Affymetrix GeneChip Human Genome HG-U133A [HG-U133A]

Gene expression in human small intestinal mucosa in vivo is mediated by iron-induced oxidative stress

rawData

scan

processedDataMatrix

Human intervention study with two doses of iron (as ferrous gluconate via intestinal perfusion) to study the effect on genome-wide gene expression in the small intestine, in order to obtain detailed information about intestinal transcriptomics in vivo.

dose

individual

Transcription profiling of human samples from intervention study with two doses of iron (as ferrous gluconate via intestinal perfusion) to study the effect on genome wide gene expression in the small intestine

Human intervention study with two doses of iron (as ferrous gluconate via intestinal perfusion) to study the effect on genome-wide gene expression in the small intestine, in order to obtain detailed information about intestinal transcriptomics in vivo.


Affymetrix:Protocol:ExpressionStat

Title: Affymetrix CHP Analysis (ExpressionStat). Description:

Affymetrix:Protocol:Hybridization-EukGE-WS2v4[]

Title: Affymetrix EukGE-WS2v4 Hybridization. Description:

Affymetrix:Protocol:Percentile

Title: Affymetrix CEL Analysis (Percentile). Description:

P-MEXP-8236

two pools were created: pool1: person 1 and person 2 pool2: persons 3,4 an 5

SCANPRTCL-iron-study

The probe arrays were scanned at 560 nm using a confocal laser-scanning microscope (Hewlett Packard GeneArray Scanner G2500A).

P-MEXP-8248

Labelled cRNA was prepared using the BioArray High Yield RNA Transcript Labelling Kit (Enzo, Farmingdale, NY, USA). 

P-MEXP-8496

This study was designed to conform to a randomized cross-over design. Each subject was tested on two separate days. Baseline duodenal biopsies, taken by standard forceps in the proximal horizontal part of the duodenum (15 cm distally from the pylorus), were obtained by gastroduodenoscopy. Biopsies were imbedded in tissue-tek (Electron Microscopy Sciences, Washington, PA, USA), snap-frozen in melting isopentane and liquid nitrogen respectively, and stored at -80ºC until analysis. After obtaining the mucosal samples, a guide wire was inserted with the distal tip positioned about 60 cm distally from the pylorus, facilitated by the duodenoscopy. After retraction of the endoscope, a double lumen perfusion catheter (home made from PVC tubing, inner diameter 2.5 mm, outer diameter 4 mm) was inserted over the guide wire into the proximal small intestine with the tip of one lumen, which served as an injection port, located in the proximal descending duodenum and the tip of the second lumen, with three small holes in the last 3 cm to serve as a sample port, 40 cm distally from the injection port. After positioning, the guide wire was removed. The whole procedure was performed under short interval fluoroscopic control. To check positioning of the injection port in the duodenum throughout the experiment, intra-luminal pH was continuously measured at 5 cm proximal of the injection port by a pH electrode (Single Crystal Antimony Multi-Use pH Catheter, Synectics Medical, Queluz, Portugal). The 40-cm segment of the proximal small intestine was perfused with saline at 10 ml/min using a peristaltic pump for 195 min to obtain steady state conditions. After reaching steady state,  300 mL saline was perfused for 90 min.  All ingoing solutions were kept on 37 degrees C in a water bath. Fifteen minutes after the perfusion experiment, the perfusion catheter was removed and a second gastroduodenoscopy was performed to obtain tissue samples from the same intestinal region after the perfusion. 

P-MEXP-8497

This study was designed to conform to a randomized cross-over design. Each subject was tested on two separate days. Baseline duodenal biopsies, taken by standard forceps in the proximal horizontal part of the duodenum (15 cm distally from the pylorus), were obtained by gastroduodenoscopy. Biopsies were imbedded in tissue-tek (Electron Microscopy Sciences, Washington, PA, USA), snap-frozen in melting isopentane and liquid nitrogen respectively, and stored at -80ºC until analysis. After obtaining the mucosal samples, a guide wire was inserted with the distal tip positioned about 60 cm distally from the pylorus, facilitated by the duodenoscopy. After retraction of the endoscope, a double lumen perfusion catheter (home made from PVC tubing, inner diameter 2.5 mm, outer diameter 4 mm) was inserted over the guide wire into the proximal small intestine with the tip of one lumen, which served as an injection port, located in the proximal descending duodenum and the tip of the second lumen, with three small holes in the last 3 cm to serve as a sample port, 40 cm distally from the injection port. After positioning, the guide wire was removed. The whole procedure was performed under short interval fluoroscopic control. To check positioning of the injection port in the duodenum throughout the experiment, intra-luminal pH was continuously measured at 5 cm proximal of the injection port by a pH electrode (Single Crystal Antimony Multi-Use pH Catheter, Synectics Medical, Queluz, Portugal). The 40-cm segment of the proximal small intestine was perfused with saline at 10 ml/min using a peristaltic pump for 195 min to obtain steady state conditions. After reaching steady state,  80 mg iron as ferrous gluconate dissolved in 300 mL saline was perfused. The iron solutions were perfused over a 30-min period. Finally, saline was perfused for another 60 min. All ingoing solutions were kept on 37 degrees C in a water bath. Fifteen minutes after the perfusion experiment, the perfusion catheter was removed and a second gastroduodenoscopy was performed to obtain tissue samples from the same intestinal region after the iron challenge. 

P-MEXP-8498

This study was designed to conform to a randomized cross-over design. Each subject was tested on two separate days. Baseline duodenal biopsies, taken by standard forceps in the proximal horizontal part of the duodenum (15 cm distally from the pylorus), were obtained by gastroduodenoscopy. Biopsies were imbedded in tissue-tek (Electron Microscopy Sciences, Washington, PA, USA), snap-frozen in melting isopentane and liquid nitrogen respectively, and stored at -80ºC until analysis. After obtaining the mucosal samples, a guide wire was inserted with the distal tip positioned about 60 cm distally from the pylorus, facilitated by the duodenoscopy. After retraction of the endoscope, a double lumen perfusion catheter (home made from PVC tubing, inner diameter 2.5 mm, outer diameter 4 mm) was inserted over the guide wire into the proximal small intestine with the tip of one lumen, which served as an injection port, located in the proximal descending duodenum and the tip of the second lumen, with three small holes in the last 3 cm to serve as a sample port, 40 cm distally from the injection port. After positioning, the guide wire was removed. The whole procedure was performed under short interval fluoroscopic control. To check positioning of the injection port in the duodenum throughout the experiment, intra-luminal pH was continuously measured at 5 cm proximal of the injection port by a pH electrode (Single Crystal Antimony Multi-Use pH Catheter, Synectics Medical, Queluz, Portugal). The 40-cm segment of the proximal small intestine was perfused with saline at 10 ml/min using a peristaltic pump for 195 min to obtain steady state conditions. After reaching steady state, 400 mg iron as ferrous gluconate dissolved in 300 mL saline was perfused. The iron solutions were perfused over a 30-min period. Finally, saline was perfused for another 60 min. All ingoing solutions were kept on 37 degrees C in a water bath. Fifteen minutes after the perfusion experiment, the perfusion catheter was removed and a second gastroduodenoscopy was performed to obtain tissue samples from the same intestinal region after the iron challenge. 

P-MEXP-8500

The RNA extraction was performed using Sigma GenElute Mammalian Total RNA Miniprep Kit (RTN-70) (Sigma-Aldrich, Oakville, ON, Canada)

Transcription profiling of human samples from intervention study with two doses of iron (as ferrous gluconate via intestinal perfusion) to study the effect on genome wide gene expression in the small intestine

Submitter Supplied Information

Samples