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Sample GSM417001 Query DataSets for GSM417001
Status Public on May 10, 2011
Title Liver biopsy from GBV-C positive subject, 7
Sample type RNA
 
Source name liver, GBV-C positive
Organism Homo sapiens
Characteristics tissue: liver
gbv-c virus status: positive
hiv virus status: positive
hcv virus status: positive
hcv genotype: 1
gender: male
Treatment protocol Ultrasound-guided liver biopsy was performed to obtain liver tissue samples from patients.
Extracted molecule total RNA
Extraction protocol Tissue was collected into RNA later and then extracted using RNAeasy MiniKit (Qiagen, Dusseldorf, Germany).
Label biotin
Label protocol 5-15ug of purified total RNA from each patient was labelled with biotin as recommended in the Affymetrix GeneChip Expression Analysis Technical Manual.
 
Hybridization protocol Affymetrix fluidics station following protocol EukGE-WS2v5_450.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner M10.
Description LB74G701
Data processing 1-way ANOVA was used to detect genes differentially expressed between GBV-C positive and negative patients using Partek Genomics suite and applying a custom CDF file (Hs133P_Hs_UG_8), available from Molecular and Behavioural Neuroscience Institute, University of Michigan. RMA was used to generate expression values.
 
Submission date Jun 12, 2009
Last update date May 10, 2011
Contact name Victoria Mary Perreau
E-mail(s) vperreau@unimelb.edu.au
Phone +61 3 8344 1835
Organization name University of Melbourne
Department Center for Neuroscience
Street address Parkville
City Melbourne
State/province Victoria
ZIP/Postal code 3010
Country Australia
 
Platform ID GPL8715
Series (1)
GSE16593 Differential expression associated with GB virus C in HCV/HIV co-infection

Data table header descriptions
ID_REF
VALUE Log base 2 RMA signal intensity

Data table
ID_REF VALUE
AFFX-BioB-3_at 7.74315
AFFX-BioB-5_at 6.56805
AFFX-BioB-M_at 7.13777
AFFX-BioC-3_at 7.83606
AFFX-BioC-5_at 7.97994
AFFX-BioDn-3_at 11.1504
AFFX-BioDn-5_at 9.27192
AFFX-CreX-3_at 12.5623
AFFX-CreX-5_at 12.1226
AFFX-DapX-3_at 5.83263
AFFX-DapX-5_at 5.63117
AFFX-DapX-M_at 5.94907
AFFX-HSAC07/X00351_3_at 12.9868
AFFX-HSAC07/X00351_5_at 12.6991
AFFX-HSAC07/X00351_M_at 13.0949
AFFX-HUMGAPDH/M33197_3_at 13.2478
AFFX-HUMGAPDH/M33197_5_at 12.9939
AFFX-HUMGAPDH/M33197_M_at 13.0597
AFFX-HUMISGF3A/M97935_3_at 11.2864
AFFX-HUMISGF3A/M97935_5_at 8.26412

Total number of rows: 18089

Table truncated, full table size 366 Kbytes.




Supplementary file Size Download File type/resource
GSM417001.CEL.gz 5.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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