Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of autumn senescence in populus Leaves

ABSTRACT: Gene expression profiling in leaves of a free-growing aspen tree (Populus tremula) in Umea in northern Sweden during natural autumn senescence (from August 17 to September 21).

ORGANISM(S): Populus tremula

SUBMITTER: Johanna Keskitalo

PROVIDER: E-MEXP-93 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A transcriptional timetable of autumn senescence.

Andersson Anders A Keskitalo Johanna J Sjödin Andreas A Bhalerao Rupali R Sterky Fredrik F Wissel Kirsten K Tandre Karolina K Aspeborg Henrik H Moyle Richard R Ohmiya Yasunori Y Bhalerao Rishikesh R Brunner Amy A Gustafsson Petter P Karlsson Jan J Lundeberg Joakim J Nilsson Ove O Sandberg Göran G Strauss Steven S Sundberg Björn B Uhlen Mathias M Jansson Stefan S Nilsson Peter P

Genome biology 20040310 4

<h4>Background</h4>We have developed genomic tools to allow the genus Populus (aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag (EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescenc ...[more]

PMID: 15059257

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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 autumn senescence in populus Leaves

Publications

A transcriptional timetable of autumn senescence.

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