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Sample GSM586094 Query DataSets for GSM586094
Status Public on May 24, 2011
Title WP_4 D1_2711246
Sample type RNA
 
Source name Gene expression data from day one post infection
Organism Homo sapiens
Characteristics tissue: Intestinal biopsy
Treatment protocol Intestinal biopsies were taken after day one and day 60 post infection with Entamoeba histolytica
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Per RNA labeling, 300 nanograms of total RNA was used in conjunction with the Affymetrix recommended protocol wt_sensetarget_label_manual (Catalog# 900672 and 901525).
 
Hybridization protocol The hybridization cocktail containing the fragmented and labeled cRNAs was hybridized to The Affymetrix Human Gene 1.0 ST GeneChips. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix. The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).
Scan protocol An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
Description Gene expression data from day one post infection
Data processing CEL files generated by the Affymetrix GCOS program (GCOS 1.2, Affymetrix) were imported into the Affymetrix Expression Consol program and an RMA (Robust Microarray Analysis) normalization was performed to generate the .Chp files.
 
Submission date Aug 23, 2010
Last update date May 24, 2011
Contact name Christopher Pan
E-mail(s) cpan@mail.nih.gov
Organization name NIH
Department NHGRI
Street address Rm 5228, Bldg 50, South Dr.
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL6244
Series (1)
GSE23750 Role of REG 1 in Entamoeba histolytica colitis

Data table header descriptions
ID_REF
VALUE RMA signal (log2 scale)

Data table
ID_REF VALUE
7892501 5.73274
7892502 5.10087
7892503 5.00155
7892504 9.39866
7892505 3.948
7892506 4.33746
7892507 4.94833
7892508 6.75759
7892509 10.2216
7892510 5.87627
7892511 4.047
7892512 8.58263
7892513 3.88305
7892514 10.7517
7892515 9.41627
7892516 7.18377
7892517 6.71005
7892518 3.46239
7892519 6.30593
7892520 9.98213

Total number of rows: 33297

Table truncated, full table size 516 Kbytes.




Supplementary file Size Download File type/resource
GSM586094.CEL.gz 4.1 Mb (ftp)(http) CEL
GSM586094.chp.gz 253.5 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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