children using 25 irradiated male family and 25 non-irradiated male family.

Grant: This study was performed under contract with the Aomori Prefectural Government, Japan.

overall_design:
We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and crossed to non-irradiated female mice (C57BL/6JNrs) and got F1 mice. After they were dead, the DNA were prepared from their tails.
At first, primary screening using 1 M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 3kb.
Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.
Identification of the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.
Finally, we performed TaqMan® Copy Number Assays to verify the mutations.
This SubSeries is a primary screening. Non-irradiated male (0mGyFM), female (0mGyFF) and their progenies (0mGyF1 to 0mGyF7) vs. reference male mouse 1.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyB family)

overall_design:
Two-condition experiment, C57BL/6JNrs tail tissue non-irradiated male (0mGyBM), female (0mGyBF) and their progenies (0mGyB1 to 0mGyB6) vs. reference male mouse.

We irradiated and non irradiated male mice (C57BL/6JNrs) for 400 days and cross to non irradiated female mice (C57BL/6JNrs) and got F1 mice.  After they dead the DNA were prepared from their tails.
At first, primary screening using １M oligo-microarray was performed.  The array was mounted autosomal fragment at intervals of an average about 3kb.
Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse.  This reference male mouse was from the same colony used in this experiment.  Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.
Identification the chromosomal location of the probe.  Probes adjacent to the probe with aberration were set at high density.  The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening.  Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.
Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyH family)

status: Public on Nov 18 2016

overall_design:
We irradiated and non irradiated male mice (C57BL/6JNrs) for 400 days and cross to non irradiated female mice (C57BL/6JNrs) and got F1 mice.  After they dead the DNA were prepared from their tails.
At first, primary screening using １M oligo-microarray was performed.  The array was mounted autosomal fragment at intervals of an average about 3kb.
Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse.  This reference male mouse was from the same colony used in this experiment.  Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.
Identification the chromosomal location of the probe.  Probes adjacent to the probe with aberration were set at high density.  The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening.  Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.
Finally, we performed TaqMan® Copy Number Assays to verify the mutations.
This SubSeries is a primary screening. non-irradiated male (0mGyHM), female (0mGyHF) and their progenies (0mGyH1 to 0mGyH3 and 0mGyH5 to 0mGyH8 ) vs. reference male mouse 1.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyE family)

overall_design:
We irradiated and non irradiated male mice (C57BL/6JNrs) for 400 days and cross to non irradiated female mice (C57BL/6JNrs) and got F1 mice.  After they dead the DNA were prepared from their tails.
At first, primary screening using １M oligo-microarray was performed.  The array was mounted autosomal fragment at intervals of an average about 3kb.
Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse.  This reference male mouse was from the same colony used in this experiment.  Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.
Identification the chromosomal location of the probe.  Probes adjacent to the probe with aberration were set at high density.  The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening.  Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.
Finally, we performed TaqMan® Copy Number Assays to verify the mutations.
This SubSeries is a primary screening. non-irradiated male (0mGyEM), female (0mGyEF) and their progenies (0mGyE1 to 0mGyE6) vs. reference male mouse 1.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyG family)

status: Public on Nov 17 2016

overall_design:
We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and crossed to non-irradiated female mice (C57BL/6JNrs) and got F1 mice. After they were dead, the DNA were prepared from their tails.
At first, primary screening using 1 M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 3kb.
Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.
Identification of the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.
Finally, we performed TaqMan® Copy Number Assays to verify the mutations.
This SubSeries is a primary screening. Non-irradiated male (0mGyGM), female (0mGyGF) and their progenies (0mGyG1 to 0mGyG6) vs. reference male mouse 1.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyD family)

overall_design:
We irradiated and non irradiated male mice (C57BL/6JNrs) for 400 days and cross to non irradiated female mice (C57BL/6JNrs) and got F1 mice.  After they dead the DNA were prepared from their tails.
At first, primary screening using １M oligo-microarray was performed.  The array was mounted autosomal fragment at intervals of an average about 3kb.
Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse.  This reference male mouse was from the same colony used in this experiment.  Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.
Identification the chromosomal location of the probe.  Probes adjacent to the probe with aberration were set at high density.  The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening.  Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.
Finally, we performed TaqMan® Copy Number Assays to verify the mutations.
This SubSeries is a primary screening. non-irradiated male (0mGyDM), female (0mGyDF) and their progenies (0mGyD1 to 0mGyD8) vs. reference male mouse 1.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Stat3f/f K5cre Skin Transcriptomes

status: Public on Oct 11 2016

city: Yokohama

first: Kosuke

last: Miyauchi

address: 1-7-22 Suehiro-sho

institute: RIKEN Center for Integrative Medical Sciences

summary: Atopic dermatitis (AD) is a common chronic skin disease, affecting >15% of children and 2-10% of adults worldwide. Understanding pathogenic mechanisms of the onset and dynamic progression of AD is required to design its effective treatments. The kinetical analysis of transcriptome in a mouse AD model revealed the pathways that led a vulnerable background and were critical to the onset of disease progress.

overall_design: Kinetical transcriptome analysis in keratinocyte specific Stat3 deficient mice

first: Kouske

first: Mariko

last: Okada-Hatakeyama

first: Reiko

last: Tanaka

first: Masato

last: Kubo


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days (Primary screening for 0mGyA family)

overall_design:
Two-condition experiment, C57BL/6JNrs tail tissue non-irradiated male (0mGyAM), female (0mGyAF) and their progenies (0mGyA1 to 0mGyA3) vs. reference male mouse.

We irradiated and non irradiated male mice (C57BL/6JNrs) for 400 days and cross to non irradiated female mice (C57BL/6JNrs) and got F1 mice.  After they dead the DNA were prepared from their tails.
At first, primary screening using １M oligo-microarray was performed.  The array was mounted autosomal fragment at intervals of an average about 3kb.
Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse.  This reference male mouse was from the same colony used in this experiment.  Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.
Identification the chromosomal location of the probe.  Probes adjacent to the probe with aberration were set at high density.  The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening.  Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.
Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: RNAseq from disomic and trisomic T cells and monocytes

status: Public on Jul 29 2016

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

summary: RNA was sequenced from Disomic and Trisomic individuals for chromosome 21 to identify consistent changes in gene expression across individuals

overall_design: Cells were cultured at subconfluency and RNA harvested for sequencing

first: Kelly

last: Sullivan

first: Ahwan

last: Pandey

first: Keith

last: Smith

first: Joaquín

last: Espinosa


title: Pediatric AML classification according to C/EBPδ expression

status: Public on Jun 21 2016

city: Padova

first: Matteo

last: Zampini

state: PD

address: corso stati uniti 4

country: Italy

institute: Istituto di Ricerca Pediatrica (IRP)  Città della Speranza

summary: We examined if pediatric AMLs rank-ordered according to C/EBPδ expression showed the activation of similar pathways. AML samples were dichotomized into groups including the upper quartile (Q1) and the lower three quartiles (Q2-4) according to their C/EBPδ expression values. Moreover, AML samples were associated to French-American-British (FAB) classification.

overall_design: 100 ng of bone marrow RNA from 85 patients with de novo AML at diagnosis were hybridized on the GeneChip® Human Transcriptome Array 2.0.

first: Claudia

last: Tregnago

first: Martina

last: Pigazzi


title: Chromatin interaction map of promoters of a human lymphoblastoid cell line using capture in situ Hi-C

status: Public on Apr 30 2016

city: Chicago

first: Noboru

middle: Jo

last: Sakabe

state: IL

address: 920 E 58th st

department: Human Genetics

institute: University of Chicago

summary: We generated an interaction map using capture in situ Hi-C in human LCL

overall_design: One sample of a human LCL was grown. In situ Hi-C was performed and the sequencing library was captured using 120 RNA probes.

first: Marcelo

last: Nobrega

first: Debora

last: Sobreira

first: Lindsey

last: Montefiori


title: Trisomy 21 consistently activates the interferon response

department: Pharmacology

institute: University of Colorado Anschutz Medical Center

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Inhibition of class I histone deacetylases 1 and 2 promotes urothelial carcinoma cell death by various mechanisms

status: Public on Jan 31 2016

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf


title: Identification of a macrophage PPARγ-GDF3 regulatory axis controlling muscle regeneration

status: Public on Oct 24 2016

city: Debrecen

first: Szilard

last: Poliska

address: Egyetem ter 1.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary:
Muscle injury was elicited by cardiotoxin injection into the tibialis anterior muscle. Macrophages were isolated 2 days post-injury from the regenerating muscle.
We used microarray to obtain global gene expression data of muscle-derived tissue macrophage subsets.

overall_design: Tissue macrophages were collected from regenerating muscle samples of three animals, Ly6C+ F4/80low and Ly6C- F4/80high macrophage subsets were sorted. The global gene expression patterns of distinct macrophage subsets were analyzed on Affymetrix microarrays.

first: Tamas

last: Varga

first: Laszlo

last: Nagy


title: RNAseq from disomic and trisomic fibroblasts and lymphoblastoids

summary: RNA was sequenced from individuals Disomic and Trisomic for chromosome 21 to identify consistent changes in gene expression across individuals

first: Leisa

last: Jackson


title: The tissue-engineered human cornea as a model to study expression of matrix metalloproteinases during corneal wound healing

status: Public on Nov 25 2015

city: Québec

first: Karine

last: Zaniolo

state: Québec

address: 1050 Chemin Sainte-Foy

department: CUO-Recherche

institute: Centre de recherche du CHU de Québec

summary: Corneal injuries remain a major cause of consultation in the ophthalmology clinics worldwide. Repair of corneal wounds is a complex mechanism that involves cell death, migration, proliferation, differentiation, and extracellular matrix (ECM) remodeling. In the present study, we used a tissue-engineered, two-layers (epithelium and stroma) human cornea as a biomaterial to study both the cellular and molecular mechanisms of wound healing. Gene profiling on microarrays revealed important alterations in the pattern of genes expressed by tissue-engineered corneas in response to wound healing. Expression of many MMPs-encoding genes was shown by microarray and qPCR analyses to increase in the migrating epithelium of wounded corneas. Many of these enzymes were converted into their enzymatically active form as wound closure proceeded. In addition, expression of MMPs by human corneal epithelial cells (HCECs) was affected both by the stromal fibroblasts and the collagen-enriched ECM they produce. Most of all, results from mass spectrometry analyses provided evidence that a fully stratified epithelium is required for proper synthesis and organization of the ECM on which the epithelial cells adhere. In conclusion, and because of the many characteristics it shares with the native cornea, this human two layers corneal substitute may prove particularly useful to decipher the mechanistic details of corneal wound healing.

overall_design: Primary cultures of human corneal epithelial cells cultivated on BSA (number of replicates: 7), Collagen type I (number of replicates: 2), Collagen type IV (number of replicates: 2), Fibronectin (number of replicates: 2), Tenascin C (number of replicates: 2) and Laminin (number of replicates: 2) matrix. Central, internal and external ring of wounded Tissue-engineered human cornea.

first: Camille

last: Couture

first: Patrick

last: Carrier

first: Jennifer

last: Lake

first: Julien

last: Patenaude

first: Lucie

last: Germain

first: Sylvain

last: Guérin


title: Illumina Sentrix 6 mouse BeadChip gene expression analysis in mouse spinal cord in the EAE model of Multiple Sclerosis

status: Public on Aug 28 2014

city: Frankfurt

first: Irmgard

last: Tegeder

state: Hessen

address: Theodor Stern Kai 7

department: Clinical Pharmacology

institute: Goethe University Frankfurt

summary:
The study assessed the efficacy of R-flurbiprofen in experimental autoimmune encephalomyelitis (EAE) models of multiple sclerosis in mice. R-flurbiprofen, also known as tarenflurbil, is the R-enantiomer of the cyclooxyygenase inhibitor S-flurbiprofen. It is ineffective in terms of cyclooxygenase inhibition and has no relevant toxicity in humans. Oral R-flurbiprofen prevented and attenuated primary progressive EAE in C57BL6/J mice and relapsing-remitting EAE in SJL mice, even if the treatment was initiated on or after the first flare of the disease. R-flurbiprofen reduced immune cell infiltration and microglia activation and inflammation in the spinal cord, brain and optic nerve and attenuated myelin destruction and EAE-evoked hyperalgesia. R-flurbiprofen treatment increased CD4+CD25+FoxP3+ regulatory T-cells, CTLA4+ inhibitory T-cells and interleukin-10, whereas the EAE-evoked upregulation of pro-inflammatory genes in the spinal cord was strongly reduced (Sentrix6 results). The effects were associated with an increase of plasma and cortical endocannabinoids but decreased spinal prostaglandins, the latter likely due to R- to S inversion. The promising results suggest potential efficacy of R-flurbiprofen in human MS.
To assess effects of R-flurbiprofen on EAE evoked gene regulations in the spinal cord a genome wide expression analysis was performed using Illumina Sentrix 6 v2 BeadChips. For the microarray study female C57BL6/J mice were immunized according to a standard protocol using the Hooke Kit™ MOG35-55/CFA emulsion PTX (EK-2110, Hooke Labs, St Lawrence, MA), which contains 200 µg myelin oligodendrocyte glycoprotein (MOG) 35-55 emulsified in 200 µl Complete Freund’s Adjuvant (CFA). The emulsion was injected subcutaneously at two sites followed by two intraperitoneal (i.p.) injections of 200 ng pertussis toxin (PTX) in phosphate buffered saline (PBS), the first 1-2 h after MOG35-55, and the second 24 h after MOG35-55. Control mice received CFA without MOG35-55 (sham mice). Treatment with R-flurbiprofen or vehicle (n = 12 per group) was started 5 days after immunization and was administered continuously via the drinking water up to the end. Spinal cords were dissected out during the flare of the disease, day 16 after immunization.

overall_design: For microarray analysis, total RNA was extracted from homogenizedlumbar  spinal cord tissue with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. RNA quality was checked  (Nanodrop ND-1000, Agilent 2100 Bioanalyzer), and subsequently biotinylated and hybridized to Mouse Sentrix-6 V2 Expression BeadChips (Illumina). Each sample consisted of pooled lumbar spinal cord tissue from 3 animals and 3 replicate samples were analyzed per group, i.e. the analysis is based on 9 mice per group. Groups were CFA-control with vehicle treatment, CFA-control with R-flurbiprofen, EAE-vehicle and EAE-R-flurbiprofen treatment. Treatment was started 5 days after immunization. For dissection, pairs were matched according to the clinical scores. QC, labeling, hybridization and raw data evaluation and normalization were done according to standard protocols at the core facilities of the Deutsche Krebsforschungszentrum, Heidelberg, Germany.


title: Effect of siRNA mediated silencing of lncRNA NRCP in cancer cells

status: Public on Dec 30 2015

city: allston

first: rajesha

last: rupaimoole

state: ma

address: 1315 commonwealth ave, apt 308

institute: UT MD Anderson Cancer Center

summary: Long noncoding RNAs (lncRNAs) significantly influence the development and regulation of genome expression in cells. Here, we demonstrate the role of lncRNA ceruloplasmin (NRCP) in cancer metabolism and elucidate functional effects leading to increased tumor progression. NRCP was highly upregulated in ovarian tumors and knockdown of NRCP resulted in significantly increased apoptosis, decreased cell proliferation, and decreased glycolysis compared with control cancer cells. In an orthotopic mouse model of ovarian cancer, siNRCP delivered via a liposomal carrier significantly reduced tumor growth compared with control treatment. We identified NRCP as an intermediate binding partner between STAT1 and RNA polymerase II, leading to increased expression of downstream target genes such as glucose-6-phosphate isomerase. Collectively, we report a previously unrecognized role of the lncRNA NRCP in modulating cancer metabolism. DOPC nanoparticle-incorporated siRNA-mediated silencing of this lncRNA in vivo demonstrates the first known preclinical model indicating therapeutic potential of modulating lncRNAs in cancer.

overall_design: SKOV3 cells were treated with sicontrol and siNRCP for 48hrs. All the tretaments were done in triplicates.

first: Anil

last: Sood

first: Rajesha

last: Rupaimoole


title: Comparison of noncoding RNA profiles in RNA from ovarian cancer patient samples

summary: We used NCode Human Long Non-coding RNA microarray  to study differential expression of noncoding RNAs in tumor samples from patients with ovarian cancer. Normal ovarian tissue samples were used as controls.

overall_design: Normal ovarian tissue isolated RNA (n=11) and Ovarian tumor tissue isolated RNA (n=29) was used to profile the expression of longnoncoding RNAs.


title: Gene expression in hippocampal sub-fields of 6.1 month old rTg4510 mice

status: Public on Jun 14 2014

city: Wallingford

first: John

last: Corradi

state: CT

address: 5 Research Parkway

institute: Bristol-Myers Squibb Company

summary: Microarrays were used to assess the gene expression patterns in the CA1, CA3, and dentate gyrus of the rTg4510 mouse line at 6.1 months of age. This line harbors a repressible mutant human Tau transgene under the Camk2a promoter. Both mice with just the tet-Transactivator alone and no transgenes ('double negative') were used as comparison groups.

overall_design: Cellular layers of the CA1, CA3, and dentate gyrus (DG) from 5 or 6 mice per genotype at age 6.1 months were laser capture dissected, RNA was isolated, and hybridization to Affymetrix microarrays performed.

first: P

last: Wes

first: A

last: Easton

first: J

first: D

last: Barten

first: L

middle: B

last: DeCarr

last: Truong

last: He

first: N

middle: X

last: Barrezueta

first: C

last: Polson

last: Bourin

first: M

middle: E

last: Flynn

first: S

last: Keenan

first: R

last: Lidge

last: Meredith

last: Natale

last: Sankaranarayanan

last: Seager

first: G

middle: W

last: Cadelina

last: Albright

last: Cacace


title: Extensive Nuclear Reprogramming Underlies Lineage Conversion into Functional Trophoblast Stem-like Cells

status: Public on Oct 01 2015

city: Jerusalem

first: Yossi

last: buganim

address: Ein Karem 91120

department: Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

summary: The generation of induced pluripotent stem cells (iPSCs) and the direct conversion approach provide an invaluable resource of cells for disease modeling, drug screening, and patient-specific cell-based therapy. However, while iPSCs are stable and resemble ESCs in their transcriptome, methylome and function, the vast majority of the directly converted cells represent an incomplete reprogramming state as evident by their aberrant transcriptome and transgene dependency. This raises the question of whether complete and stable nuclear reprogramming can be achieved only in pluripotent cells. Here we demonstrate the generation of stable and fully functional induced trophoblast stem cells (iTSCs) by transient expression of Gata3, Tfap2c and Eomes.  Similarly to iPSCs, iTSCs underwent a complete and stable reprogramming process as assessed by transcriptome and methylome analyses and functional assays such as the formation of hemorrhagic lesion and placenta contribution. Careful examination of the conversion process indicated that the cells did not go through a transient pluripotent state. These results suggest that complete nuclear reprograming can be attained in non-pluripotent cells.

overall_design: Technical duplicates of 10 samples

first: Hana

last: Benchetrit

first: Yosef

last: Buganim


title: Inhibition of class I histone deacetylases 1 and 2 promotes urothelial carcinoma cell death by various mechanisms (HDAC inhibitor treatments)

first: Karl

last: Koehrer

summary: Preliminary manuscript abstract: Class I histone deacetylases HDAC1 and HDAC2 contribute to cell proliferation and are commonly upregulated in urothelial carcinoma (UC). To evaluate whether specific inhibition of HDAC1 and HDAC2 might serve as an appropriate therapy of UC we applied specific pharmacological inhibition of HDAC1 and HDAC2 with the two selective class I HDAC inhibitors Romidepsin and Givinostat. Treatment with the pan HDAC inhibitor SAHA served as an additional control. Romidepsin and Givinostat significantly reduced proliferation and clonogenicity of UC cells with minor effects on non-tumorigenic cells. Furthermore, compounds induced primarily S-phase disturbances and non-apoptotic cell death. Results of microarray analysis of HDAC inhibitor treated cells match with observed phenotype after pharmacological HDAC1 and HDAC2 inhibition in UC cells.

overall_design: For differential gene expression analyses three independent high quality RNA preparations from VM-CUB1 and UM-UC-3 cells, treated with the HDAC inhibitors Romidepsin, Givinostat and SAHA, were compared to DMSO treated control cells.

last: Pinkerneil

last: Hoffmann

last: Deenen

first: K

last: Köhrer

first: T

last: Arent

first: W

middle: A

last: Schulz

last: Niegisch


title: A Saccharomyces cerevisiae strain with a minimal complement of glycolytic genes reveals strong redundancies in central metabolism

status: Public on Dec 06 2014

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

summary: As a result of ancestral whole genome and small-scale duplication events, the genome of Saccharomyces cerevisiae’s, and of many eukaryotes, still contain a substantial fraction of duplicated genes. In all investigated organisms, metabolic pathways, and more particularly glycolysis, are specifically enriched for functionally redundant paralogs. In ancestors of the Saccharomyces lineage, the duplication of glycolytic genes is purported to have played an important role leading to S. cerevisiae current lifestyle favoring fermentative metabolism even in the presence of oxygen and characterized by a high glycolytic capacity. In modern S. cerevisiae, the 12 glycolytic reactions leading to the biochemical conversion from glucose to ethanol are encoded by 27 paralogs. In order to experimentally explore the physiological role of this genetic redundancy, a yeast strain with a minimal set of 14 paralogs was constructed (MG strain). Remarkably, a combination of quantitative, systems approach and of semi-quantitative analysis in a wide array of growth environments revealed the absence of phenotypic response to the cumulative deletion of 13 glycolytic paralogs. This observation indicates that duplication of glycolytic genes is not a prerequisite for achieving the high glycolytic fluxes and fermentative capacities that are characteristic for S. cerevisiae and essential for many of its industrial applications and argues against gene dosage effects as a means for fixing minor glycolytic paralogs in the yeast genome. MG was carefully designed and constructed to provide a robust, prototrophic platform for quantitative studies, and is made available to the scientific community.

overall_design: The goals of the present study are to experimentally explore genetic redundancy in yeast glycolysis by cumulative deletion of minor paralogs and to provide a new experimental platform for fundamental yeast research by constructing a yeast strain with a functional ‘minimal glycolysis’. To this end, we deleted 13 minor paralogs, leaving only the 14 major paralogs for the S. cerevisiae glycolytic pathway. The cumulative impact of deleting all minor paralogs was investigated by two complementary approaches.  A first, quantitative analysis focused on the impact on glycolytic flux under a number of controlled cultivation conditions that, in wild-type strains, result in different glycolytic fluxes. These quantitative growth studies were combined with transcriptome, enzyme-activity and intracellular metabolite assays to capture potential small phenotypic effects. A second, semi-quantitative characterization explored the phenotype of the ‘minimal glycolysis’ strain under a wide array of experimental conditions to identify potential context-dependent phenotypes

first: Marcel

last: van den Broek

first: Daniel

last: Solis-Escalante

first: Pascale

last: Daran-Lapujade


title: Gene expression in hippocampal sub-fields of 4.5 month old rTg4510 mice

first: John

last: Corradi

summary: Microarrays were used to assess the gene expression patterns in the CA1, CA3, and dentate gyrus of the rTg4510 mouse line at 4.5 months of age. This line harbors a repressible mutant human Tau transgene under the Camk2a promoter. Both mice with just the tet-Transactivator alone and no transgenes ('double negative') were used as comparison groups.

overall_design: Cellular layers of the CA1, CA3, and dentate gyrus (DG) from 5 or 6 mice per genotype at ages 4.5 months were laser capture dissected, RNA was isolated, and hybridization to Affymetrix microarrays performed.

first: P

last: Wes

first: A

last: Easton

first: J

first: D

middle: M

last: Barten

first: L

last: DeCarr

last: Truong

last: He

first: N

last: Barrezueta

last: Polson

last: Bourin

last: Flynn

last: Keenan

last: Lidge

last: Meredith

last: Natale

last: Sankaranarayanan

last: Seager

last: Cadelina

last: Albright


title: Age-dependent gene expression in the hippocampus of rTg4510 mice

last: Corradi

summary: Microarrays were used to assess the adult hippocampal gene expression patterns in the rTg4510 mouse line at various ages. This line harbors a repressible mutant human Tau transgene under the Camk2a promoter. Both mice with just the tet-Transactivator alone and no transgenes ('double negative') were used as comparison groups.

overall_design: Hippocampi from (1-4) mice per genotype at ages ranging from 1.7 to 10.8 months of age were dissected, RNA isolated, and hybridization to Affymetrix microarrays performed.

last: Wes

last: Easton

first: C

first: M

first: S

first: R

first: G

last: Cacace


title: Differential gene expression in the proximal neck of human abdominal aortic aneurysm

status: Public on May 30 2013

city: Townsville

first: Erik

last: Biros

address: James Cook Drive

institute: James Cook University

summary: The aim of this study was to assess the gene expression profile of biopsies obtained from the neck of human AAAs.

overall_design: Genome-wide expression analysis of AAA neck specimen obtained from 14 patients with AAA (mean maximum aortic diameter=62.6±18.0 mm). Relative aortic gene expression was compared with that of 8 control aortic specimen of organ donors.

first: Gabor

last: Gäbel

first: Jan

last: Lindeman

first: Philip

last: Walker

first: Jonathan

last: Golledge


title: Hsa-miR-375 in early breast cancer

status: Public on Jun 18 2015

city: Salzburg

first: Franz

last: Zehentmayr

address: Müllner Hauptstraße

country: Austria

institute: RadArt

summary: Purpose of the current study was to identify miRs that can differentiate between patients with and without local relapse after breast conserving therapy in early stage breast cancer, which is especially important in the context of individualized treatment selection.

overall_design: The study was conducted in a pilot and a validation phase. First, 32 patients were screened for the most de-regulated miRs in a panel of 1250 miRs by microarray technology. Second, the candidate miRs were analyzed in an independent cohort of 115 patients using reverse transcription quantitative polymerase chain reaction (RT-qPCR).

first: Barbara

last: Zellinger


title: ImmGen Microarray Phase 2

status: Public on Apr 24 2012

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary: Gene-expression microarray datasets generated as part of the Immunological Genome Project (ImmGen) for samples that use a different set of amplification reagents (Ambion WT Expression Kit, not the Affymetrix GeneChip WT cDNA Synthesis and Amplification Kits).

overall_design: This Series record provides access to Immunological Genome Project data submitted to GEO.


title: Ocular fibroblast types differ in their mRNA profiles - implications for fibrosis prevention after aqueous shunt implantation

status: Public on Sep 25 2012

city: Greifswald

first: Joerg

last: Mostertz

address: F.-L.-Jahnstr 15

department: Competence Center Functional Genomics

institute: Greifswald University

summary: Surgical glaucoma therapy is characterized by implantation of an aqueous shunt either draining into the extraocular Tenon’s space or the intraocular suprachoroidal space. In both cases the long term drainage is hampered by fibrotic reactions around the outflow region of the shunt. The prevention of fibrosis should extend the operating life of the shunt. For an aqueous shunt draining from the anterior chamber into the choroidal space fibroblasts from the choroidea and/or the sclera are most likely responsible for a fibrotic response around the outflow region of such a shunt.  A detailed characterization of fibroblasts derived from choroidea and sclera should provide information whether a fibrosis reaction can be inhibited by cell type specific agents. Therefore, we have decided to generate mRNA profiles of fibroblasts from the choroidea, sclera and Tenon’s space in order to look for potential pharmacological targets for fibrosis prevention. The three fibroblast types investigated share fibroblast specific gene expression patterns, concerning extracellular matrix proteins as collagens and fibronectin, but also show distinct mRNA patterns, which we plan to search for targets responsible for fibrotic processes which hopefully can be targeted by specific antifibrotic drugs.

overall_design: Three human fibroblast cell type cultures from different ocular tissues were established: sclera fibroblasts (hSF), choroidea fibroblasts (hCF), and Tenon’s space fibroblasts (hTF). For the gene expression analysis n = 5 for  hCF, n = 4 for hSF, and n = 5 for hTF donor cells were cultivated from different donors. After appropriate cultivation, cells were harvested, RNA was extracted, purified and quantity and quality was assessed. All total RNA samples were analyzed by Affymetrix' Whole-Transcript Expression Analysis & Profiling Human Gene ST Arrays, respectively. In this set-up, we run = 5 arrays for  hCF, n = 4 arrays for hSF, and n = 5 arrays for hTF i.e. one array per biological replicate. No technical replication was carried out. Microarray data analysis was carried out by using the Rosetta Resolver® system for gene expression data analysis (Rosetta Biosoftware, Seattle, WA, USA). In brief, the raw signals of the probes were summarized using RMA thereby generating probe set specific signal intensities. Chips were normalized by using quantile normalization. To compare RNA expression levels of genes in hCF, hSF and hTF, normalized expression signals of genes from corresponding samples were averaged and fold changes were calculated. To assess differences in mean signal intensities between experimental groups, ANOVA (analysis of variance, with Benjamini Hochberg test correction) and a post-hoc Scheffe test was performed. Rosetta Resolver ratio built statistics to correct for possible signal intensity bias were also considered. Only genes (1) an absolute fold change of ≥ 1.5 together with a Scheffe test p value ≤ 0.05 in at least one of the three pairwise comparisons hCF vs. hTF, hSF vs. hTF and hCF vs. hSF, resp., as well as (2) a ratio built p value ≤ 0.05 were deemed differentially expressed genes (DEG) and considered for further evaluation.

first: Marian

last: Loebler

first: Rudolf

last: Guthoff


title: Neuronal differentiation-associated gene profiling of the CHB50 cell line

status: Public on Dec 01 2006

city: Bryan

first: Rajesh

last: Miranda

address: 8447 Riverside Parkway

institute: Texas A&M University

summary:
To identify neuronal differentiation associated gene candidates
Keywords: Compared differentiated (-tsTA/+p53 condition) CHB50 cells to proliferating (+tsTA/-p53 condition) CHB50 cells

overall_design: We compared two, dual labeled, 9K mouse cDNA arrays, where one channel (Ch1) corresponds to the control (proliferation) condition and channel two corresponds to the treatment (differentiation) condition"

first: Cynthia

last: Camarillo

middle: C