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Sample GSM30859 Query DataSets for GSM30859
Status Public on Nov 21, 2004
Title Down syndrome heart CDH5
Sample type RNA
 
Source name Fetal heart at 18 weeks of gestation
Organism Homo sapiens
Characteristics Heart tissue from fetus with Down syndrome and septal defects.
age: 18 gestation weeks
Biomaterial provider Bank of fetal tissues at Federico II University - Naples
Extracted molecule total RNA
Extraction protocol Total RNA was extracted by Trizol
Label Biotin
Label protocol In vitro transcription was performed to obtain biotin labeled cRNA according to Affymetrix protocols described at http://www.affymetrix.com/support/technical/manuals.affx
 
Hybridization protocol according to Affymetrix protocols described at http://www.affymetrix.com/support/technical/manuals.affx
Scan protocol according to Affymetrix protocols described at http://www.affymetrix.com/support/technical/manuals.affx
Description The heart tissue was explanted from a human fetus with chromosome 21 trisomy and atrio-ventricular septal defects, following therapeutic abortion. The posterior half representing all the four heart chambers was dissected by a longitudinal cut. Total RNA was extracted and PolyA+ mRNA was obtained to prepare biotinilated target cRNA according to Affymetrix protocols (http://www.affymetrix.com/support/technical/manuals/expression_manual.affx). Target cRNA was hybridized to Affymetrix HG-U133A chip using an Affymetrix GeneChip Instrument System according to the procedures described at http://www.affymetrix.com/support/downloads/manuals/expression_s2_manual.pdf.
Image data were analyzed using the Affymetrix expression analysis software. The Affymetrix software Microarray Suite (MAS 5.0) assigned to each probe set of the chip an average difference value corresponding to the expression level of the gene it represents and an absolute call that indicates whether the transcript is present in the sample. Data sets were scaled to a total targeted fluorescence of 100.
Keywords = Down syndrome
Keywords = heart gene expression
Data processing Affymetrix CEL files were imported into GeneSping 7.2 software (Agilent Technologies Inc.) and normalized by MAS5 algorithm
 
Submission date Sep 21, 2004
Last update date Sep 11, 2009
Contact name Lucio Nitsch
E-mail(s) nitsch@unina.it
Phone +39-0817463621
Fax +39-0817701016
Organization name Unversity of Naples Federico II
Department Biologia e Patologia Cellulare e Molecolare
Street address Via Pansini 5
City Napoli
ZIP/Postal code 80131
Country Italy
 
Platform ID GPL96
Series (1)
GSE1789 heart gene expression in Down syndrome

Data table header descriptions
ID_REF
VALUE average difference value assigned by Affymetrix MAS 5.0, corresponding to the expression level of the gene that each probe set represents.
ABS_CALL the flag that indicates if the transcript is present (P), absent (A) or marginal (M)

Data table
ID_REF VALUE ABS_CALL
1007_s_at 196.3 P
1053_at 40.6 P
117_at 47.2 P
121_at 93.7 P
1255_g_at 7 A
1294_at 53.5 P
1316_at 17 P
1320_at 15 A
1405_i_at 9.4 A
1431_at 2.8 A
1438_at 4.8 A
1487_at 132 P
1494_f_at 28.7 A
1598_g_at 768.9 P
160020_at 124.5 P
1729_at 40.4 P
1773_at 32.5 A
177_at 40.7 P
179_at 84.9 P
1861_at 54.5 P

Total number of rows: 22283

Table truncated, full table size 387 Kbytes.




Supplementary data files not provided

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