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Sample GSM170766 Query DataSets for GSM170766
Status Public on Jul 01, 2008
Title Prostate tumor patient 13 (MicroRNA Array)
Sample type RNA
 
Source name Adenocarcinoma (NOS) of the prostate
Organism Homo sapiens
Characteristics race: African American
smoking status: Current
gleason sum: 6
pt stage: 2
extraprostatic extension: None
perineural invasion: Yes
seminal vesicle invasion: No
are surgical margins involved: All surgical margins are free of tumor
angio lymphatic invasion: No
Extracted molecule total RNA
Extraction protocol TRIzol
Label biotin
Label protocol Refer to Liu et al (PNAS 101: 9740-9744 (2004)). 5 ug of total RNA was labeled in reverse transcription at 37C for 90 mins by using biotin-labeled rand-octomer oligo primer. The RT reaction mix was further denatured by using 0.5 N NaOH / 1 mM EDTA at 65C for 15 mins and neutralized by 1 M Tris HCl pH 7.6. Biotin signal was detected with an Alexa 647-Streptavidin conjugate.
 
Hybridization protocol The chips were hybridized on Tecan HS 4800 hybridization station. Chips were pre-hybridized at 25C for 30 min in the buffer of 6x SSPE/ 30% formamide/ 1x Denhardt's solution. The chips were further hybridized with labeled target in 6x SSPE/ 30% formamide at 25C for 18 hr. Hybridization, post-hybridization washing in 0.75x TNT (Tris, sodium, Tween 20) (see PNAS) at 37C for 40 mins. The chips were stained by streptavidin-alexa647 (1:500) dilution in TNT for 30 mins. Post-staining washing in 1x TNT FOR 40 min. Rinse with water and spin dry.
Scan protocol Arrays were scanned on the GenePix scanner and analyzed using the GenePix Pro software package.
Description Race: African American, Smoking Status: Current, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No
Data processing median-centralized normalized
 
Submission date Feb 21, 2007
Last update date Apr 16, 2015
Contact name Robert Scott Hudson
Organization name NIH
Department NCI
Lab The Laboratory of Human Carcinogenesis
Street address National Cancer Institute Room Blgd.37/3044
City Bethesda
State/province MD
ZIP/Postal code 20852
Country USA
 
Platform ID GPL4700
Series (1)
GSE7055 Expression of microRNAs and Protein-coding Genes Associated with Perineural Invasion in Prostate Cancer

Data table header descriptions
ID_REF Concatenated positional information
Flag -50 denotes spot flags and values <5
VALUE same as UNF_VALUE but with flagged values removed
UNF_VALUE median-centralized normalized data (in log scale)

Data table
ID_REF Flag VALUE UNF_VALUE
1-1-1 0 9.012095451 9.012095451
1-1-10 0 6.00069046 6.00069046
1-1-11 0 9.64546299 9.64546299
1-1-12 -50 5.80477047
1-1-13 -50 4.881391525
1-1-14 0 12.21570396 12.21570396
1-1-2 -50 6.23286438
1-1-3 -50 6.00069046
1-1-4 -50 4.667266846
1-1-5 -50 7.13193512
1-1-6 -50 5.608372688
1-1-7 -50 4.110873222
1-1-8 0 10.47255898 10.47255898
1-1-9 -50 4.023410797
1-10-1 0 7.531205177 7.531205177
1-10-10 0 5.308813095 5.308813095
1-10-11 -50 5.345338821
1-10-12 -50 6.193335533
1-10-13 -50 4.482842445
1-10-14 -50 0.023410559

Total number of rows: 8164

Table truncated, full table size 228 Kbytes.




Supplementary file Size Download File type/resource
GSM170766.gpr.gz 443.7 Kb (ftp)(http) GPR
Processed data included within Sample table

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