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Sample GSM2539097 Query DataSets for GSM2539097
Status Public on Nov 07, 2018
Title WT 0hrs sham rep_1
Sample type RNA
 
Source name WT 0hrs sham
Organism Mus musculus
Characteristics genotype: WT
treatment: sham
reperfusion time: 0hrs
Treatment protocol A subset of animals undergoing I/R (n=4 in 3 hour and 6 hour reperfusion groups) received 0.6 mg/g body weight FITC dextran (4,000 kD at a concentration of 80 mg/ml; Sigma-Aldrich, St. Louis, MO) by gavage 3 hours before euthanasia. At euthanasia, plasma was harvested and the FITC concentration quantitated by fluorometry against a FITC-dextran standard curve.
Growth protocol Animal work was approved by the Duke University and the National Institutes of Health (NIH)/National Institute of Neurological Disorders and Stroke (NINDS) Animal Care and Use Committees (ACUC) respectively. Initial studies were performed in C57BL/6 mice obtained from Jackson Lab (Bar Harbor, ME). Experiments in the previously established Ubc9 transgenic mice (Ubc9Tg) were performed in the “H3” and “N2” founder lines [25]. For mesenteric I/R, mice were anesthetized with 1% isoflurane-supplemented by a one-time administration of 80mg/kg ketamine, 5mg/kg xylazine intraperitoneally, and 0.05mg/kg buprenorphine subcutaneously. A midline laparotomy was then made and a 2-3cm ileal loop isolated and rendered ischemic by placing aneurysm clips (Kent Scientific, Torrington,CT) on the peripheral branches of the superior mesenteric artery as well as across the intestine itself to block flow through collaterals. Ischemia was maintained for 15, 30, or 45 minutes when the clamps were removed, and the incision closed. During the procedure, the body temperature was maintained at 37°C rectal temperature using a feedback-controlled heating pad. For the reperfusion phase of injury, mice were kept in a heated box with supplemental oxygen for a variable amount of time (0.5, 1, 3, or 6 hours) without anesthesia. After euthanasia, tissue was rapidly removed and snap frozen in liquid nitrogen for RNA and protein isolation or transferred into 4% paraformaldehyde (PFA) for paraffin embedding. To achieve snapshot images representative of in vivo SUMO expression and distribution, a subset of mice were euthanized, and perfused with 0.9% NaCl (10 ml) followed by 4% PFA (30 ml) via transcardiac puncture. The intestines were then removed, placed in 4% PFA overnight, transferred to PBS, and embedded in paraffin.
Extracted molecule total RNA
Extraction protocol RNA was isolated using a commercially available kit (Macherey-Nagel, Bethlehem, PA), which includes a DNAse digestion step.
Label Biotin
Label protocol Total RNA was labeled on a sample-by-sample basis according to the manufacturer’s guidelines for use with the Mouse Clariom S GeneChip (Affymetrix, Santa Clara, CA).
 
Hybridization protocol Labeled cRNA were hybridized to the Mouse Clariom S GeneChip (Affymetrix, Santa Clara, CA) in blinded interleaved fashion.
Scan protocol The Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate one .CEL file per hybridized cRNA.
Description WT 0hrs sham
Data processing The Expression Console (Affymetrix) was used to summarize the data contained across all .CEL files and generate 28,846 SST-RMA normalized transcript cluster expression values.
 
Submission date Mar 16, 2017
Last update date Nov 09, 2018
Contact name Kory R Johnson
E-mail(s) johnsonko@ninds.nih.gov
Phone 301-402-1956
Organization name NINDS/NIH
Department DIR IT & Bioinformatics
Lab Bioinformatics Section
Street address 10/3B01, 9000 Rockville Pike
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL23038
Series (1)
GSE96733 Ubc9 overexpression and SUMO1 deficiency blunt inflammation after intestinal ischemia/reperfusion.

Data table header descriptions
ID_REF
VALUE SST-RMA

Data table
ID_REF VALUE
AFFX-BkGr-GC03_st 6.754437
AFFX-BkGr-GC04_st 6.990019
AFFX-BkGr-GC05_st 7.105891
AFFX-BkGr-GC06_st 6.759146
AFFX-BkGr-GC07_st 5.695014
AFFX-BkGr-GC08_st 4.534454
AFFX-BkGr-GC09_st 3.96243
AFFX-BkGr-GC10_st 3.595746
AFFX-BkGr-GC11_st 3.297711
AFFX-BkGr-GC12_st 2.978803
AFFX-BkGr-GC13_st 2.658643
AFFX-BkGr-GC14_st 2.554114
AFFX-BkGr-GC15_st 2.555272
AFFX-BkGr-GC16_st 2.71829
AFFX-BkGr-GC17_st 2.886477
AFFX-BkGr-GC18_st 3.374522
AFFX-BkGr-GC19_st 6.752642
AFFX-BkGr-GC20_st 7.164182
AFFX-BkGr-GC21_st 7.009103
AFFX-BkGr-GC22_st 7.200821

Total number of rows: 28846

Table truncated, full table size 777 Kbytes.




Supplementary file Size Download File type/resource
GSM2539097_SAMPLE_1.CEL.gz 1.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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