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Sample GSM2496295 Query DataSets for GSM2496295
Status Public on Feb 22, 2017
Title Asx subject at Day 1 [3266_246792_HG-U133A_2_39856_DU11-04S01136]
Sample type RNA
 
Source name Whole peripheral blood at Day 1
Organism Homo sapiens
Characteristics phenotype: asymptomatic
time: Day 1
Treatment protocol Subjects were orally administered ETEC strain H10407 in a bicarbonate solution, with random assignment to a dose of either 1 × 10^5 or 1 × 10^6 colony-forming units.
Extracted molecule total RNA
Extraction protocol RNA isolation was completed using the PAXgene Blood miRNA Kit. PAXgene Blood RNA Tubes were first centrifuged to pellet the samples, then washed with water and resuspended. After digestion with Proteinase K, the samples were homogenized by centrifugation through PAXgene Shredder spin columns. Isopropanol was added to the samples to optimize binding conditions, and the samples were then centrifuged through PAXgene RNA spin columns, where total RNA >18 nucleotides (including miRNA) was bound to the silica-membrane. The bound RNA was treated with DNase to remove genomic DNA contamination and washed. Pure RNA was then eluted.
Label biotin
Label protocol Total RNA specimens were converted into double-stranded cDNA using an olgio dT-T7 primer. Double stranded cDNA was then used as a template for an invitro transcription reaction to produce a biotinylated cRNA target. The biotinylated cRNA was fragmented and hybridized to the appropriate GeneChip microarray
 
Hybridization protocol A hybridization cocktail is prepared, including the fragmented target, and probe array controls. It is then hybridized to the probe array during a 16-hour incubation
Scan protocol Following hybridization, arrays are washed and stained using standard Affymetrix procedures before scanning on the Affymetrix GeneChip Scanner and data extraction using Affymetrix GCOS software.
Description Gene expression at Day 1 for Asx subject
Data processing The data were RMA normalized with the Bioconductor Affy package.
 
Submission date Feb 21, 2017
Last update date Nov 30, 2020
Contact name Sunil Suchindran
E-mail(s) ss240@duke.edu
Organization name Duke University
Department Center for Applied Genomics and Precision Medicine
Street address 101 Science Drive
City Durham
State/province NC
ZIP/Postal code 27708
Country USA
 
Platform ID GPL571
Series (1)
GSE95104 Transcriptomic Analysis of the Host Response and Innate Resilience to Enterotoxigenic Escherichia coli Infection in Humans
Relations
Reanalyzed by GSE162329

Data table header descriptions
ID_REF
VALUE RMA normalized intensity

Data table
ID_REF VALUE
1007_s_at 8.185038453
1053_at 7.573638327
117_at 9.776902402
121_at 9.236929293
1255_g_at 3.798278787
1294_at 9.663837151
1316_at 5.853148644
1320_at 4.886669689
1405_i_at 11.96133976
1431_at 4.283355651
1438_at 6.059146247
1487_at 8.883744067
1494_f_at 6.874338823
1598_g_at 8.780610201
160020_at 8.562264488
1729_at 10.3993348
177_at 5.264031085
1773_at 7.035360749
179_at 9.431792512
1861_at 7.707072744

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM2496295_3266_246792_HG-U133A_2_39856_DU11-04S01136.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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