title: Differential cytogenomics and miRNA signature of the Acute Myeloid Leukemia Kasumi-1 cell line CD34+38- compartment

status: Public on Feb 11 2010

city: Buffalo

first: Jeffrey

last: Conroy

address: Elm & Carlton Sts

institute: Roswell Park Cancer Institute

type: Non-coding RNA profiling by genome tiling array

summary: The t(8;21) Acute Myeloid Leukaemia (AML) Kasumi-1cell line with N822K KIT mutation, is  a  model system for leukemogenesis. As AML initiating cells reside in the CD34+CD38– fraction, we addressed the refined cytogenomic characterization and miRNA expression of Kasumi-1 cell line and its FACS-sorted subpopulations focussing on this compartment. By conventional cytogenetics, Spectral Karyotyping and array-CGH the cytogenomic profile of Kasumi-1 cells evidenced only subtle regions differentially represented in CD34+CD38– cells.

overall_design:
Cell culture
The human AML Kasumi-1 cell line (AML M2, AML1-ETO) was obtained from DMSZ (Braunschweig GERMANY) and maintained in RPMI 1640 (PBI International, Milan, Italy) with 10% fetal bovine serum (FBS; HyClone Laboratories, Logan, UT, USA).

Immunophenotypic characterization
Kasumi-1 cells, after washing and blocking, were stained with the following antibodies: Cy7-phycoerythrine (PE) conjugated anti-CD34, PE conjugated anti-CD38, allophycocyanin (APC) conjugated anti-CD117, PE conjugated anti-CD33, fluorescein-5-isothiocyanate (FITC) anti -CD3, CD4, CD8, CD14, CD16, CD19, CD20 and FITC conjugated anti-CD13, CD235a, CD41 (Becton Dickinson, BD Biosciences). The analysis was performed using a FacsCalibur instrument (Becton Dickinson, BD Biosciences).

Cell sorting
Kasumi-1 cells were stained with anti-CD34 and anti-CD38 antibodies as described above. Cell sorting was performed using a Facs Vantage SE Laser 488nm Interprise Coherent flow cytometer (Becton Dickinson, BD Biosciences), and gates were set up to exclude not viable cells and debris. The purity of sorted fractions was assessed to ensure sort quality.

Nucleic acid extraction
DNA was isolated from FACS-sorted CD34-, CD34+CD38- Kasumi-1 subpopulations and Kasumi-1 total cell line using the NucleoSpin Tissue kit (Macherey-Nagel, Gmbh & Co. KG), according to the manufacturer’s instructions. DNA quality and concentration were evaluated using spectrophotometer NANODROP 1000 ( Thermo Fischer Scientific Inc.). DNA was conserved at -20°C until use.

Array CGH
An oligonucleotide array, containing 244,000 probes designed for human CGH, was utilized (Agilent Technologies, Palo Alto, CA). It is composed of 60-mer oligonucleotides at an average spatial resolution of 6.4 Kb.
Labelling and Hybridization of DNA: respectively 1μg of reference DNA  (pooled normal female control) and test sample genomic DNA (either Kasumi-1 total cell line and sorted CD34- and CD34+CD38- cells) were individually fluorescently labelled using the Agilent Genomic DNA Labelling kit, Direct Method, as described by the manufacturer (Agilent Technologies, Palo Alto, CA). The labelled DNA was hybridized to the Agilent human 244K CGH array (Agilent Technologies, Palo Alto, CA) according to the manufacturer’s instructions. Chip was scanned with an Agilent microarray scanner to generate high-resolution (5 µm) images.
-Image and data Analysis: Image analysis was performed using the Feature Extraction version 9.5.1.1 (Agilent Technologies, Palo Alto, CA) and the Agilent’s CGH-v4_95_Feb07 protocol. The results of Feature Extraction were imported into CGH Analytics version 3.4.27 (Agilent Technologies, Palo Alto, CA). Aberration calls were made using Agilent’s ADM-1 algorithm with a threshold of 10, comparing the Kasumi-1 DNA sample versus the control DNA sample. Array CGH was performed by Empire Genomics, Buffalo, NY, USA.

first: Laura

last: Pedranzini

first: Federica

last: Mottadelli

first: Simona

last: Ronzoni

first: Franca

last: Rossella

first: Manuela

last: Ferracin

first: Ivana

last: Magnani

first: Gaia

last: Roversi

first: Patrizia

last: Colapietro

first: Massimo

last: Negrini

first: Pier

last: Pelicci

first: Lidia

last: Larizza


title: The pitfalls of platform comparison: DNA copy number array technologies assessed

status: Public on Dec 03 2009

city: Cambridge

first: Christina

last: Curtis

address: Robinson Way

department: Computational Biology/Oncology

country: United Kingdom

institute: University of Cambridge

type: Genome variation profiling by genome tiling array

summary: A study of the relative merits of four leading copy number profiling platforms.

overall_design: Breast tumours and their corresponding matched normals or a set of pooled normals, cancer cell-lines, and HapMap samples were hybridized to the Affymetrix SNP5.0, Agilent 244A,  Illumina HumanCNV370-duo BeadChips, and Nimblegen 385k array.

first: Andy

middle: G

last: Lynch

first: Mark

middle: J

last: Dunning

first: Inmaculada

last: Spiteri

first: John

middle: C

last: Marioni

first: James

last: Hadfield

first: Suet-Feung

last: Chin

last: Brenton

first: Simon

last: Tavaré

first: Carlos

last: Caldas


title: Tumor sample array-CGH profiles

status: Public on Nov 01 2009

city: New York

first: Cameron

last: Brennan

state: NY

address: 1275 York Avenue

country: USA

institute: MSKCC

summary: Array-CGH profiling of a panel of 24 gliomas

overall_design: Tumor tissue snap-frozen and maintained at -80c, DNA extracted and hybridized in 2-channel experiment with common reference: pooled male genomic DNA

middle: W


title: Deregulated expression of cytokine receptor gene, CRLF2, is involved in lymphoid transformation in BCP-ALL

status: Public on Jul 18 2009

city: Newcastle Upon Tyne

first: Vikki

last: Rand

state: Tyne and Wear

address: Paul O'Gorman Building, Newcastle University

department: Northern Institute for Cancer Research

institute: Newcastle University

summary:
Deregulated expression of cytokine receptor gene, CRLF2, is involved in lymphoid transformation in B-cell precursor acute lymphoblastic leukemia
We report two novel, cryptic chromosomal abnormalities in precursor B-cell acute lymphoblastic leukemia (BCP-ALL): a translocation, either t(X;14)(p22;q32) or t(Y;14)(p11;q32), in 33 patients and an interstitial deletion, either del(X)(p22.33p22.33) or del(Y)(p11.32p11.32), in 64 patients, involving the pseudoautosomal region (PAR1) of the sex chromosomes. The incidence of these abnormalities was 5% in childhood ALL (0.8% with the translocation, 4.2% with the deletion). Patients with the translocation were older (median age 16 years), whilst the patients with the deletion were younger (median age 4 years). The two abnormalities result in deregulated expression of the cytokine receptor, cytokine receptor-like factor 2, CRLF2 (also known as thymic stromal-derived lymphopoietin receptor, TSLPR). Over-expression of CRLF2 was associated with activation of the JAK-STAT pathway in cell lines and transduced primary B-cell progenitors, sustaining their proliferation and indicating a causal role of CRLF2 over-expression in lymphoid transformation. In Down Syndrome (DS) ALL and two non DS BCP-ALL cell lines, CRLF2 deregulation was associated with mutations of the JAK2 pseudokinase domain suggesting oncogenic cooperation, as well as highlighting a link between non DS ALL and JAK2 mutations.
Keyword(s): Global copy number analysis using Agilent oligonucleotide arrays

overall_design: DNA copy number analysis of 16 acute lymphoblastic leukaemia samples (13 diagnostic, 1 diagnostic and relapse pair and 2 cell-lines) was performed using Agilent 244K and 105K custom microarrays. These samples were hybridised against gender matched reference DNA.


title: Genomic Copy-Number Variations in Hepatoblastoma Patients Revealed by Array Comparative Genomic Hybridization

status: Public on Oct 01 2010

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

summary:
Purpose: Hepatoblastoma (HB) is a malignant pediatric hepatic progenitor cell tumor with uncertain etiology. To discover genomic biomarkers associated with this malignancy, we conduct the study.
Experimental Design: A panel of ten cases and two pairs of identical twins for HB were screened using high-resolution array-based comparative genomic hybridization (array CGH) technology. Genomic DNA from the peripheral blood was subject to our laboratory investigation.
Results: In total of the twelve HB cases tested, we identified four high recurrent copy-number variations (CNVs) including gain on 1p13.3 (25%) and losses on 5p15.33 (33.3%), 16q12.2 (33.3%), and 19q13.42 (25%). Additionally, the twin study indicated that microdeletions of 3p12.1 and 12p13.2 correlated with hepatoblastoma occurrence. Among these candidate CNVs, 5p15.33 and 16q12.2 not only the most prevalent genomic deletion in this survey, but also encompassed hepatic expressed gene, Zinc finger, DHHC-type containing 11B (ZDHHC11B) and Zinc finger, DHHC-type containing 11 (ZDHHC11) map to 5p15.33; carboxylesterase 4-like (CES4) map to 16q12.2. Furthermore, the microdeletion of 5p15.33 was associated with high mortality rate (3/3; P = 0.018) in patients with native liver. Currently, the only surviving patient with 5p15.33 microdeletion is who has receipt liver transplantation.
Conclusions: These results suggested that losses on 3p12.1, 5p15.33, 12p13.2 and 16q12.2 may be pathogenic for HB. In addition, HB patient who affected by 5p15.33 microdeletion seems to carry high risk of mortality unless undergo liver transplantation. Thus, 5p15.33 microdeletion was suggested as potential prognostic biomarker for poor survival in hepatoblastoma.

overall_design: A panel of ten cases and two pairs of identical twins for HB were screened using high-resolution array-based comparative genomic hybridization (array CGH). Genomic DNA from the peripheral blood was subject to our laboratory investigation. For array CGH experiment, we used commercial human male and female genomic DNA as control samples.In order to build up list of HB candidate CNVs, a strategy organized into two phases was designed. In phase one, the copy-number polymorphisms (CNPs) found in healthy control were excluded. Thus, two array hybridization experiments were performed with gender-matched DNA pools from healthy Taiwanese and Caucasian (Promega, Madison, WI, USA). Then the CNVs observed in these two arrays including microdeletions on 3q26.1, 4q13.2, 7q34, 9q33.2, 19q13.41, and Xp11.4, and amplification on 1p36.12, 1p22.1, 2p24.1, 7p22.3, 8q24.3, 9q34.11, 10q26.3, 11p15.4, 14q32.34, 17p11.2, 17q25.3, 19p13.3, 20q11.22, 21q22.3, 22q11.21, and 22q13.33 which were excluded from subsequent data analysis. We also excluded the CNVs observed in the healthy siblings of the two identical twins. In phase two, CNVs with altered patterns (i.e. gain or loss) that were inconsistent among patients were extracted from candidate list.

first: C

middle: H

first: J

middle: F

last: Wu

first: M

last: Chang


title: Osteosarcoma Copy Number Analysis

status: Public on Sep 08 2009

city: Toronto

first: Bekim

last: Sadikovic

state: Ontario

address: 555 University Avenue

country: Canada

institute: The SickKids Hospital and Princess Margaret Hospital

summary:
Osteosarcoma (OS) is a very aggressive bone tumor characterized by highly abnormal complex karyotypes.This a-CGH is a part of an expriment whose aim was to identify, genomic imbalance, DNA methylation and gene expression profiles in a panel osteosarcoma tumors.
Keywords: comparative genomic hybridization

overall_design: The Agilent Human Genome CGH microarray 244A (Agilent Technologies, Inc., Palo Alto, USA) were used for U2OS array-CGH experiments. Three μg of Human Genomic DNA from multiple anonymous male donors (Promega Corporation, Madison, USA) and 3 μg of test genomic tumour DNA sample were digested with AluI (5 units) and RsaI (5 units) (Promega) for a minimum of 2 hours at 37C. Digestion quality was assessed by the DNA 1000 LabChip Kit (Agilent 2100 Bioanalyzer, Agilent Technologies). Labelling reactions were performed using the Agilent Genomic DNA Labeling Kit PLUS (Agilent Technologies, Inc., Palo Alto, USA) according to the manufacturer’s directions. Briefly, the reference and sample DNA were labelled with 1.5 - 3 mM Cy5-dUTP or Cy3-dUTP (Agilent Technologies, Inc., Palo Alto, USA), and purified using a Centricon YM-30 filter (Millipore, Billerica, USA). Probe mixture of Cy3-labelled sample DNA, Cy5-labelled reference DNA, 50 μl of 1.0mg/ ml of human Cot-1 DNA (Invitrogen, USA), 52 μl of Agilent 10X Blocking Agent and 260 μl of Agilent 2X Hybridization Buffer (Agilent Technologies, Inc.) was denatured at 100C for 1 minute 30 seconds and incubated at 37C for 30 minutes. The probe was applied to the array using an Agilent microarray hybridization chamber, and hybridized for 40 hours at 65C in a rotating oven (Robbins Scientific, Sunnyvale, USA) at 20 rpm. Arrays were washed according to the manufacturer’s recommendations; air dried, and scanned using an Agilent 2565AA DNA microarray scanner (Agilent Technologies, Inc), and processed using Agilent’s Feature Extraction software. Dye-swapped duplicate experiments were carried out.


title: Comprehensive Mapping of Paediatric High Grade Glioma

status: Public on Dec 01 2010

city: Nottingham

first: Jennifer

middle: Helen

last: Barrow

address: Queen's Medical Centre

department: Clinical Sciences

institute: University of Nottingham, Children's Brain Tumour Research Centre

summary: Overall paediatric high grade glioma (pHGG)  has a poor prognosis, in part due to the lack of understanding of  the underlying biology. We therefore used high resolution 244k oligo array comparative genomic hybridisation (oligo aCGH) (Agilent Technologies) to analyse DNA from 38 formalin-fixed paraffin embedded pHGG samples, including 13 DIPG (ten pre-treatment samples and three post-mortem). The pattern of gains and losses were distinct from those seen in HGG arising in adults. In particular we found 1q gain in 22% of our cohort compared to 9% in adults. Homozygous loss at 8p12 was seen in 6/38 (15%) of pHGG. This deletion has not been previously reported in adult or paediatric high grade gliomas. The minimal deleted region is of the gene ADAM3A and homozygous deletion of ADAM3A was confirmed by quantitative real time PCR (qPCR). This novel homozygous deletion of ADAM3A in pHGG merits further study.  Loss of CDKN2A/CDKN2B was seen in 4/38 (10%) samples by oligo a CGH, confirmed by FISH on TMAs and was restricted to supratentorial tumours. Amplification of the 4q11-13 region was detected in 8% of cases and included PDGFRA and KIT, subsequent qPCR analysis was consistent with amplification of PDGFRA. MYCN amplification was seen in 2/38 samples (5%) and was shown to be significantly associated with anaplastic astrocytomas (p=0.03). Overall DIPG shared similar spectrum of changes to supratentorial HGG with some notable differences including high frequency of 17p loss and 14q loss and lack of CDKN2A/CDKN2B deletion. To our knowledge, this study examines the largest DIPG cohort to date using high-throughput genetic techniques.

overall_design: 38 high grade glioma samples including 13 DIPG (ten pre-treatment samples and three post-mortem) analysed by Agilent 244K array CGH. Samples BSG 1, 2, 3, 5, 6, 7, 8, 9, 10 and 11 are the ten pre-treatment DIPG samples. Samples BSG 4, 12 and 13 are the three post-treatment DIPG samples.


title: DNA packaging of human and murine spermatozoal chromatin

status: Public on Jun 09 2009

city: Leeds

first: David

last: Miller

address: Clarendon Way

department: Leeds Institute for Genetics and Health Therapeutics

institute: Leeds University

type: Genome binding/occupancy profiling by genome tiling array

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: U2OS array-CGH

status: Public on May 01 2009

summary:
Osteosarcoma (OS) is a very aggressive bone tumor characterized by highly abnormal complex karyotypes.This a-CGH is a part of an expriment whose aim was to identify, genomic imbalance, DNA methylation and gene expression profiles of osteosarcoma cell lines.
Keywords: comparative genomic hybridization

overall_design: The Agilent Human Genome CGH microarray 44k and 244A (Agilent Technologies, Inc., Palo Alto, USA) were used for U2OS array-CGH experiments.  Three μg of Human Genomic DNA from multiple anonymous male donors (Promega Corporation, Madison, USA) and 3 μg of test genomic DNA sample were digested with AluI (5 units) and RsaI (5 units) (Promega) for a minimum of 2 hours at 37C.  Digestion quality was assessed by the DNA 1000 LabChip Kit (Agilent 2100 Bioanalyzer, Agilent Technologies).  Labelling reactions were performed using the Agilent Genomic DNA Labeling Kit PLUS (Agilent Technologies, Inc., Palo Alto, USA) according to the manufacturer’s directions. Briefly, the reference and sample DNA were labelled with 1.5 - 3 mM Cy5-dUTP or Cy3-dUTP (Agilent Technologies, Inc., Palo Alto, USA), and purified using a Centricon YM-30 filter (Millipore, Billerica, USA).  Probe mixture of Cy3-labelled sample DNA, Cy5-labelled reference DNA, 50 μl of 1.0mg/ ml of human Cot-1 DNA (Invitrogen, USA), 52 μl of Agilent 10X Blocking Agent and 260 μl of Agilent 2X Hybridization Buffer (Agilent Technologies, Inc.) was denatured at 100C for 1 minute 30 seconds and incubated at 37C for 30 minutes.  The probe was applied to the array using an Agilent microarray hybridization chamber, and hybridized for 40 hours at 65C in a rotating oven (Robbins Scientific, Sunnyvale, USA) at 20 rpm. Arrays were washed according to the manufacturer’s recommendations; air dried, and scanned using an Agilent 2565AA DNA microarray scanner (Agilent Technologies, Inc), and processed using Agilent’s Feature Extraction software. Dye-swapped duplicate experiments were carried out.


title: Integrative genomic profiling of human prostate cancer

status: Public on Jun 24 2010

first: Barry

middle: Stephen

last: Taylor

address: 1275 York Avenue, Box #460

institute: Memorial Sloan-Kettering Cancer Center

middle: S

first: Nikolaus

last: Schultz

first: Haley

last: Hieronymus

first: Charles

middle: L

last: Sawyers


title: DNA packaging  of human spermatozoal chromatin

summary:
During mammalian spermiogenesis, the majority of the nucleosomes packaging the
male haploid genome are replaced by protamines to produce a highly compact
chromatin architecture that is critical to male fertility. We have carried out a genomewide
survey of human spermatozoal chromatin using both a salt and micrococal nuclease approach to characterise the DNA sequences
that remain packaged by histones.

overall_design:
Weak salt solutions or limited digestion with micrococcal nuclease
facilitates the release of a nucleosome-rich chromatin from mature spermatozoa.  Whole genome CGH arrays were used to map the
histone and protamine bound portions of spermatozoal DNA.

first: Ali

last: Arpanahi

first: Martin

last: Brinkworth

first: Stephen

middle: A

first: Adrian

middle: E

last: Platts

first: Myriam

last: Saida

first: Philip

last: Tedder

last: Iles


title: PTEN and the PI3K/AKT Pathway in T-Cell Acute Lymphoblastic Leukemia

status: Public on Dec 01 2009

city: Houston

first: Alexei

last: Protopopov

state: TX

address: 1901 East Rd

department: IACS

institute: UT MD Anderson Cancer Center

summary: To comprehensively analyze the PTEN-PI3K-AKT pathway in T-ALL, we examined diagnostic DNA samples from a series of children with T-ALL by array CGH and sequence analysis, and identified genetic lesions in PTEN, PI3K or AKT in 47.7 % (n = 21 of 44) of cases.  Furthermore, we identified a striking clustering of PTEN mutations in exon 7 in primary T-ALL patient samples, all of which encode mutations predicted to truncate the C2 domain without disrupting the phosphatase domain of PTEN.  Induction chemotherapy failed in three of the four patients whose lymphoblasts harbored PTEN deletions at the time of diagnosis, while no induction failures occurred in the 12 cases with PTEN exon 7 mutations (P = 0.007), suggesting that PTEN deletion has more adverse therapeutic consequences than mutational disruptions that preserve the phosphatase domain.  These findings provide a firm rationale for the development of therapies targeting the PI3K-AKT pathway in T-ALL.

overall_design: We performed array-CGH with genomic DNAs from 47 pediatric T-ALL diagnostic specimens, 7 of which were reported in a previous publication. For the array-CGH, test DNA was always labeled by Cy3, and reference (pooled male DNA) - by Cy5. Single polarity hybridizations were performed, no dye-swap. Event-free survival was analyzed in the 44 pediatric T-ALL cases analyzed by both CGH and sequencing.  Kaplan-Meier curves were generated using GraphPad Prism version 4.01, and differences between groups were compared by Gehan-Breslow-Wilcoxon Test.

first: Alejandro

last: Gutierrez

first: Takaomi

last: Sanda

first: Ruta

last: Grebliunaite

first: Arkaitz

last: Carracedo

first: Leonardo

last: Salmena

first: Yebin

last: Ahn

first: Suzanne

last: Dahlberg

first: Donna

last: Neuberg

first: Lisa

last: Moreau

first: Stuart

last: Winter

first: Richard

last: Larson

first: Jianhua

last: Zhang

first: Lynda

last: Chin

first: Pier

last: Pandolfi

first: Lewis

last: Silverman

last: Hunger

last: Sallan

first: Thomas

last: Look


title: Human GBM tumor vs Normal Human DNA

status: Public on Apr 29 2008

city: Boston

first: Yonghong

last: Xiao

state: MA

address: 450 Brookline Ave., HIM218A

institute: Dana-Farber Cancer Institute

summary:
We have developed a nonheuristic genome topography scan (GTS) algorithm to characterize the patterns of genomic alterations in human glioblastoma (GBM), identifying frequent p18INK4C and p16INK4A codeletion. Functional reconstitution of p18INK4C in GBM cells null for both p16INK4A and p18INK4C resulted in impaired cell-cycle progression and tumorigenic potential. Conversely, RNAi-mediated depletion of p18INK4C in p16INK4A-deficient primary astrocytes or established GBM cells enhanced tumorigenicity in vitro and in vivo. Furthermore, acute suppression of p16INK4A in primary astrocytes induced a concomitant increase in p18INK4C. Together, these findings uncover a feedback regulatory circuit in the astrocytic lineage and demonstrate a bona fide tumor suppressor role for p18INK4C in human GBM wherein it functions cooperatively with other INK4 family members to constrain inappropriate proliferation.
Keywords: comparative genomic hybridization

overall_design: DNA copy number abberation of human glioblastoma tumors were obtained by comparative genomic hybridization of GBM tumor vs. normal human DNA. 11 human GBM samples were analyzed on Agilent human 244A human cgh array (G4411B). Normal Human DNA was used as reference. Some samples were hybridized with dye-swap replica.

first: Ruprecht

last: Wiedemeyer

first: Cameron

last: Brennan

first: Timothy

middle: P

last: Heffernan

first: John

last: Mahoney

first: Alexei

last: Protopopov

first: Hongwu

last: Zheng

first: Graham

last: Bignell

first: Frank

last: Furnari

first: Webster

middle: K

last: Cavenee

first: William

last: Hahn

first: Koichi

last: Ichimura

first: V.

last: Collins

first: Gerald

last: Chu

first: Michael

middle: R

last: Stratton

first: Keith

last: Ligon

first: P.

last: Futreal


title: Chromosomal aberration of ESCC and HSCC cell lines

status: Public on Dec 01 2008

city: Tsurumi-ku, Yokohama

first: Katsuyuki

last: Hayashi

state: Kanagawa

address: 1-1-43, Suehiro-cho

department: Business Development

country: Japan

institute: DNA Chip Research Inc

summary:
In order to identify putative targets in squamous cell carcinoma (SCC), a survey of parallel chromosomal alterations and gene expression studies in 10 SCC cell lines were performed using array-CGH and microarray techniques. The most frequent changes were gains of 11q13.1-13.3 and losses of 18q12.1-23 in SCC. Furthermore, the expression levels of the sets of genes at both these loci in SCC were measured using microarray analysis. By combining the array-CGH with the microarray data, 10 genes at 11q13.1-13.3 and 6 genes at 18q12.1-23 whose expression correlated with chromosomal alterations were identified.

Keywords: comparative genomic hybridization

overall_design: Genomic DNAs from 10 cell lines and normal diploid cells were subjected to array CGH analysis to identify genomic alterations in the each cell lines. These DNAs were labeled with Cy5 and Cy3, respectively.

first: Takashi

last: Sugimoto


title: Genome-wide analysis of skeletal muscle gene expression in Lin28A Tg mice

status: Public on Apr 07 2010

first: Hao

last: Zhu

address: 7th Floor Karp, 300 Longwood Ave.

department: Hematology/Oncology

institute: Children's Hospital of Boston

summary: To identify mechanisms involved in growth and glucose metabolism, we performed whole genome mRNA expression analysis in five week old quadraceps muscle from 2 CD-1 background male Lin28A Tg and 2 WT littermates (all male) in which there was 7 fold overexpression of Lin28A, a RNA binding protein that enhances Igf2 translation and suppresses the let-7 microRNA biogenesis.

overall_design: Total RNA was harvested and processed using RNeasy mini kits from Qiagen. All RNA samples were DNase treated. The Illumina Ref-8 microarray platform was used to generate data.


title: Experiment to determine DNA copy number of the HCE-T cell line relative to normal duploid cell

status: Public on Apr 15 2008

city: Kyoto

first: Satoshi

last: Kawasaki

address: 465, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

department: Ophthalmology

institute: Kyoto Prefectural University of Medicine

summary:
Purpose. Simian virus 40 (SV40)-immortalized human corneal epithelial (HCE-T) cells have been widely used as an in vitro model of human corneal epithelial cells. To better understand the nature of this cell line, we assessed it for genomic aberrations and cellular heterogeneity.
Methods. For the quantitative measurement of genomic aberrations, array based comparative genomic hybridization (CGH) analysis was performed. For identification of cellular heterogeneity, cell morphology, growth kinetics, trans-epithelial electrical resistance and transcriptional efficiency were analyzed. We also carried out real-time PCR and chromosomal fluorescent in situ hybridization (cFISH) against some gained or lost loci in order to assess genomic heterogeneity. To assess differences in the gene expression profiles between HCE-T cells and normal corneal epithelial cells, we collected expressed sequence tags (ESTs) for this cell line. Southern blotting and inverse PCR analyses were used to determine the genomic integration site of the SV40 large T antigen gene (LTAG).
Results. Array CGH analysis indicated that the genomic content of HCE-T cells is different from the normal healthy genome. Our results from cellular functional assays, real-time PCR and cFISH strongly showed that HCE-T cells consist of a not insignificant number of heterogeneous cell populations. The genomic integration site of the SV40 large T antigen was at p22.1 of chromosome 9.
Conclusions. Our results indicate that HCE-T cells have an altered genomic content and that they are composed of heterogeneous cell populations. This should be considered when conducting experiments or interpreting the results of studies which use this cell line.
Keywords: comparative genomic hybridization

overall_design: Genomic DNAs from HCE-T cells, immortalized cell line of human corneal epithelial cells and normal female duploid cells were subjected to array CGH analysis to identify genomic alterations in the HCE-T cells. These DNAs were labeled with Cy5 and Cy3, respectively.

first: Kenta

last: Yamasaki

first: Robert

middle: D

last: Young

first: Hideki

last: Fukuoka

first: Mina

last: Nakatsukasa

first: Hidetoshi

last: Tanioka

first: Shigeru

last: Kinoshita


title: Genomic Run-On (GRO) experiment for the YPD to YPGal time course

status: Public on Jul 29 2004

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

summary:
Timecourse analyses (0 to 850 min) of exponentially growing BQS252 yeast after shift from YPD to YPGal galactose medium.
Total RNA in vivo labeled by run-on, or cDNA labelling using random decamers included.
Genomic DNA also examined.
Keywords: other

overall_design: This study focus on the transcriptional activity of RNA pol II in yeast genes. S. cerevisiae cells grown in YPD to middle exponential phase and transferred to YPGal were subjected to Genomic Run On. Data were normalized by the ArrayStat software. Home-made macroarrays containing 6035 ORF were used.

first: J

last: Garcia-Martinez


title: Human TALL tumor vs Normal Human DNA

status: Public on Jun 05 2007

city: boston

first: bin

last: feng

address: 44 binney street

institute: dfci

summary:
Highly rearranged and mutated cancer genomes present major challenges in the identification of pathogenetic events driving the cancer process.  Here, we engineered lymphoma-prone mice with chromosomal instability to assess the utility of mouse models in cancer gene discovery and the extent of cross-species overlap in cancer-associated copy number aberrations.  Integrating with targeted re-sequencing, our comparative oncogenomic studies efficiently identified FBXW7 and PTEN as commonly deleted or mutated tumor suppressors in human T-cell acute lymphoblastic leukemia/lymphoma (T-ALL).  More generally, the murine cancers acquire widespread recurrent clonal amplifications and deletions targeting loci syntenic to alterations present in not only human T-ALL but also diverse tumors of hematopoietic, mesenchymal and epithelial types. These results thus support the view that murine and human tumors experience common biological processes driven by orthologous genetic events as they evolve towards a malignant phenotype.  The highly concordant nature of genomic events encourages the use of genome unstable murine cancer models in the discovery of biologically relevant driver events in human cancer.
Keywords: comparative genomic hybridization

overall_design: 26 human TALL samples were analyzed. Normal Human DNA was used as reference. Each sample was hybridized with dye-swap replica.

first: B

last: Feng

first: R

last: Maser

first: K

last: Wong

first: A

last: Protopopov

first: E

last: Lin

last: O'Neil

last: Gutierrez

first: T

last: Look

first: L

last: Chin

last: Depinho


title: Cancer Process Study


title: TR heat-shock

status: Public on Apr 19 2011

summary: Within a GRO experiment, samples for Transcription rate (TR) analysis were taken at 0, 4, 11, 16, 26 and 40 minutes after heat stress (from 25ºC to 37ºC) and subjected to run-on. Analysis was done in filters also used for RA analysis of aliquots from the same cultures.

overall_design: The analysis includes 3 repeats of stress treatment of the W3030-1a strain. The same times were used for sampling in each repeat of the experiment. A single genomic DNA hybridization on every one of the filters is used for normalization between gene probes.


title: Terbutyl stress mRNA

status: Public on May 23 2008

summary:
mRNA amount analysis of W303-1a yeast strain growing in exponential phase in YPD subjected to terbutyl stress
Keywords: time course

overall_design: Transcriptomic analysis of three independent replicates the yeast strain growing in exponential phase. Each time point replicate has been hybridized on a different macroarray (F5-F10). A single DNA genomic hybridization from the same labeling reaction was done on the same macroarrays for normalization.

first: José

last: Pérez-Ortín

last: García-Martínez


title: Terbutyl stress TR

summary:
Transcription rate (TR) analysis of W303-1a yeast strain growing in exponential phase in YPD subjected to terbutyl stress
Keywords: time course

overall_design: Transcription rate analysis by means of GRO of three independent replicates the yeast strain growing in exponential phase. Each time point replicate has been hybridized on a different macroarray (F5-F10). A single DNA genomic hybridization from the same labeling reaction was done on the same macroarrays for normalization.


title: Microenvironment Cell Populations Affymetrix 133 A

status: Public on Sep 02 2016

city: Seattle

first: Etienne

last: Becht

address: 1100 Fairview Ave N

institute: Fred Hutchison Cancer Research Center

type:
Expression profiling by array
Third-party reanalysis

summary: Human tissues harbour a wide array of cellular populations, often including both immune and lymphoid cell populations, endothelial cells and fibroblasts. The goal of this study was to identify transcriptomic markers of these cell populations, in order to quantify their abundances using transcriptomic data. The present super-series is composed of a large number of transcriptomic profiles of these cell populations. These profiles were obtained from public repositories, normalized using the fRMA R package (which allows a consistent normalization of profiles across public series), and consistently annotated. This series corresponds to Affymetrix 133 A profiles. Sample's annotation is available as supplementary material.

overall_design: 1594 gene expression profiles from immune cell populations, non-immune non-malignant cell populations and non-hematopoietic cancer cell lines were gathered from 81 different studies. Data was normalized using the fRMA R package, version 1.18.0, and frma133afrmavecs version 1.3.0. fRMA was applied to single series independantly, and the resulting gene expression matrices were then concatenated.

first: Nicolas

last: Giraldo

first: Florent

last: Petitprez

first: Samuel

last: Mouyal

first: Catherine

last: Sautès-Fridman

first: Wolf

last: Fridman

first: Aurélien

last: de Reyniès


title: Microenvironment Cell Populations Affymetrix 133 Plus 2.0 series

summary: Human tissues harbour a wide array of cellular populations, often including both immune and lymphoid cell populations, endothelial cells and fibroblasts. The goal of this study was to identify transcriptomic markers of these cell populations, in order to quantify their abundances using transcriptomic data. The present super-series is composed of a large number of transcriptomic profiles of these cell populations. These profiles were obtained from public repositories, normalized using the fRMA R package (which allows a consistent normalization of profiles across public series), and consistently annotated. This series corresponds to Affymetrix 133 Plus 2.0 profiles. Sample's annotation is available as supplementary material.

overall_design: 1936 gene expression profiles from immune cell populations, non-immune non-malignant cell populations and non-hematopoietic cancer cell lines were gathered from 81 different studies. Data was normalized using the fRMA R package, version 1.18.0, and frmahgu133plus2frmavecs version 1.3.0. fRMA was applied to single series independantly, and the resulting gene expression matrices were then concatenated.


title: Microenvironment Cell Populations Affymetrix HuGene 1.0ST

summary: Human tissues harbour a wide array of cellular populations, often including both immune and lymphoid cell populations, endothelial cells and fibroblasts. The goal of this study was to identify transcriptomic markers of these cell populations, in order to quantify their abundances using transcriptomic data. The present super-series is composed of a large number of transcriptomic profiles of these cell populations. These profiles were obtained from public repositories, normalized using the fRMA R package (which allows a consistent normalization of profiles across public series), and consistently annotated. This series corresponds to Affymetrix HuGene 1.0ST profiles. Sample's annotation is available as supplementary material.

overall_design: 3224 gene expression profiles from immune cell populations, non-immune non-malignant cell populations and non-hematopoietic cancer cell lines were gathered from 81 different studies. Data was normalized using the fRMA R package, version 1.18.0, and hugene.1.0.st.v1frmavecs version 1.0.0. fRMA was applied to single series independantly, and the resulting gene expression matrices were then concatenated.