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| Status |
Public on Nov 15, 2012 |
| Title |
Global Gene Expression Profiles of Visceral Adipose in Females with Type 2 Diabetes. |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Gene expression profiles of biopsy samples of visceral adipose of three female patients of type 2 diabetes and three non-diabetic female patients were generated using Illumina HumanHT-12 v3 Expression BeadChip arrays. The primary indications of surgery were non-infective and non-malignant conditions, namely, cholelethiasis, hernia and trauma.
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| Overall design |
Three biological replicates with four technical replicates each were used to generate expression profiles. Total cellular RNA from biopsy samples was isolated using mirVana™ miRNA Isolation Kit (Ambion, Austin, TX). The quantity and the quality of RNA samples were determined using Nanodrop-1000 (Thermo Fischer Scientific, Wilmington, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), in that order. RNA samples with a RIN (RNA Integrity Number) value between 5-8 were used for expression profiling. Starting with 500 ng of total RNA, Illumina TotalPrepTM RNA Amplification Kit was used for preparing first and second strand cDNA, purification of cDNA, in vitro transcription to synthesize biotin labeled cRNA, and purification of the labeled cRNA, in that sequence. The quantitation of cRNA was performed using Nanodrop-1000. Illumina HumanHT-12 v3 Expression BeadChip arrays were hybridized with 750 ng of labeled cRNA samples. Hybridization and washing were perforemd according to the manufacturer's protocol. The arrays were scanned and read using Illumina iScan System, and the data extraction, average normalization and downstream analysis performed using Illumina GenomeStudio V2010.1.
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| Contributor(s) |
Jain P, Vig S, Bharadwaj D, Dutta M, Mathur S, Sharma A |
| Citation(s) |
23308243 |
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| Submission date |
May 11, 2011 |
| Last update date |
Aug 16, 2018 |
| Contact name |
Abhay Sharma |
| E-mail(s) |
abhaysharma@igib.res.in
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| Phone |
+91-11-27666156
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| Fax |
+91-11-27667602
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| Organization name |
CSIR-Institute of Genomics and Integrative Biology (IGIB)
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| Department |
Functional Genomics Unit
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| Street address |
Delhi University campus, Mall Road
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| City |
Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110007 |
| Country |
India |
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| Platforms (1) |
| GPL6947 |
Illumina HumanHT-12 V3.0 expression beadchip |
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| Samples (24)
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| GSM722948 |
Non-diabetic visceral adipose female 1 |
| GSM722949 |
Non-diabetic visceral adipose female 2 |
| GSM722950 |
Non-diabetic visceral adipose female 3 |
| GSM722951 |
Non-diabetic visceral adipose female 4 |
| GSM722952 |
Non-diabetic visceral adipose female 5 |
| GSM722953 |
Non-diabetic visceral adipose female 6 |
| GSM722954 |
Non-diabetic visceral adipose female 7 |
| GSM722955 |
Non-diabetic visceral adipose female 8 |
| GSM722956 |
Non-diabetic visceral adipose female 9 |
| GSM722957 |
Non-diabetic visceral adipose female 10 |
| GSM722958 |
Non-diabetic visceral adipose female 11 |
| GSM722959 |
Non-diabetic visceral adipose female 12 |
| GSM722960 |
Diabetic visceral adipose female 1 |
| GSM722961 |
Diabetic visceral adipose female 2 |
| GSM722962 |
Diabetic visceral adipose female 3 |
| GSM722963 |
Diabetic visceral adipose female 4 |
| GSM722964 |
Diabetic visceral adipose female 5 |
| GSM722965 |
Diabetic visceral adipose female 6 |
| GSM722966 |
Diabetic visceral adipose female 7 |
| GSM722967 |
Diabetic visceral adipose female 8 |
| GSM722968 |
Diabetic visceral adipose female 9 |
| GSM722969 |
Diabetic visceral adipose female 10 |
| GSM722970 |
Diabetic visceral adipose female 11 |
| GSM722971 |
Diabetic visceral adipose female 12 |
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| Relations |
| BioProject |
PRJNA139939 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE29231_RAW.tar |
6.2 Mb |
(http)(custom) |
TAR |
| GSE29231_non-normalized.txt.gz |
9.5 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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