Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of human nodal peripheral T-cell lymphomas

ABSTRACT: Microarray technology was used to monitor the level of expression of 7,657 human genes in a set of 35 nodal peripheral T-cell lymphomas.

INSTRUMENT(S): G2565BA DNA microarray scanner [Agilent]

ORGANISM(S): Homo sapiens

DISEASE(S): unspecified peripheral T-cell lymphoma

SUBMITTER: Beatriz Martinez

PROVIDER: E-TABM-191 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Identification of a proliferation signature related to survival in nodal peripheral T-cell lymphomas.

Cuadros Marta M Dave Sandeep S SS Jaffe Elaine S ES Honrado Emiliano E Milne Roger R Alves Javier J Rodríguez Jose J Zajac Magdalena M Benitez Javier J Staudt Louis M LM Martinez-Delgado Beatriz B

Journal of clinical oncology : official journal of the American Society of Clinical Oncology 20070618 22

<h4>Purpose</h4>Nodal peripheral T-cell lymphomas (PTCLs) constitute a heterogeneous group of neoplasms, suggesting the existence of molecular differences contributing to their histologic and clinical variability. Initial expression profiling studies of T-cell lymphomas have been inconclusive in yielding clinically relevant insights. We applied DNA microarrays to gain insight into the molecular signatures associated with prognosis.<h4>Materials and methods</h4>We analyzed the expression profiles ...[more]

PMID: 17577022

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Project description:In this study, we employ high-density oligonucleotide microarrays to characterize the MutaMouse FE1 cell line at various stages of cell growth, in primary MutaMouse lung epithelial cell cultures, and in whole lung. Global transcriptional analysis and real-time RT-PCR was applied to (1) further define the cellular origin of the FE1 cell line and its responses under different culture conditions (media and substratum), (2) provide insight into the transcriptional differences in cellular processes between FE1 cultures compared to whole lung tissues, more specifically in toxicological response, and (3) preliminarily examine FE1 culture response to exposure of benzo(a)pyrene compared to whole animals. Total RNA samples from 3 cell culture types (50% FE1, %100 FE1, and Primary lung) or MutaMouse lung were labeled with Cyanine 5-CTP, and universal reference total RNA (Stratagene, CA, USA) was labeled with Cyanine 3-CTP (Perkin Elmer Life Sciences, Woodbridge, ON, Canada) using Agilent linear Amplification kits (Agilent Tech. Inc. Mississauga, ON, Canada) following the manufacturer's instruction. Briefly, double-stranded cDNA was synthesized using MMLV-RT with T7 promoter primer, starting with 5 ug total RNA. Cyanine-labeled cRNA targets were in vitro transcribed using T7 RNA polymerase. The synthesized cRNA was precipitated by LiCl and fragmented at 60 degrees C for 30 min with fragmentation solution. Cy5- sample cRNA and Cy3- reference cRNA were hybridized to Agilent mouse development microarrays (containing ~20,000 unique 60 mer oligonucleotides; Agilent Tech. Inc. Mississauga, ON, Canada) at 60 degrees C overnight with Agilent hybridization solution and washed according to manufacturer's instruction. Arrays were scanned on a VersArray ChipReader (BioRad Laboratories Ltd., Waterloo, Ontario, Canada), and data were acquired with ImaGene 5.5 (BioDiscovery, Inc. CA, USA). Present calls were determined as signals that were greater than the mean plus three times the standard deviation of the average of the negative control spots.

Dataset Information

Transcription profiling of human nodal peripheral T-cell lymphomas

Publications

Identification of a proliferation signature related to survival in nodal peripheral T-cell lymphomas.

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