GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE3297 Query DataSets for GSE3297
Status Public on Sep 14, 2005
Title Laparoscopic Donor Nephrectomy Gene Expression Profiling Compared to Healthy Control Kidneys
Organism Homo sapiens
Experiment type Expression profiling by array
Summary We compared gene expression profiles from six donor kidneys prior to surgical manipulation to six kidneys removed after laparoscopic donor nephrectomy (LDN) and several hours of CO2 pneumoperitoneum. Biopsies were obtained from renal cortex and hybridized to Affymetrix HG-U133A GeneChips. For control kidneys we identified 1380 genes present on all 6 samples that had a signal intensity greater than 1000. Functional classification of these revealed genes for cellular signaling (201; 15%), regulation of transcription (156; 11%), cellular transport (144; 10%) and cellular metabolism (111; 8%). A class comparison between the controls and LDN kidneys yielded 865 differentially expressed genes. Functional classification of the 502 genes differentially up-regulated in LDN kidneys identified associations with apoptosis, cell adhesion, cell signaling, regulation of cell growth/proliferation, immune/inflammation, ischemia/stress response and proteolysis/peptidolysis. These data demonstrate an altered renal transcriptome induced by several hours of CO2 pneumoperitoneum and laparoscopic surgery characterized by up-regulation of ischemia and injury associated genes.
Keywords: Comparative Expression
Overall design Twelve healthy adult kidney donors signed a consent form, and were approved for donation according to the usual evaluation and practice of the Cleveland Clinic Renal Transplant Program. To avoid potentially significant differences in gene expression based on race and/or ethnicity, only white recipients were selected. The patients were divided into two groups; six controls from open donor nephrectomy and six from LDN. Demographic information included age, gender, race, HLA type, and renal function data including serum creatinine (mg/dL), GFR measured by iothalamate clearance (cc/min.), and urine protein excretion (mg/24 hr). Each patient was given general anesthesia and had a diuresis induced with saline, mannitol, and furosemide. The controls had an extraperitoneal flank incision made, and with only minimal manipulation of the kidney two subcapsular core renal biopsies were obtained using a 15-gauge spring-loaded needle. For the LDN cases two core renal biopsies were obtained using the same needles after the kidneys underwent 2 to 3 hours of C02 pneumoperitoneum. Study biopsies went immediately into 1.5 mL of RNALater (Ambion, Austin, TX), and were stored at –80 0C until they were processed.
Biopsy specimens were homogenized in 1 mL of Trizol (Invitrogen, Carlsbad, CA); total RNA was purified using an RNeasy column (Qiagen, Valencia, CA); and quality confirmed with an Agilent 2100 BioAnalyzer (Palo Alto, CA). Standard Affymetrix GeneChip (Santa Clara, CA) protocols were used, and labelled samples were hybridized to HG-U133A GeneChip arrays containing 22,283 probe sets representing over 14,500 human genes. Data was analyzed using Signal intensities generated using GeneChip Operating System version 1.0 and were subsequently analysed by Robust Multichip Average Express (RMA Express) using all Affymetrix .CEL files as a training set. BRB ArrayTools ( was used to perform class comparisons (significance level of p < 0.005), and create dendrograms. We used NetAffyx ( to annotate the differentially expressed genes according to biological function based on the Gene Ontology database. A Heatmap was created using Cluster and TreeView software
Contributor(s) Kurian SM, Flechner SM, Kaouk J, Modlin C, Goldfarb D, Cook DJ, Head SR, Salomon DR
Citation(s) 16278587
Submission date Sep 12, 2005
Last update date Aug 10, 2018
Contact name Sunil Kurian
Phone 858-784-7759
Organization name The Scripps Research Institute
Department Molecular and Experimental Medicine
Street address 10550 N Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL96 [HG-U133A] Affymetrix Human Genome U133A Array
Samples (12)
GSM74199 Laparoscopic Donor 1
GSM74200 Laparoscopic Donor 2
GSM74201 Laparoscopic Donor 3
BioProject PRJNA92805

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap