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Sample GSM718641 Query DataSets for GSM718641
Status Public on Jul 01, 2012
Title Ejaculate resulting in pregnancy, F5
Sample type RNA
 
Source name ejaculate after 30 min liquefaction
Organism Homo sapiens
Characteristics tissue: ejaculate
ivf outcome: pregnancy
motility (a+b) [%]: 68
ejaculate volume: 3.9
concentration [10e6/ml]: 48
oocytes in metaphase ii: 11
age of woman [years]: 27
fertilisation ratio [%] (2pn/mii): 81.8
cumulative embryo score: 45.00
pregnancies: 1
Treatment protocol Human ejaculates were liquefied for 30 min at 37°C, and an aliquot of 1 mL was washed once by centrifugation in PBS (500 g).
Extracted molecule total RNA
Extraction protocol RNA was extracted from the ejaculates by a specially designed two-fold genomic DNA pre-elimination protocol (Rneasy Micro). Details are to be found under http://www.dr-spiess.de/supp/MHRCappallo2011/RNA.pdf.
Label biotin
Label protocol 50 - 500 ng total RNA were amplified with the MessageAmp III Kit (Ambion, USA), and Biotin-UTP was incorporated as a label.
 
Hybridization protocol Hybridization was conducted for 20h at 37°C, and arrays were washed in 1x TNT (10 min, RT) and 1x TNT (60 min, 46°C). Staining with Cy5-Streptavidin was done for 30 min at RT. Then, arrays were washed 2 times with 1x TNT for 10 min and 0.2x SSPE for 30s. They were spin-dried in a centrifuge at 2000 rpm for 2 min.
Scan protocol Scanning was done on a ScanArray Gx Scanner (Perkin Elmer) at PMT 70/LP 90% setting and 5um resolution. Images were acquired with the ScanArray Express 3.0 software (Perkin Elmer).
Description F5
Data processing Scan images were converted to raw values by the CodeLink Expression analysis software (GE Healthcare, USA). Genes with lower than 5th percentile expression values over all samples were removed. Normalization was by quantile normalization using the Bioconducter package 'affy'.
 
Submission date May 02, 2011
Last update date Jul 01, 2012
Contact name Andrej-Nikolai Spiess
E-mail(s) a.spiess@uke.uni-hamburg.de
Phone +49-40-42803-1585
Fax +49-40-42803-1554
URL http://www.dr-spiess.de
Organization name University Hospital Hamburg-Eppendorf
Department Andrology
Lab Molecular Andrology
Street address Martinistr. 52
City 20246 Hamburg
State/province n/a
ZIP/Postal code n/a
Country Germany
 
Platform ID GPL2895
Series (1)
GSE29002 The transcriptome of ejaculates used for successful/failed in vitro-fertilization

Data table header descriptions
ID_REF
VALUE Normalized log2 signal intensity

Data table
ID_REF VALUE
1002 13.20472899
1004 13.31327053
1006 11.94998
1007 13.01514647
1009 12.43205818
1011 11.37263525
1013 11.64619147
1014 11.22482773
1016 10.1829581
1017 11.3262147
1019 10.3094632
1020 11.57307789
1021 12.29954198
1023 10.98369113
1027 14.07380432
1032 11.20300119
1037 9.800882455
1041 11.92657895
1044 10.87215134
1047 10.63360392

Total number of rows: 20783

Table truncated, full table size 377 Kbytes.




Supplementary file Size Download File type/resource
GSM718641.TXT.gz 3.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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