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Sample GSM1253065 Query DataSets for GSM1253065
Status Public on Jun 27, 2014
Title Convalescent Patient 39
Sample type RNA
 
Source name Whole Blood of Dengue infected patient at convalescent time point
Organism Homo sapiens
Characteristics subject id: 39
infection: DENV
status: convalescent
tissue: whole blood
Treatment protocol Blood was collected on CPT tubes (Vacutainer® with Sodium Citrate; BD). Whole blood specimens were preserved on RNALater buffer (Ambion) and stored in -80oC
Extracted molecule total RNA
Extraction protocol RNA was isolated using the RiboPure-Blood kit (Ambion) and alpha and beta globin mRNA was depleted by GLOBINclear™ Kit (Ambion) according to the manufacturer’s protocol. All RNA samples were checked for purity using a ND-1000 spectrophotometer (NanoDrop Technologies) and for integrity by electrophoresis on a 2100 BioAnalyzer (Agilent Technologies).
Label biotin
Label protocol Total RNA sample quality was evaluated by spectrophotometer to determine quantity, protein contamination and organic solvent contamination, and an Agilent 2100 Bioanalyzer was used to check for RNA degradation. Two-round in vitro transcription amplification and labeling was performed starting with 50 ng intact, total RNA per sample, following the Affymetrix protocol.
 
Hybridization protocol Two-round in vitro transcription amplification and labeling was performed starting with 50 ng intact, total RNA per sample, following the Affymetrix protocol. Samples were hybridized on Human U133 Plus 2.0 Arrays (using GeneTitan platform).
Scan protocol Scanning was performed on a 7th generation GeneChip Scanner 3000, and the Affymetrix GCOS software was used to perform image analysis and generate raw intensity data.
Description convalescent_39
Data processing RMA normalization was performed using Expression Console software.
 
Submission date Oct 28, 2013
Last update date Jun 27, 2014
Contact name Helder I. Nakaya
E-mail(s) hnakaya@usp.br
Phone +551126481130
Organization name Universidade de São Paulo
Lab csbiology.com
Street address AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17
City SÃO PAULO
State/province SÃO PAULO
ZIP/Postal code 05508000
Country Brazil
 
Platform ID GPL13158
Series (1)
GSE51808 Systems biological analysis of immunity to dengue

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
AFFX-BioB-5_at 7.95662
AFFX-BioB-M_at 9.28176
AFFX-BioB-3_at 8.86341
AFFX-BioC-5_at 9.77938
AFFX-BioC-3_at 9.82285
AFFX-BioDn-5_at 11.6727
AFFX-BioDn-3_at 12.5585
AFFX-CreX-5_at 13.3491
AFFX-CreX-3_at 13.6052
AFFX-DapX-5_at 5.54958
AFFX-DapX-M_at 8.56041
AFFX-DapX-3_at 10.6022
AFFX-LysX-5_at 5.75545
AFFX-LysX-M_at 6.86209
AFFX-LysX-3_at 8.15328
AFFX-PheX-5_at 5.73008
AFFX-PheX-M_at 6.87335
AFFX-PheX-3_at 8.02616
AFFX-ThrX-5_at 4.23241
AFFX-ThrX-M_at 6.76411

Total number of rows: 54715

Table truncated, full table size 1159 Kbytes.




Supplementary file Size Download File type/resource
GSM1253065_1444BP0049_82310_A05.CEL.gz 2.1 Mb (ftp)(http) CEL
GSM1253065_1444BP0049_82310_A05.rma.chp.gz 378.0 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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